The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
John Doebley - One of the best experts on this subject based on the ideXlab platform.
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defining the role of the mads box gene zea agamous like1 a target of selection during maize domestication
Journal of Heredity, 2018Co-Authors: James B. Holland, Alessandra M York, David M Wills, Zhou Fang, John DoebleyAbstract:Genomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, Teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time. To determine the trait(s) controlled by zagl1 that was (were) the target(s) of selection during maize domestication, we created a set of recombinant chromosome isogenic lines that differ for the maize versus Teosinte alleles of zagl1 and which carry cross-overs between zagl1 and its neighbor genes. These lines were grown in a randomized trial and scored for flowering time and domestication related traits. The results indicated that the maize versus Teosinte alleles of zagl1 affect flowering time as expected, as well as multiple traits related to ear size with the maize allele conferring larger ears with more kernels. Our results suggest that zagl1 may have been under selection during domestication to increase the size of the maize ear.
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a gene for genetic background in zea mays fine mapping enhancer of Teosinte branched1 2 to a yabby class transcription factor
Genetics, 2016Co-Authors: Chin Jian Yang, Anthony J Studer, Lisa E Kursel, Madelaine E Bartlett, Clinton J Whipple, John DoebleyAbstract:The effects of an allelic substitution at a gene often depend critically on genetic background, i.e., the genotypes at other genes in the genome. During the domestication of maize from its wild ancestor (Teosinte), an allelic substitution at Teosinte branched (tb1) caused changes in both plant and ear architecture. The effects of tb1 on phenotype were shown to depend on multiple background loci, including one called enhancer of tb1.2 (etb1.2). We mapped etb1.2 to a YABBY class transcription factor (ZmYAB2.1) and showed that the maize alleles of ZmYAB2.1 are either expressed at a lower level than Teosinte alleles or disrupted by insertions in the sequences. tb1 and etb1.2 interact epistatically to control the length of internodes within the maize ear, which affects how densely the kernels are packed on the ear. The interaction effect is also observed at the level of gene expression, with tb1 acting as a repressor of ZmYAB2.1 expression. Curiously, ZmYAB2.1 was previously identified as a candidate gene for another domestication trait in maize, nonshattering ears. Consistent with this proposed role, ZmYAB2.1 is expressed in a narrow band of cells in immature ears that appears to represent a vestigial abscission (shattering) zone. Expression in this band of cells may also underlie the effect on internode elongation. The identification of ZmYAB2.1 as a background factor interacting with tb1 is a first step toward a gene-level understanding of how tb1 and the background within which it works evolved in concert during maize domestication.
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a gene for genetic background in zea mays fine mapping enhancer of Teosinte branched1 2 etb1 2 to a yabby class transcription factor
bioRxiv, 2016Co-Authors: Chin Jian Yang, Anthony J Studer, Lisa E Kursel, Madelaine E Bartlett, Clinton J Whipple, John DoebleyAbstract:The effects of an allelic substitution at a gene often depend critically on genetic background, the genotype at other genes in the genome. During the domestication of maize from its wild ancestor (Teosinte), an allelic substitution at Teosinte branched (tb1) caused changes in both plant and ear architecture. The effects of tb1 on phenotype were shown to depend on multiple background loci including one called enhancer of tb1.2 (etb1.2). We mapped etb1.2 to a YABBY class transcription factor (ZmYAB2.1) and showed that the maize alleles of ZmYAB2.1 are either expressed at a lower level than Teosinte alleles or disrupted by insertions in the sequences. tb1 and etb1.2 interact epistatically to control the length of internodes within the maize ear which affects how densely the kernels are packed on the ear. The interaction effect is also observed at the level of gene expression with tb1 acting as a repressor of ZmYAB2.1 expression. Curiously, ZmYAB2.1 was previously identified as a candidate gene for another domestication trait in maize, non-shattering ears. Consistent with this proposed role, ZmYAB2.1 is expressed in a narrow band of cells in immature ears that appears to represent a vestigial abscission (shattering) zone. Expression in this band of cells may also underlie the effect on internode elongation. The identification of ZmYAB2.1 as a background factor interacting with tb1 is a first step toward a gene-level understanding of how tb1 and the background within which it works evolved in concert during maize domestication.
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mapping prolificacy qtl in maize and Teosinte
Journal of Heredity, 2016Co-Authors: Liyan Yang, Wei Xue, Chin Jian Yang, Qi Cheng, John DoebleyAbstract:Teosinte, the ancestor of maize, possesses multiple ears at each node along its main stalk, whereas maize has only a single ear at each node. With its greater ear number, Teosinte is referred to as being more prolific. The grassy tillers 1 (gt1) gene has been identified as a large-effect quantitative trait locus underlying this prolificacy difference between maize and Teosinte, and the causal polymorphism for the difference was mapped to a 2.7kb control region 5' of the gt1 ORF. The most common maize haplotype (M1) at the gt1 control region confers low prolificacy. A prior study reported that 29% of maize varieties possess the Teosinte haplotype (T) for the control region, although these varieties are nonprolific. This observation suggested that these maize lines might possess an additional factor, other than gt1, suppressing prolificacy in maize. We discovered that the factor suppressing prolificacy in maize varieties with the gt1 T haplotype mapped to a 3.20 cM interval, which includes gt1 Subsequent DNA sequence analysis revealed that the maize varieties with the apparent T haplotype actually possess a distinct maize haplotype (M2) that is similar, but not identical, to the T haplotype in sequence but is associated with a nonprolific phenotype similar to the M1 haplotype. Our data indicate that the M2 haplotype or a closely linked factor confers a nonprolific phenotype. Our data suggest that 2 different alleles or haplotypes (M1 and M2) of gt1 were selected during domestication, and that nonprolificacy in all maize varieties is likely a result of allele substitutions at gt1.
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evidence for a natural allelic series at the maize domestication locus Teosinte branched1
Genetics, 2012Co-Authors: Anthony J Studer, John DoebleyAbstract:Despite numerous quantitative trait loci and association mapping studies, our understanding of the extent to which natural allelic series contribute to the variation for complex traits is limited. In this study, we investigate the occurrence of a natural allelic series for complex traits at the Teosinte branched1 (tb1) gene in natural populations of Teosinte (Zea mays ssp. parviglumis, Z. mays ssp. mexicana, and Z. diploperennis). Previously, tb1 was shown to confer large effects on both plant architecture and ear morphology between domesticated maize and Teosinte; however, the effect of tb1 on trait variation in natural populations of Teosinte has not been investigated. We compare the effects of nine Teosinte alleles of tb1 that were introgressed into an isogenic maize inbred background. Our results provide evidence for a natural allelic series at tