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<h1 class="title toc-ignore">Publications</h1>

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<p>Journal names have been intentionally excluded. Lab member names are in bold and co-first authors indicated with *. Links are provided to the published article and when possible an open-access version (pre- or post-print) of the paper. Click on a triangle for the article abstract.</p>
<pre><code>## Warning in url(url, open = &quot;rb&quot;, encoding = &quot;UTF-8&quot;): URL
## &#39;https://api.crossref.org/works/10.6084%2Fm9.figshare.12781307.v1&#39;: status was
## &#39;Couldn&#39;t resolve host name&#39;</code></pre>
<pre><code>## DOI sync skipped: cannot open the connection to &#39;https://api.crossref.org/works/10.6084%2Fm9.figshare.12781307.v1&#39;</code></pre>
<div id="preprints" class="section level3">
<h3>Preprints</h3>
<details>
<summary>
Maize genetic diversity is largely unstructured by human ethnolinguistic diversity in its center of origin [<a href="https://www.biorxiv.org/content/10.64898/2026.02.02.703385v1">preprint</a>]<br />
<strong>Snodgrass S</strong>, <strong>Li F</strong>, <strong>Mambakkam S</strong>, Medina-Muñoz SG, <strong>Sparreo L</strong>, <strong>Menon MB</strong>, <strong>Perez C</strong>, …[5 authors]… , Runcie DE, Coop GM, <strong>Ross-Ibarra J</strong>
</summary>
<p style="margin-left: 30px">
Population structure and environmental features often capture major axes of genetic variation in many species. Yet the impacts of human activity often remain unquantified. For domesticated species that rely on human activity for survival and dispersal, human movements and cultural differences may play key roles patterning genetic diversity. Maize is a staple crop of enormous cultural importance to indigenous peoples of the Americas, but cannot survive or disperse without farmers. Using publicly available genotyping and passport data from almost 2,000 traditional maize varieties, more than 500 whole genome sequences of humans from Mexico, and indigenous linguistic maps, we quantify anthropogenic effects on maize genetic diversity in the Americas. Maize shows very little overall structure, highlighting the effectiveness of indigenous farmers in moving and mixing maize populations. While principal components of maize diversity show meaningful correlations to human genetic diversity, our linear modeling suggests little additional impact of human population structure beyond shared geography. Though differences in maize diversity are often patterned by language locally, we find only weak genome-wide effects at larger spatial scales. Despite the relatively weak global signal of anthropogenic effects, linguistic GWAS, outlier FST analyses, and selection scans identified loci associated with specific languages. Leveraging landscape-level sequencing data, we highlight how anthropogenic factors have shaped patterns of maize genetic diversity across Mesoamerica.
</p>
</details>
<p>
</p>
<details>
<summary>
The origins and adaptive consequences of polyploidy in a dominant prairie grass. [<a href="https://www.biorxiv.org/content/10.1101/2025.11.25.690567v1">preprint</a>]<br />
<strong>Phillips A</strong>, AuBuchon-Elder T, …[23 authors including <strong>Cameron B</strong>, <strong>Cryan EP</strong>, <strong>Julianna Porter</strong>]… Kellogg EA, <strong>Ross-Ibarra J</strong>
</summary>
<p style="margin-left: 30px">
Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species <em>Andropogon gerardi</em>, a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 populations and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9x <em>A. gerardi</em> cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9x cytotype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9x <em>A. gerardi</em>, the establishment of 9x may lower overall population fitness due to the lower reproductive viability of 9x individuals.
</p>
</details>
<p>
</p>
<details>
<summary>
The dominance of gene expression controlled by trans-eQTL hotspots contributes to phenotypic heterosis in maize [<a href="https://www.biorxiv.org/content/10.1101/2025.11.03.686376v1?ct=">preprint</a>]<br />
Xu G, Yang X, Zhang M, Kang C, Tian Z, Qi Y, Luo M, Liu P, <strong>Ross-Ibarra J</strong>, Yang J, Liu H
</summary>
<p style="margin-left: 30px">
Heterosis, or hybrid vigor, is a key phenomenon in genetics research and agricultural production, and has been primarily attributed to non-additive genetic effects such as dominance â€” a prevailing consensus shaped by decades of empirical research and theoretical debate. Although dominance may arguably arise from distal modifiers, their selective advantage is debated due to presumably small individual effects. To address this longstanding question, particularly how genetic dominance manifests at the transcriptomic level and contributes to phenotypic heterosis, we integrated transcriptomic and phenotypic data from a large population of maize hybrids and their inbred parents. We found that â‰ˆ 30% of the expressed seedling genes in a significant proportion of hybrids exhibited expression patterns deviating from the average of the two parents, indicative of non-additivity. Further analysis suggests that while hybrid gene expression per se is primarily regulated by cis-eQTLs, expression dominance (or non-additivity) is disproportionately controlled by trans-eQTLs. These trans-eQTLs cluster into hotspots that regulate the non-additivity of hundreds of target genes, mostly within co-expression networks, and are notably enriched for transcription factors (TFs). Focusing on one such hotspot, we functionally validated a classical maize gene ZmR1, a basic helix-loop-helix (bHLH) TF associated with multiple seedling trait heterosis, as a candidate regulator of expression dominance across hundreds of genes. Overexpression of ZmR1 enhances expression dominance of downstream genes and increases phenotypic heterosis in both seedling and adult traits. Further experiments confirmed its direct regulatory role in modulating genes involved in anthocyanin biosynthesis and lignin metabolism, driving transcriptome-level dominance. These results provide empirical support for the modifier hypothesis under an omnigenic model, suggesting that heterosis arises not from the modification of a single geneâ€²s inheritance but through the coordinated regulation of hundreds of phenotype-associated genes, thereby helping to reconcile the long-standing debate over the genetic basis of dominance in heterosis.
</p>
</details>
<p>
</p>
<details>
<summary>
Genome-wide selection on transposable elements in maize. [<a href="https://www.biorxiv.org/content/10.1101/2025.09.16.676665v1">preprint</a>]<br />
<strong>Liu B</strong>, Munasinghe M, <strong>Fairbanks RA</strong>, Hirsch CN, <strong>Ross-Ibarra J</strong>
</summary>
<p style="margin-left: 30px">
While most evolutionary research has focused on single nucleotide polymorphisms (SNPs), transposable elements (TEs) represent a major but understudied source of mutations that can influence organismal fitness. Previous studies on TEs often overlook the mechanisms and rates of transposition, rely on short-read sequencing that limits TE detection, or focus on small genomes such as Arabidopsis or Drosophila. In this study, we leveraged high-quality, long-read genome assemblies from 26 maize inbreds to investigate natural selection on TEs. We developed a novel and interpretable method, Î¦SFS, which incorporates TE age and improves resolution for detecting selection. Using this approach, we identified key factors influencing selection on TEs: (1) the distance to the nearest gene, (2) the pre-insertion DNA methylation level at the insertion site, and (3) intrinsic TE characteristics, including copy number and expression level. This work represents the first application of long-read genome assemblies to study TE selection in a major crop species with a typical plant genome size. Our Î¦SFSmethod offers a broadly applicable framework for detecting selection on TEs, and the factors uncovered provide new insights into the evolutionary dynamics and trade-offs between TEs and host genes.
</p>
</details>
<p>
</p>
<details>
<summary>
Heritability and QTL mapping of aerial roots and other yield component traits with implications for N2 fixation in <em>Zea </em>mays*. [<a href="https://www.biorxiv.org/content/10.1101/2025.09.10.675198v1">preprint</a>]<br />
Oâ€™Donnell1 DA, <strong>Yang J</strong>, Zamora P, <strong>Lorant A</strong>, …[3 authors]… Bennett A, <strong>Ross-Ibarra J</strong>
</summary>
<p style="margin-left: 30px">
<em>Zea </em>mays* L. spp. <em>mays</em> (hereafter maize) populations from an indigenous community of Mexico have been reported to perform well using traditional cultivation practices that exclude industrial fertilizers despite low soil nitrate levels. The local maize cultivar is characterized by extended maturity, tall stature, and presence of thick aerial roots that secrete an abundance of polysaccharide-rich root exudate, or mucilage, that is implicated in the recruitment of diazotrophic microbes to facilitate biological nitrogen fixation. Here we estimate the broad sense heritability of traits related to nitrogen fixation in a panel of <em>Zea</em> entries spanning pre-domestication, post- domestication and post-improvement, and identify QTL via F2:F3 families for traits including aerial root node counts and various other yield related traits (i.e. germination rate, time to reproductive maturity, total biomass and nitrogen content of shoot and grain). Across two separate field studies, aerial root node count (AR) demonstrates heritability of 64% and 73%, and genetic mapping reveals three distinct QTL distributed on chromosomes 1 and 9. Further, we report novel QTL for germination rate via stand counts after direct sowing (SC), Plant Total Nitrogen (PTN), Plant Dry Mass (PDM), and a joint QTL for Grain Total Nitrogen (GTN) and Grain Dry Mass (GDM). Finally, we identify overlap between QTL for multiple traits (including AR and SC) and regions of elevated introgression from wild <em>Zea </em>mays* L. spp. <em>mexicana</em> (hereafter mexicana) into Totontepec maize, with a greater degree of overlap than expected under a uniform genomic distribution suggesting adaptive introgression from mexicana. Given its pronounced aerial root morphology, we propose that mexicana is the ancestral source for prominent aerial roots and corresponding abundant mucilage production in Totontepec maize and other maize traditional varieties.
</p>
</details>
<p>
</p>
<details>
<summary>
Extensive genome evolution distinguishes maize within a stable tribe of grasses [<a href="https://www.biorxiv.org/content/10.1101/2025.01.22.633974v1">preprint</a>]<br />
Stitzer MC, Seetharam AS, Scheben A …[35 authors including <strong>Phillips AR</strong>]… <strong>Ross-Ibarra J</strong>, Romay MC, Kellogg EA, Buckler ES, Hufford MB
</summary>
<p style="margin-left: 30px">
Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy â€“ a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives <em>Zea</em> and <em>Tripsacum</em>. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus <em>Zea</em>, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.
</p>
</details>
<p>
</p>
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<!--     <summary>**Other papers by lab members** -->
<!-- </summary> -->
<!--     <p style="margin-left: 30px"> -->
<!-- **Regina Fairbanks**     -->
<!--     DiVito Evans, A., Fairbanks, R. A., Schmidt, P., & Levine, M. T. (2023). Histone methylation regulates reproductive diapause in Drosophila melanogaster. PLoS genetics, 19(9), e1010906.  -->
<!-- **Mitra Menon** -->
<!--     Sun, X., Xiang, Y., Dou, N. et al. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize. Nat Biotechnol 41, 120â€“127 (2023).  -->
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</div>
<div id="section" class="section level3">
<h3>2025</h3>
<details>
<summary>
<p><a href="https://www.pnas.org/doi/abs/10.1073/pnas.2503748122">An ancient origin of the naked grains of maize</a> [<a href="https://www.biorxiv.org/content/10.1101/2024.12.02.626434v1">preprint</a>]<br />
<strong>Fairbanks R</strong>, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Adaptation to novel environments requires genetic variation, which may either predate the novel environment or arise as new mutations. The relative importance of standing genetic variation vs. <em>de novo</em> mutations in adaptation remains a fundamental question in evolutionary biology. Selection during domestication has been long used as a model to understand evolutionary processes, providing information not only on the phenotypes selected but also, in many cases, an understanding of the causal loci. Of the multiple causal loci that have been identified in maize, the selected allele can be found segregating in natural populations, consistent with their origin as standing genetic variation. The sole exception to this pattern is the well-characterized domestication locus <em>tga1</em>, which has long been thought to be an example of selection on a <em>de novo</em> mutation. Here, we use a large dataset of maize and teosinte genomes to reconstruct the origin and evolutionary history of <em>tga1</em>. We first estimated the age of  using a genealogy-based method, finding that the allele arose approximately 41,000-49,000 years ago, predating the beginning of maize domestication. We also identify, for the first time, <em>tga1-maize</em> in teosinte populations, indicating the allele can survive in the wild. Finally, we compare observed patterns of haplotype structure and mutational age distributions near <em>tga1</em> with simulations, finding that patterns near <em>tga1</em> in maize better resemble those generated under simulated selective sweeps on standing variation. These multiple lines of evidence suggest that maize domestication likely drew upon standing genetic variation at <em>tga1</em> and cement the importance of standing variation in driving adaptation during domestication.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://www.cell.com/iscience/fulltext/S2589-0042(25)02323-5">Plant Domestication Revisited: Genomic Insights into Origins, Mechanisms, and Convergent Evolution</a><br />
<strong>Cao Y</strong>, Yan JY, <strong>Ross-Ibarra J</strong>, Yang N</p>
</summary>
<p style="margin-left: 30px">
Plant domestication is a complex evolutionary process shaped by genic and regulatory variation, selection, and gene flow between crops and their wild relatives. Hybridization and introgression have been pivotal in both initial domestication and post-domestication adaptation, while cis-regulatory elements and epigenetic modifications mediate transcriptional divergence underlying key traits, including those of the domestication syndrome. In this review, we synthesize recent advances in the evolutionary origins and molecular mechanisms of domestication in major crops, with emphasis on maize, rice, and wheat. We highlight the roles of interspecific hybridization and adaptive introgression in shaping dynamic domestication trajectories and enhancing environmental adaptation. We then examine how cis-regulatory elements drive phenotypic innovation through modulation of gene expression, transposable element activity, and epigenetic reprogramming. Finally, we discuss convergent domestication, showing how deep conservation of homologous loci and lineage-specific innovations in regulatory networks shape agronomic traits across diverse lineages. Together, these insights provide an integrative framework for domestication genomics and highlight how multi-omics approaches can simultaneously advance evolutionary understanding and guide future crop improvement.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011714">The utility of environmental data from traditional varieties for climate-adaptive maize breeding</a> [<a href="https://www.biorxiv.org/content/10.1101/2024.09.19.613351v1">preprint</a>]<br />
<strong>Li F</strong>, <strong>Gates DJ</strong>, Buckler ES …[8 authors]… Hearne S, <strong>Ross-Ibarra J</strong>, Runcie DE</p>
</summary>
<p style="margin-left: 30px">
Maintaining crop yields in the face of climate change is a major challenge facing plant breeding today. Considerable genetic variation exists in ex-situ collections of traditional crop varieties, but identifying adaptive loci and testing their agronomic performance in large populations in field trials is costly. Here, we study the utility of climate and genomic data for identifying promising traditional varieties to incorporate into maize breeding programs. To do so, we use phenotypic data from more than 4,000 traditional maize varieties grown in 13 trial environments. First, we used genotype data to predict environmental characteristics of germplasm collections to identify varieties that may be locally adapted to target environments. Second, we used environmental GWAS (envGWAS) to identify genetic loci associated with historical divergence along climatic gradients, such as the putative heat shock protein Hsftf9 and the large-scale adaptive inversion Inv4m. Finally, we compared the value of environmental data and envGWAS-prioritized loci to genomic data for prioritizing traditional varieties. We find that maize yield traits are best predicted by genomic data, and that envGWAS-identified variants provide little direct predictive information over patterns of population structure. We also find that adding environment-of-origin variables does not improve yield component prediction over kinship or population structure alone, but could be a useful selection proxy in the absence of sequencing data. While our results suggest little utility of environmental data for selecting traditional varieties to incorporate in breeding programs, environmental GWAS is nonetheless a potentially powerful approach to identify individual novel loci for maize improvement, especially when coupled with high density genotyping.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyaf085/8126661">Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize</a> [<a href="https://biorxiv.org/cgi/content/short/2023.08.08.551183v1">preprint</a>]<br />
Engelhorn J, <strong>Snodgrass SJ</strong>, Kok A, Seetharam AS …[15 authors]… Frommer WB, <strong>Ross-Ibarra J</strong>, Hartwig T</p>
</summary>
<p style="margin-left: 30px">
Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped nearly two-hundred thousand genetic variants (termed binding-QTLs) linked to cis-element occupancy. The functional significance of binding-QTLs is supported by three lines of evidence: i) they coincide with known causative loci that regulate traits, including novel alleles of Upright Plant Architecture2, Trehalase1, and the MITE transposon site of ZmNAC111 under drought; ii) their allelic bias is mirrored between inbred parents and by ChIP-seq; iii) partitioning genetic variation across genomic regions demonstrates that binding-QTLs capture the majority of heritable trait variation across ~70% of 143 phenotypes. Our study provides a promising approach to make previously hidden cis-variation more accessible for genetic studies and multi-target engineering of complex traits.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyaf085/8126661?login=false">Molecular evolution of a reproductive barrier in maize and related species</a> [<a href="https://www.biorxiv.org/content/10.1101/2024.12.02.626474v1">preprint</a>]<br />
<strong>Cryan, E</strong>, <strong>Phinney G</strong>, Seetharam AS, Evans MMS, Kellogg EA, Zhan J, Meyers BC, Kliebenstein D, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Three cross-incompatibility loci each control a distinct reproductive barrier in domesticated maize (<em>Zea </em>mays* ssp. <em>mays</em>) and its wild teosinte relatives. These three loci, Teosinte crossing barrier 1 (Tcb1), Gametophytic factor 1 (Ga1), and Ga2, each play a key role in preventing hybridization between populations and are proposed to maintain the barrier between domesticated and wild subspecies. Each locus encodes a matching pair of silk- and pollen-active pectin methylesterases (PMEs). To investigate the diversity and molecular evolution of these gametophytic factor loci, we identified existing and improved models of the responsible genes in a new genome assembly which contains active versions of all three loci. We then examined fifty-two assembled genomes from seventeen species to classify haplotype diversity and identify sites under diversifying selection during the evolution of the causal genes. We show that Ga2, the oldest of these three loci, was duplicated to form Ga1 at least 12 million years ago. Tcb1, the youngest locus, arose as a duplicate of Ga1 before or around the time of diversification of the <em>Zea</em> genus. We find evidence of positive selection during evolution of the functional genes at an active site in the pollen-expressed PME and predicted surface sites in both the silk- and pollen-expressed PMEs. The most common allele at the Ga1 locus is a conserved ga1 allele (ga1-O), which is non-coding due to conserved stop codons in full-length gene copies that are between 610 thousand and 1.5 million years old. We show that the ga1-O allele is associated with and likely generates 24 nt siRNAs in developing pollen-producing tissue, and these siRNAs map to functional Ga1 alleles. In previously-published crosses, the ga1-O allele associates with reduced function of the typically dominant functional alleles for the Ga1 and Tcb1 barriers. Taken together, this seems to be an example of a type of epigenetic trans-homolog silencing known as paramutation functioning at a locus controlling a reproductive barrier.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><strong>Other papers by lab members</strong></p>
</summary>
<p style="margin-left: 30px">
<p><strong>Regina Fairbanks</strong></p>
<pre><code> A.T. Lin, R.A. Fairbanks, J. Barba-Montoya, H. Liu,  &amp; L. Kistler,   A legacy of genetic entanglement with wolves shapes modern dogs, Proc. Natl. Acad. Sci. U.S.A. 122 (48) e2421768122, https://doi.org/10.1073/pnas.2421768122 (2025).

Zhang, M.-H., Nie, Z.-L., Fairbanks, R.A., Liu, J., Literman, R., Johnson, G., Handy, S. and Wen, J. (2025), Phylogenomic insights into species relationships, reticulate evolution, and biogeographic diversification of the ginseng genus Panax (Araliaceae), with an emphasis on the diversification in the Himalayan-Hengduan Mountains. J. Syst. Evol., 63: 99-114. https://doi.org/10.1111/jse.13138</code></pre>
</p>
</details>
<p>
</p>
</div>
<div id="section-1" class="section level3">
<h3>2024</h3>
<details>
<summary>
<p><a href="https://academic.oup.com/g3journal/article/15/2/jkae281/7913450">A unified VCF data set from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize</a>.<br />
[<a href="https://www.biorxiv.org/content/10.1101/2024.04.30.591904v1">preprint</a>]<br />
Andorf CM, <strong>Ross-Ibarra J</strong>, Seetharam AS, Hufford MB, Woodhouse MR</p>
</summary>
<p style="margin-left: 30px">
Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison. To address these continuity issues, The Maize Genetics and Genomics Database has collaborated with researchers in the maize community to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, coverage, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool to filter, visualize, and download genotype sets based on genomic locations and accessions of interest. MaizeGDB plans to host regular updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="">Teosinte populations exhibit weak local adaptation to their rhizosphere biota despite strong effects of biota source on teosinte fitness and traits</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.04.20.440703v1">preprint</a>]<br />
<strong>O’Brien AM</strong>, Sawers RJH, Gasca-Pineda J, Baxter, I, Eguiarte LE, <strong>Ross-Ibarra J</strong>, Strauss SY</p>
</summary>
<p style="margin-left: 30px">
While biotic interactions often impose selection, species and populations vary in whether they are locally adapted to biotic interactions. Evolutionary theory predicts that environmental conditions drive this variable local adaptation by altering the fitness impacts of species interactions. To investigate the influence of an environmental gradient on adaptation between a plant and its associated rhizosphere biota, we cross-combined teosinte <em>Zea </em>mays* ssp. <em>mexicana</em>) and rhizosphere biota collected across a gradient of decreasing temperature, precipitation, and nutrients in a greenhouse common garden experiment. We measured both fitness and phenotypes expected to be influenced by biota, including concentrations of nutrients in leaves. Independent, main effects of teosinte and biota source explained most variation in teosinte fitness and traits. For example, biota from warmer sites provided population-independent fitness benefits across teosinte hosts. Effects of biota that depended on teosinte genotype were often not specific to their local hosts, and most traits had similar relationships to fitness across biota treatments. However, we found weak patterns of local adaptation between teosinte and biota from colder sites, suggesting environmental gradients may alter the importance of local adaptation in teosinte-biota interactions, as evolutionary theory predicts.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://rdcu.be/dQg54">Teosinte Pollen Drive guides maize domestication and evolution by RNAi</a> [<a href="https://www.biorxiv.org/content/10.1101/2023.07.12.548689v1">preprint</a>]<br />
Berube B, Ernst E, Cahn J …[3 authors]… Scheben A, Siepel A, <strong>Ross-Ibarra J</strong>, Kermicle J, Martienssen RA.</p>
</summary>
<p style="margin-left: 30px">
Meiotic drivers subvert Mendelian expectations by manipulating reproductive development to bias their own transmission. Chromosomal drive typically functions in asymmetric female meiosis, while gene drive is normally postmeiotic and typically found in males. Using single molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive, an instance of gene drive in hybrids between maize (<em>Zea </em>mays* ssp. <em>mays</em>) and teosinte mexicana (<em>Zea </em>mays* ssp. <em>mexicana</em>), that depends on RNA interference (RNAi). 22nt small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-Like 2 (Dcl2) and target Teosinte Drive Responder 1 (Tdr1), which encodes a lipase required for pollen viability. Dcl2, Tdr1, and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas, and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize. A survey of maize landraces and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least 3 chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive likely played a major role in maize domestication and evolution, and offers an explanation for the widespread abundance of “self” small RNAs in the germlines of plants and animals.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><strong>Other papers by lab members</strong></p>
</summary>
<p style="margin-left: 30px">
<p><strong>Alyssa Phillips</strong></p>
<pre><code> Current genomic deep learning architectures generalize across grass species but not alleles. Travis Wrightsman, Taylor H. Ferebee, M. Cinta Romay, Taylor AuBuchon-Elder, Alyssa R. Phillips, Michael Syring, Elizabeth A. Kellogg, Edward S. Buckler. bioRxiv 2024.04.11.589024; doi: https://doi.org/10.1101/2024.04.11.589024

  Phillips, A. R. 2024. Variant calling in polyploids for population and quantitative genetics. Applications in Plant Sciences 12(4): e11607. https://doi.org/10.1002/aps3.11607</code></pre>
</p>
</details>
<p>
</p>
</div>
<div id="section-2" class="section level3">
<h3>2023</h3>
<details>
<summary>
<p><a href="https://www.science.org/doi/10.1126/science.adg8940">Two teosintes made modern maize</a>. [<a href="https://www.biorxiv.org/content/10.1101/2023.01.31.526540v1">preprint</a>]<br />
<strong>Yang N</strong>*, Wang Y*, Liu X* …[20 authors including <strong>Mambakkam S</strong> and <strong>Menon M</strong>]… Stitzer MC, Runcie DE, Yan J, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Despite its global importance as a crop with broad economic, dietary, and cultural importance, the origins of maize and its closest wild relatives remained the topic of vigorous debate for nearly a century. Molecular analyses ultimately concluded that maize was domesticated once from a common ancestor with its closest extant relative, the lowland wild grass <em>Zea </em>mays* ssp. <em>parviglumis</em>. But neither the current genetic model nor earlier models based on archaeological data account for the totality of available data, and recent work has highlighted the potential contribution of a second wild relative, the highland Zea <em>mays</em> ssp. mexicana. Here we present a detailed population genetic analysis of the contributions of both wild taxa to modern maize diversity using the largest sample of traditional maize varieties sequenced to date. We show that all modern maize can trace its origin to an ancient admixture event between domesticated ancient maize and Zea <em>mays</em> ssp. mexicana in the highlands of Mexico ca 5300 cal BP, some 4,000 years after domestication began. We show that variation in admixture is a key component of modern maize genetic and phenotypic diversity, both at the level of individual loci and as a factor driving a substantial component of additive genetic variation across a number of agronomic traits. Our results clarify the long-debated origin of modern maize, highlight the potential contributions of crop wild relatives to agronomic improvement, and raise new questions about the anthropogenic mechanisms underlying multiple waves of dispersal throughout the Americas.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://elifesciences.org/reviewed-preprints/92405">Not so local: the population genetics of convergent adaptation in maize and teosinte.</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.09.09.459637v1">preprint</a>]<br />
<strong>Tittes S</strong>, <strong>Lorant A</strong>, <strong>McGinty S</strong> …[4 authors]… Tenaillon MI, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
What is the genetic architecture of local adaptation and what is the geographic scale that it operates over? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea <em>mays</em> subsp.<em>parviglumis</em>). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are frequently shared by several populations, and often between the subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, post domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, out results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations, but smaller than the species range.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://www.nature.com/articles/d41586-023-02895-w">Genetic modification can improve crop yields â€” but stop overselling it</a><br />
Khaipho-Burch M, Cooper M, Crossa J, de Leon N …[5 authors]… Ronald P, <strong>Ross-Ibarra J</strong>, Weigel D, Buckler ES
</summary>
<p style="margin-left: 30px">
With a changing climate and a growing population, the world increasingly needs more-productive and resilient crops. But improving them requires a knowledge of what actually works in the field.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msad170/7231441?utm_source=authortollfreelink&amp;utm_campaign=mbe&amp;utm_medium=email&amp;guestAccessKey=4c4e0dab-22b0-4c6d-be4f-009119c216fd">Unraveling prevalence and effects of deleterious mutations in maize elite lines across decades of modern breeding</a><br />
Sun S, Wang B, Li C, Xu G, Yang J, Hufford MBH, <strong>Ross-Ibarra J</strong>, Wang H, Wang L
</summary>
<p style="margin-left: 30px">
Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than non-deleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in non-differentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://t.co/CM6xxYYmzy">Diamonds in the Not-So-Rough: Wild Relative Diversity Hidden in Crop Genomes</a> [<a href="https://osf.io/pk8uy/">preprint</a>]<br />
Flint-Garcia S, Hannes Dempewolf H, Feldmann MJ, Morrell PL, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Cultivated species have reduced genetic diversity relative to their closest wild relatives. Domestication also changes the type and effect of polymorphic variants in domesticates. Cultivated species selected for productivity under optimal growth environments have often lost genetic variants that contributed to adaptation to diverse and now rapidly changing environments. Selection for yield can also cause harmful variants segregating in wild relative populations to either be lost to purifying selection or fixed in domesticates. Preservation and effective utilization of the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. Most crops show evidence of admixture and gene flow with their wild relatives during the course of evolution. We argue that allelic diversity from crop wild relatives likely already exists in cultivated populations conserved in germplasm repositories. These alleles have been tested by evolution in an agronomic background. Many are of sufficient age that the twofold sieve of recombination and selection have separated them from linked deleterious variants. Surveying domesticated traditional varieties for functionally relevant variation from wild relatives may thus greatly facilitate the identification and incorporation of useful wild diversity into modern breeding programs.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://academic.oup.com/g3journal/article/13/6/jkad073/7099442">A happy accident: a novel turfgrass reference genome</a> [<a href="https://www.biorxiv.org/content/10.1101/2022.03.08.483531v1">preprint</a>]<br />
<strong>Phillips AR</strong>*, Seetharam AR*, AuBuchon-Elder T …[6 authors]… Kellogg E, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genome’s relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in three North American wild P. pratensis populations. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and biologists interested in this complex species.
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</p>
<details>
<summary>
<p><strong>Other papers by lab members</strong></p>
</summary>
<p style="margin-left: 30px">
<p><strong>Regina Fairbanks</strong></p>
<pre><code>DiVito Evans, A., Fairbanks, R. A., Schmidt, P., &amp; Levine, M. T. (2023). Histone methylation regulates reproductive diapause in Drosophila melanogaster. PLoS genetics, 19(9), e1010906. </code></pre>
<p><strong>Mitra Menon</strong></p>
<pre><code>Sun, X., Xiang, Y., Dou, N. et al. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize. Nat Biotechnol 41, 120â€“127 (2023). </code></pre>
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</details>
<p>
</p>
</div>
<div id="section-3" class="section level3">
<h3>2022</h3>
<details>
<summary>
<a href="https://academic.oup.com/mbe/article/39/11/msac239/6795225">Allele-specific expression reveals multiple paths to highland adaptation in maize</a> [<a href="https://www.biorxiv.org/content/10.1101/2022.07.15.500250v1?rss=1">preprint</a>]<br />
Hu H, Crow T, Nojoomi S, …[5 authors]… EstÃ©vez-Palmas JM, <strong>Ross-Ibarra J</strong>, Runcie DE.
</summary>
<p style="margin-left: 30px">
Maize is a staple food of smallholder farmers living in highland regions up to 4,000 meters above sea level worldwide, and Mexican and South American highlands are two major highland maize growing regions. Maize landraces show numerous adaptations to highland environments, and population genetic data suggests the highland populations largely independently from local lowland populations on each continent. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America (MSA) with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousand of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution etween Mexico and South America, including 17 flowering-related genes. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hudnreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying adaptation. Principal component analyses of these 20 loci provided evidence of multiple mechanisms underlying this convergent adaptation: the spread of adaptive allele through migration and the recruitment of different, but functionally similar, alleles in different populations. Our findings reveal a complex genetic architecture of cis-regulatory alleles underlying adaptation to highlands in maize. Although the vast majority of evolutionary changes associated with highland adaptation were region-specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.
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</p>
<details>
<summary>
<p><a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001814#ack">Conflict over fertilization underlies the transient evolution of reinforcement.</a> [<a href="https://www.biorxiv.org/content/10.1101/2020.11.10.377481v1">preprint</a>]<br />
<strong>Rushworth C</strong>, Wardlaw AW, <strong>Ross-Ibarra J</strong>, Brandvain YB.</p>
</summary>
<p style="margin-left: 30px">
When two populations or species hybridize, their offspring often experience reductions in fitness relative to either parental population. The production of low fitness hybrids may be prevented by the evolution of increased prezygotic isolation; a process known as reinforcement. Theoretical challenges to the evolution of reinforcement are generally cast as a coordination problem — e.g., linkage disequilibrium between trait and preference loci is difficult to maintain in the face of recombination. However, the evolution of reinforcement also poses a potential conflict between mates. For example, the opportunity costs to hybridization may differ between the sexes or species. This is particularly likely for postmating prezygotic isolation, as the ability to fertilize both conspecific and heterospecific eggs is beneficial to male gametes, but heterospecific mating may incur a cost for female gametes. Motivated by this problem, we develop a population genetic model of interspecific conflict over reinforcement, inspired by `gametophytic factors’, which act as postmating prezygotic barriers among Zea <em>mays</em> subspecies. We demonstrate that this conflict results in the transient evolution of reinforcement –â€“ after female preference for a conspecific gamete trait rises to high frequency, male traits adaptively introgress into the other population. Ultimately the male gamete trait fixes in both species, and prezygotic isolation returns to pre-reinforcement levels. We interpret geographic patterns of isolation among Z. <em>mays</em> subspecies in light of these findings, and suggest when and how this conflict can be mediated. Our results suggest that sexual conflict may pose an understudied obstacle to the evolution of reinforcement via postmating prezygotic isolation.
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</p>
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<summary>
<a href="https://www.nature.com/articles/s41588-022-01184-y">Genome sequencing reveals evidence of adaptive variation in the genus <em>Zea</em></a> [<a href="https://www.biorxiv.org/content/10.1101/2022.06.03.494450v1">preprint</a>]<br />
Chen L, Luo J, Minliang Jin, <strong>Yang N</strong> …[27 authors including <strong>Phillips AR</strong> and <strong>Cameron B</strong>]… <strong>Ross-Ibarra J</strong>, Yan J.
</summary>
<p style="margin-left: 30px">
Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single nucleotide polymorphisms (SNPs) and nearly 9 million Insertion/Deletion (InDel) polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations to traits such as waterlogging, perenniality and regrowth. We focus in detail on adaptive alleles in highland teosinte and temperate maize and highlight the key role of flowering time related pathways in highland and high latitude adaptation. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity of the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.
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</p>
<details>
<summary>
<a href="http://rilab.ucdavis.edu/pdfs/li22natplants.pdf">Genomic Insights into Historical Improvement of Heterotic Groups during Modern Hybrid Maize Breeding</a><br />
Li C, Guan H, Jing X, Li Y …[18 authors]… <strong>Ross-Ibarra J</strong>, Li Y, Wang T, Wang H
</summary>
<p style="margin-left: 30px">
Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. To dissect the genomic basis underlying breeding improvement of heterotic groups, we assembled 1,604 historically utilized maize inbred lines belonging to various female and male heterotic groups, and conducted phenotyping and genomic sequencing analyses. We find that the female heterotic groups (FHGs) and male heterotic groups (MHGs) have undergone convergent changes in a common set of plant architecture- and yield-related traits across the breeding eras for increased tolerance to higher planting density and increased yield. In addition, we find that the FHGs and MHGs have experienced divergent changes for three ear-related traits associated with kernel dehydration rate and mechanical harvesting. Using genome-wide selection scans and association analyses, we identify a large number of candidate genes that contributed to the improvement of agronomic traits of the female and male parental lines. Moreover, we observe increased genetic differentiation between the FHGs and MHGs across the breeding eras, and find positive correlation between increase of heterozygosity levels in the differentiated genes with heterosis in hybrids. Further, we validate the function of two selected genes affecting flowering time/ear height and kernel length/kernel weight in inbred lines, and a differentiated gene promoting ear length/ear weight in hybrids. This study provides insights into the genomic basis of hybrid maize breeding, and should enable future genomics-informed maize breeding.
</p>
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</p>
<details>
<summary>
<a href="https://onlinelibrary.wiley.com/doi/10.1002/evl3.285">The genomic signature of wild-to-crop introgression during the domestiation of scarlet runner bean (<em>Phaseolus coccineus L.</em>)</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.02.03.429668v1">preprint</a>]<br />
Guerra-Garcia A, Rojas-Barrera IC, <strong>Ross-Ibarra J</strong>, Papa R, PiÃ±ero D.
</summary>
<p style="margin-left: 30px">
The scarlet runner bean is an open-pollinated legume from the highlands of Mesoamerica that is cultivated in small-scale agriculture for its dry seeds and immature pods. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 SNVs) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck, followed by a population expansion. Introgression from wild to domesticated populations was detected, but not in the opposite direction. This asymmetric introgression might contribute to the recovery of genetic variation and it has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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</p>
<details>
<summary>
<a href="https://pnas.org/doi/full/10.1073/pnas.2100036119">An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.01.25.426574v4">preprint</a>]<br />
Barnes AC*, RodrÃguez-Zapata F*, BlÃ¶cher-JuÃ¡rez KA*, <strong>Gates DJ</strong> …[22 authors]… <strong>Ross-Ibarra J</strong>, Hufford M, Sawers RJH, RellÃ¡n-Ãlvarez R.
</summary>
<p style="margin-left: 30px">
Native Americans domesticated maize (Zea <em>mays</em> ssp. <em>mays</em>) from lowland teosinte<em>parviglumis</em> (Zea <em>mays</em> ssp.<em>parviglumis</em>) in the warm Mexican southwest and brought it to the highlands of MÃ©xico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability, and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 (HPC1), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea <em>mays</em> ssp. mexicana and has been maintained in maize breeding lines from the Northern US, Canada and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.
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<p>
</p>
<details>
<summary>
<p><a href="https://academic.oup.com/gbe/article/14/2/evac016/6519160?login=false">Controlling for variable transposition rate with an age-adjusted site frequency spectrum</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.08.16.456262v1">preprint</a>]<br />
<strong>Horvath R</strong>, <strong>Menon M</strong>, Stitzer MC, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Recognition of the important role of transposable elements (TEs) in eukaryotic genomes quickly led to a burgeoning literature modeling and estimating the effects of selection on TEs. Much of the empirical work on selection has focused on analyzing the site frequency spectrum (SFS) of TEs. But TEs differ from standard evolutionary models in a number of ways that can impact the power and interpretation of the SFS. For example, rather than mutating under a clock-like model, transposition often occurs in bursts which can inflate particular frequency categories compared to expectations under a standard neutral model. If a TE burst has been recent, the excess of low frequency polymorphisms can mimic the effect of purifying selection. Here, we investigate how transposition bursts affect the frequency distribution of TEs and the correlation between age and allele frequency. Using information on the TE age distribution, we propose an age-adjusted site frequency spectrum to compare TEs and neutral polymorphisms to more effectively evaluate whether TEs are under selective constraints. We show that our approach can minimize instances of false inference of selective constraint, but also allows for a correct identification of even weak selection affecting TEs which experienced a transposition burst and is robust to at least simple demographic changes. The results presented here will help researchers working on TEs to more reliably identify the effects of selection on TEs without having to rely on the assumption of a constant transposition rate.
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</details>
<p>
</p>
<details>
<summary>
<p><a href="https://academic.oup.com/g3journal/article/12/3/jkac013/6520465">Analysis of genotype by environment interactions in a maize mapping population</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.07.21.453280v1">preprint</a>]<br />
<strong>Hudson AI</strong>, <strong>Odell SG</strong>, Dubreuil P, Tixier M-H, Praud S, Runcie DE, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Genotype by environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype by environment interaction in a maize multi-parent advanced generation intercross population grown across five environments. We found that genotype by environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. In order to understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype by environment variance. We also performed a genome-wide association study to identify markers associated with genotype by environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype by environment interactions in this population.
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</details>
<p>
</p>
<details>
<summary>
<p><a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009797">Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.09.01.458502v1">preprint</a>]<br />
Holland JB, Samayoa LF, Olukolu BA, Yang CJ …[7 authors]… <strong>Yang J</strong>, <strong>Ross-Ibarra J</strong>, Buckler ES, Doebley JF.</p>
</summary>
<p style="margin-left: 30px">
Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to rare large-effect variation versus potentially more common variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load predicted from sequence data in the maize population. For many traits - and more commonly in maize - genetic variation among self-fertilized families was less than expected based on additive and dominance variance estimated in outcrossed families, suggesting that a negative covariance between additive and homozygous dominance effects limits the variation available to selection under partial inbreeding. We identified quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect recessive variation underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following to the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against large effect variants, but polygenic load is harder to purge and segregating mutational burden increased in maize compared to teosinte.
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</p>
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<summary>
<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8896015/">A B73 x Palomero Toluqueo mapping population reveals local adaptation in Mexican highland maize</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.09.15.460568v1">preprint</a>]<br />
Perez-Limon S, Li M, …[13 authors]… <strong>Ross-Ibarra J</strong>, Flint-Garcia S, Diaz-Garcia L, RellÃ¡n-Ãlvarez R, Sawers RJH</p>
</summary>
<p style="margin-left: 30px">
Generations of farmer selection have produced a unique collection of traditional maize varieties adapted to the environmental challenges of the central Mexican highlands. In addition to agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterized a recombinant inbred line population derived from the cross of the B73 reference line and the Mexican highland maize variety Palomero Toluqueo. Evaluation over multiple years in lowland and highland field sites in Mexico identified genomic regions linked to yield components and putatively adaptive morphological traits. A region on chromosome 7 associated with ear weight showed antagonistic allelic effects in lowland and highland fields, suggesting a trade-off consistent with local adaptation. We identified several alleles of highland origin associated with characteristic highland traits, including reduced tassel branching, increased stem pigmentation and the presence of stem macrohairs. The oligogenic architecture of characteristic morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.
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</details>
<p>
</p>
<details>
<summary>
<p><strong>Other papers by lab members</strong></p>
</summary>
<p style="margin-left: 30px">
</p>
</details>
<p>
</p>
</div>
<div id="section-4" class="section level3">
<h3>2021</h3>
<details>
<summary>
<p><a href="https://academic.oup.com/g3journal/article/12/3/jkac011/6509518?login=true">Modeling Allelic Diversity of Multi-parent Mapping Populations Affects Detection of Quantitative Trait Loci</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.07.14.452335v1">preprint</a>]<br />
<strong>Odell SG</strong>, <strong>Hudson AI</strong>, Praud S, Dubreuil P, Tixier M-H, <strong>Ross-Ibarra J</strong>, Runcie DE</p>
</summary>
<p style="margin-left: 30px">
The search for quantitative trait loci (QTL) that explain complex traits such as yield and flowering time has been ongoing in all crops. Methods such as bi-parental QTL mapping and genome-wide association studies (GWAS) each have their own advantages and limitations. Multi-parent advanced generation intercross (MAGIC) populations contain more recombination events and genetic diversity than bi-parental mapping populations and reduce the confounding effect of population structure that is an issue in association mapping populations. Here we discuss the results of using a MAGIC population of doubled haploid (DH) maize lines created from 16 diverse founders to perform QTL mapping. We compare three models that assume bi-allelic, founder, and ancestral haplotype allelic states for QTL. The three methods have different power to detect QTL for a variety of agronomic traits. Although the founder approach finds the most QTL, there are also QTL unique to each method, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time QTL, qDTA8, which contains vgt1, suggests a potential epistatic interaction and highlights the strengths and weaknesses of each method. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and show the limitations of binary SNP data for identifying multi-allelic QTL.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://journals.plos.org/plosgenetics/article/comments?id=10.1371/journal.pgen.1009810">Selective sorting of ancestral introgression in maize and teosinte along an elevational cline</a> [<a href="https://www.biorxiv.org/content/10.1101/2021.03.05.434040v1">preprint</a>]<br />
Calfee E, <strong>Gates DJ</strong>, <strong>Lorant A</strong>, <strong>Perkins MT</strong>, Coop G, <strong>Ross-Ibarra J</strong>.</p>
</summary>
<p style="margin-left: 30px">
While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea <em>mays</em> ssp. <em>mays</em>), and its wild teosinte relative. Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (&gt; 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of Zea <em>mays</em> ssp. mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed &gt;1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low Fst between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized Inv4m and a new 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. The bulk of our ancestry selection outliers show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize landrace populations.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009768">The Genomic Ecosystem of Transposable Elements in Maize</a> [<a href="https://www.biorxiv.org/content/10.1101/559922v1">preprint</a>][<a href="https://github.com/mcstitzer/maize_genomic_ecosystem">github</a>][<a href="https://mcstitzer.shinyapps.io/maize_te_families/">interactive</a>]<br />
<strong>Stitzer MC</strong>, Anderson SN, Springer NM, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://science.sciencemag.org/content/373/6555/655.abstract"><em>De novo</em> assembly, annotation, and comparative analysis of 26 diverse maize genomes</a>. [<a href="https://www.biorxiv.org/content/10.1101/2021.01.14.426684v1">preprint</a>]<br />
Hufford MB, Seetharam AS …[40 authors including <strong>Hudson AI</strong> and <strong>Tittes S</strong>]… <strong>Ross-Ibarra J</strong>, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK.</p>
</summary>
<p style="margin-left: 30px">
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further reveal the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that overlap QTL and contribute to changes in gene expression.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://genome.cshlp.org/content/early/2021/05/27/gr.266528.120.abstract#aff-4">Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize</a>. [<a href="https://www.biorxiv.org/content/10.1101/2020.07.11.192575v2">preprint</a>]<br />
Song B, Buckler ES, Wang H, Wu Y, …[4 authors including <strong>D Gates</strong>]… Bradbury PJ, <strong>Ross-Ibarra J</strong>, Hufford MB, Romay MC.</p>
</summary>
<p style="margin-left: 30px">
DNA sequencing technology has advanced so quickly, identifying key functional regions using evolutionary approaches is required to understand how those genomes work. This research develops a sensitive sequence alignment approach to identify functional constrained non-coding sequences in the Andropogoneae tribe. The grass tribe Andropogoneae contains several crop species descended from a common ancestor ~18 million years ago. Despite broadly similar phenotypes, they have tremendous genomic diversity with a broad range of ploidy levels and transposons. These features make Andropogoneae a powerful system for studying conserved non-coding sequence (CNS), here we used it to understand the function of CNS in maize. We find that 86% of CNS comprise known genomic elements e.g., cis-regulatory elements, chromosome interactions, introns, several transposable element superfamilies, and are linked to genomic regions related to DNA replication initiation, DNA methylation and histone modification. In maize, we show that CNSs regulate gene expression and variants in CNS are associated with phenotypic variance, and rare CNS absence contributes to loss of gene expression. Furthermore, we find the evolution of CNS is associated with the functional diversification of duplicated genes in the context of the maize subgenomes. Our results provide a quantitative understanding of constrained non-coding elements and identify functional non-coding variation in maize.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab119/6255756">Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces</a> [<a href="https://www.biorxiv.org/content/10.1101/2020.07.31.227629v1">preprint</a>]<br />
<strong>Wang L</strong>, <strong>Josephs EB</strong>, Lee KM, Roverts LM, RellÃ¡n-Ãlvarez R, <strong>Ross-Ibarra J</strong>, Hufford MB.</p>
</summary>
<p style="margin-left: 30px">
Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal strong evidence of parallel adaptation at the level of individual SNPs, genes and pathways in four independent highland maize populations, even though most SNPs show unique patterns of local adaptation. The majority of selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyab061/6237897?searchresult=1">Gene body methylation is under selection in <em>Arabidopsis thaliana</em>.</a> [<a href="https://www.biorxiv.org/content/10.1101/2020.09.04.283333v1">preprint</a>]<br />
Muyle A, <strong>Ross-Ibarra J</strong>, Seymour DK, Gaut BS.</p>
</summary>
<p style="margin-left: 30px">
In plants, mammals and insects, some genes are DNA methylated in the CG dinucleotide context, a phenomenon called gene body methylation. It has long been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 868 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of gene body methylation at the gene level. We used two outgroups to infer the ancestral methylation state of orthologs. Using the A. thaliana gene body methylation site frequency spectrum and a population genetics model specifically designed for epigenetic data, we find that genes with ancestral gene body methylation are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes are under selection to remain unmethylated. The estimated selection coefficients are small, on the order of magnitude of selection acting on codon usage. We also find that A. thaliana is losing gene body methylation more often than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. We investigated the potential function of gene body methylation through its link with gene expression level. We show that, within genes with polymorphic methylation states in A. thaliana wild populations, the gene body methylated state is consistently associated with the highest gene expression level. Our work suggests that gene body methylation has a small effect on fitness, but substantial enough for natural selection to act on it.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://www.nature.com/articles/s41477-020-00834-5.epdf?sharing_token=_mN9oSJzgPbS9Ldsr01s8dRgN0jAjWel9jnR3ZoTv0OIqw-nLs7dqtihevHgjRdBgKyJmnWQSkGOUEc4hulR2jnTLjP4fqtKbSUSzA7iWbyA0E0YEvXdfVUO_1_dmi2uNdJtrPRcKz9O_jp58VwFcP02Yhzr7I3YNxgg8Oit1Xk%3D">Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize</a> [<a href="https://doi.org/10.1101/777623">preprint</a>][<a href="https://github.com/GoreLab/Sorghum-HapMap">github</a>]<br />
Lozano R, Gazave E, dos Santos JPR, Stetter MG …[4 authors]… Mockler T, Buckler ES, <strong>Ross-Ibarra J</strong>, Gore MA</p>
</summary>
<p style="margin-left: 30px">
Sorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analyzed 13M variants identified from whole genome resequencing (WGS) of 468 sorghum lines together with 25M variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes, and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the â€œdomestication costâ€ hypothesis that predicts a higher deleterious burden among domesticates compared to wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy higher than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing them for removal through genome editing and breeding.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><strong>Other papers by lab members</strong></p>
</summary>
<p style="margin-left: 30px">
<p><strong>Cathy Rushworth</strong></p>
<pre><code>Rushworth, C.A., and T. Mitchell-Olds. 2021. The evolution of sex is tempered by costly hybridization in Boechera (rock cress). Journal of Heredity 112(1): 67-77 https://doi.org/10.1093/jhered/esaa041.

Rushworth, C.A., R.S. Baucom, B.K. Blackman, M. Neiman, M.E. Orive, A. Sethuraman, J. Ware, and D.R. Matute. 2021. Who are we now? A demographic assessment of the evolution societies. Evolution 75(2): 208-218 https://onlinelibrary.wiley.com/doi/10.1111/evo.14168.

Carley, L.N., J.P. Mojica, B. Wang, C.-Y. Chen, Y.-P. Lin, K.V.S.K. Prasad, E. Chan, C.-W. Hsu, R. Keith, C.L. NuÃ±ez, C.F. Olson-Manning, C.A. Rushworth, M.R. Wagner, J. Wang, P.-M. Yeh, M. Reichelt, K. Ghattas, J. Gershenzon, C.-R. Lee, and T. Mitchell-Olds. 2021. Ecological factors influence balancing selection on leaf chemical profiles of a wildflower. Nature Ecology and Evolution https://doi.org/10.1038/s41559-021-01486-0.</code></pre>
<p><strong>Mitra Menon</strong></p>
<pre><code>Menon, M., Bagley, J.C., Page, G.F.M. et al. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Commun Biol 4, 160 (2021). https://doi.org/10.1038/s42003-020-01632-7</code></pre>
<p><strong>Silas Tittes</strong></p>
<pre><code>Oâ€™Hara, N. B., Franks, S. J., Kane, N. C., Tittes, S., &amp; Rest, J. S. (2021). Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population. BMC Ecology and Evolution, 21(1), 1-11.  </code></pre>
</p>
</details>
<p>
</p>
</div>
<div id="section-5" class="section level3">
<h3>2020</h3>
<details>
<summary>
<a href="https://www.nature.com/articles/s41467-020-19333-4">Adaptive evolution of DNA methylation reshaped gene regulation in maize</a> [<a href="https://www.biorxiv.org/content/10.1101/2020.03.13.991117v1">preprint</a>] [<a href="https://github.com/jyanglab/msfs_teo">github</a>]<br />
Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, Springer NM, <strong>Ross-Ibarra J</strong>, Yang J
</summary>
<p style="margin-left: 30px">
DNA methylation is a ubiquitous chromatin feature â€“ in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea <em>mays</em> ssp.<em>parviglumis</em>) to investigate the adaptive and phenotypic consequences of methylation variations in maize. By using a novel estimation approach, we inferred the methylome site frequency spectrum (mSFS) to estimate forward and backward methylation mutation rates and selection coefficients. We only found weak evidence for direct selections on methylations in any context, but thousands of differentially methylated regions (DMRs) were identified in population-wide that are correlated with recent selections. Further investigation revealed that DMRs are enriched in 5â€™ untranslated regions, and that maize hypomethylated DMRs likely helped rewire distal gene regulation. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, our HiChIP data indicated that the interactive loops between DMRs and respective downstream genes were present in B73, a modern maize line, but absent in teosinte. And functional analyses suggested that these DMRs likely served as cis-acting elements that modulated gene regulation after domestication. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008791">The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication</a><br />
Chen Q, Fernando Samayoa L, Yang CJ, …[5 authors]… <strong>Lorant A</strong>, Buckler ES, <strong>Ross-Ibarra J</strong>, Holland JB, Doebley JF
</summary>
<p style="margin-left: 30px">
The genetics of domestication has been extensively studied ever since the rediscovery of Mendelâ€™s law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high F ST ) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is â€œmissingâ€ in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://www.g3journal.org/content/ggg/early/2020/05/28/g3.120.401196.full.pdf">Loss of diversity and accumulation of genetic load in doubled-haploid lines from European maize landraces</a> [<a href="https://www.biorxiv.org/content/10.1101/817791v1">preprint</a>][<a href="https://github.com/LZeitler/eurodh-scripts/blob/master/README.org">github</a>]<br />
<strong>Zeitler L</strong>, <strong>Ross-Ibarra J</strong>, <strong>Stetter MGS</strong>
</summary>
<p style="margin-left: 30px">
Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in  programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve useful genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift, and document patterns of heterozygosity and polymorphism at conserved sites that suggest an important role for deleterious recessive load in determining diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that while landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs they come at the cost of decreased genetic diversity and increased genetic load.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://drive.google.com/file/d/1UxPN_Yf2HQ0OOJdqbP537Bwxlm2N1EkL/view?usp=sharing">Genome-wide selection and genetic improvement during modern maize breeding</a><br />
Wang B, Lin Z, Li X, Zhao Y …[17 authors]… Hufford MB, <strong>Ross-Ibarra J</strong>, He H, Wang H.
</summary>
<p style="margin-left: 30px">
Modern crop breeding has made a profound impact on food production to sustain population growth during the past century; however, systematic analyses of the genomic basis underlying the dramatic increase in crop yields during modern breeding remain limited in scope. Here we report an analysis of the genomic and phenotypic changes associated with modern maize breeding across a chronological sampling of 350 elite inbred lines representing multiple eras of both Chinese and U.S. germplasm. We document a number of convergent phenotypic changes in both countries. Using genome-wide association and selection scan methods, we identify 160 loci underlying adaptive agronomic phenotypes and more than 1,800 genomic regions representing the targets of selection during modern breeding. We functionally validate two candidate genes underpinning variation in ear height and tassel branch number using CRISPR knockout mutants. In sum, this work demonstrates the utility of breeding-era approach for identifying breeding signatures and lays the foundation for future genomics-enabled maize breeding."
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://www.sciencedirect.com/science/article/pii/S1369526620300339">Evolutionary insights into plant breeding</a> [<a href="https://agrixiv.org/akdt8">preprint</a>]<br />
<strong>Turner-Hissong SD</strong>, Mabry ME, Beissinger TM, <strong>Ross-Ibarra J</strong>, Pires JC
</summary>
<pre><code>&lt;p style=&quot;margin-left: 30px&quot;&gt;Crop domestication is a fascinating area of study, as evidencedby a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can be used to inform selection strategies. Future advances in crop improvement will rely on the integration of population genetics with  plant  breeding  methodology,  and  the  development  of  community  resources  to  support research in a variety of crop life histories and reproductive strategies. We highlight recent advances in the role of selective sweeps and demographic history in shaping genetic architecture, how these breakthroughs can inform selection strategies, and the application of precision gene editing to leverage these connections.</code></pre>
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="http://library.oapen.org/bitstream/handle/20.500.12657/23339/1006816.pdf?sequence=1#page=292">Genomics of long- and short- term adaptation in maize and teosinte</a> [<a href="https://peerj.com/manuscripts/31241/">preprint</a>]<br />
<strong>Lorant A</strong>, <strong>Ross-Ibarra J</strong>, Tenaillon M</p>
</summary>
<p style="margin-left: 30px">
We review studies on short and long term adaptation, both natural and artificial, in maize and teosinte.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://www.genetics.org/content/214/4/1019">The temporal dynamics of background selection in non-equilibrium populations</a> [<a href="https://www.biorxiv.org/content/10.1101/618389v1">preprint</a>][<a href="https://github.com/RILAB/BGS_sims/">github</a>]<br />
Torres R, <strong>Stetter MG</strong>, Hernandez R, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
We use simulations to show that the effects of nonequilibrium population dynamics on linked selection differ qualitatively from predictions under equilibrium models, calling into question inferences about the efficacy of selection made from summary statistics.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><strong>Other papers by lab members</strong></p>
</summary>
<p style="margin-left: 30px">
<p><strong>Catherine Rushworth</strong></p>
<pre><code>Rushworth, C.A., R.S. Baucom, B.K. Blackman, M. Neiman, M.E. Orive, A. Sethuraman, J. Ware, and D.R. Matute. 2021. Who are we now? A demographic assessment of the evolution societies. In press, Evolution. Early View: https://onlinelibrary.wiley.com/doi/10.1111/evo.14168.

Rushworth, C.A., and T. Mitchell-Olds. 2021. The evolution of sex is tempered by costly hybridization in Boechera (rock cress). Journal of Heredity Early View: https://doi.org/10.1093/jhered/esaa041.

Rushworth, C.A., Y. J. Brandvain, and T. Mitchell-Olds. 2020. Identifying the fitness consequences of sex in complex natural environments. Evolution Letters 4-6: 516-529. https://dx.doi.org/10.1002/evl3.194

Jordon-Thaden, I., J. Beck, C.A. Rushworth, M.D. Windham, N. Diaz, J. Cantley, C. Martine, and C.J. Rothfels. 2020. RADseq for any lab: a basic two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera. Applications in Plant Sciences 8(4): e11344.  </code></pre>
<p><strong>Silas Tittes</strong></p>
<pre><code>Tittes, Silas. &quot;rdmc: an open source R package implementing convergent adaptation models of Lee and Coop (2017).&quot; G3: Genes, Genomes, Genetics 10.9 (2020): 3041-3046.

Wooliver, R., Tittes, S. B., &amp; Sheth, S. N. (2020). A resurrection study reveals limited evolution of thermal performance in response to recent climate change across the geographic range of the scarlet monkeyflower. Evolution, 74(8), 1699-1710.

Comeault, A. A., Wang, J., Tittes, S., Isbell, K., Ingley, S., Hurlbert, A. H., &amp; Matute, D. R. (2020). Genetic diversity and thermal performance in invasive and native populations of African fig flies. Molecular biology and evolution, 37(7), 1893-1906.</code></pre>
</p>
</details>
<p>
</p>
</div>
<div id="section-6" class="section level3">
<h3>2019</h3>
<details>
<summary>
<p>Single gene resolution of locally adaptive genetic variation in Mexican maize [<a href="https://www.biorxiv.org/content/10.1101/706739v1">preprint</a>]<br />
<strong>Gates DJ</strong>, Runcie D, Janzen GM, Romero Navarro A …[4 authors]… Buckler ES, Hearne S, Hufford MB, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
We present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="http://www.g3journal.org/cgi/pmidlookup?view=long&amp;pmid=31506319">Dynamic patterns of transcript abundance of transposable element families in maize</a> [<a href="https://www.biorxiv.org/content/10.1101/668558v1">preprint</a>]<br />
Anderson SN, <strong>Stitzer MC</strong>, Zhou P, <strong>Ross-Ibarra J</strong>, Hirsch CD, Springer NM</p>
</summary>
<p style="margin-left: 30px">
We develop an approach to estiamte family-level expression in transposable elements. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. We also assay expression among different maize genotypes and use a mapping population to identify what proportion of copies in a family contribute to expression."
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14489">Transposable elements contribute to dynamic genome content in maize</a> [<a href="https://www.biorxiv.org/content/10.1101/547398v1?rss=1">preprint</a>]<br />
Anderson SN*, <strong>Stitzer MC</strong>*, Brohammer AB*, Peng Zhou P, Noshay JM, Hirsch CD, <strong>Ross-Ibarra J</strong>, Hirsch CN, Springer NM</p>
</summary>
<p style="margin-left: 30px">
We identify hundreds of thousands of variable transposable elements among a small set of maize genome assemblies. We find evidence of a large number of genes impacted by TEs, including TEs in genes and genes in TEs, and evidence of recent transposition as well.""
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://www.genetics.org/content/213/1/143">Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize</a> [<a href="https://www.biorxiv.org/content/10.1101/588715v1">preprint</a>]<br />
Wei X, Anderson SN, Wang X, …[<strong>Bilinski P</strong>, <strong>Stitzer MC</strong>, <strong>Ross-Ibarra J</strong> and 4 other authors]… Chen X, Springer NM, Doebley JF</p>
</summary>
<p style="margin-left: 30px">
We describe a phenomenon we name ‘hybrid decay’ triggered by backcrossing between domesticated maize and a specific teosinte population, resulting in genome instability, activation of transposable elements, and altered epigenetics ."
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13818">Adaptive phenotypic divergence in teosinte differs across biotic contexts</a> [<a href="https://www.biorxiv.org/content/10.1101/382770v2">preprint</a>] [<a href="https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13857">perspective</a>]<br />
<strong>O’Brien AM</strong>, Sawers RJH, Strauss SY, <strong>Ross-Ibarra J</strong></p>
</summary>
<p style="margin-left: 30px">
We show that rhizosphere biota impact adaptive divergence of phenotypic traits in teosinte along an environmental cline. This work suggests an important role for biotic interactions in determining the outcome of local adaptation.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://peerj.com/articles/6815/">Characterization of introgression from the teosinte <em>Zea </em>mays* ssp. <em>mexicana</em> to Mexican highland maize</a> [<a href="https://peerj.com/preprints/27489/">preprint</a>]<br />
Gonzalez-Segovia E, PÃ©rez-Limon S, C CÃntora-MartÃnez C, Guerrero-Zavala A, Jansen G, Hufford MB, <strong>Ross-Ibarra J</strong>, Ruairidh J H Sawers</p>
</summary>
<p style="margin-left: 30px">
We look for introgression from teosinte in the genomes of two highland landraces and use QTL mapping to test for functional relevance of introgressed regions.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><a href="https://www.genetics.org/content/211/3/989">Detecting adaptive differentiation in structured populations with genomic data and common gardens</a> [<a href="https://www.biorxiv.org/content/early/2018/07/13/368506">preprint</a>] [<a href="https://github.com/emjosephs/qpc-maize">github</a>]<br />
<strong>Josephs EB</strong>, Berg JJ, <strong>Ross-Ibarra J</strong>, Coop G</p>
</summary>
<p style="margin-left: 30px">
We develop methods to detect polygenic adaptation on phenotypes from common gardens and GWAS panels.
</p>
</details>
<p>
</p>
<details>
<summary>
<p><strong>Other papers by lab members</strong></p>
</summary>
<p style="margin-left: 30px">
<p><strong>Taylor Perkins</strong></p>
<pre><code>Perkins, M. Taylor, Tetyana Zhebentyayeva, Paul H. Sisco, and J. Hill Craddock. â€œGenome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis.â€ bioRxiv (2019): 680371.

Craddock, J. Hill, and M. Taylor Perkins. â€œChestnut (Castanea spp. Miller) Breeding.â€ In Advances in Plant Breeding Strategies, vol. 4. (J.M. Al-Khayri et al., eds.)(in press), 55 pages. Springer Nature Switzerland AG, Basel.  </code></pre>
<p><strong>Michelle Stitzer</strong></p>
<pre><code>Roessler, Kyria, Aline Muyle, Concepcion M. Diez, Garren RJ Gaut, Alexandros Bousios, Michelle C. Stitzer, Danelle K. Seymour, John F. Doebley, Qingpo Liu, and Brandon S. Gaut. &quot;The genome-wide dynamics of purging during selfing in maize.&quot; Nature plants (2019): 1-11.

Noshay, Jaclyn M., Sarah N. Anderson, Peng Zhou, Lexiang Ji, William Ricci, Zefu Lu, Michelle C. Stitzer et al. &quot;Monitoring the interplay between transposable element families and DNA methylation in maize.&quot; PLoS genetics 15, no. 9 (2019): e1008291.

Marcela K. Tello-Ruiz, Cristina F. Marco, Fei-Man Hsu, Rajdeep S. Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C. Stitzer, Rachael Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay C. Barone, Cornel Ghiban, Demitri Muna, Andrew C. Olson, Liya C. Wang, Doreen C. Ware, David A. Micklos bioRxiv 654848; doi: https://doi.org/10.1101/654848

Stitzer, Michelle C., and Philipp Brand. &quot;Digest: Hybrid incompatibilities and introgression in wild monkeyflowers.&quot; Evolution 72, no. 11 (2018): 2565-2566.</code></pre>
</p>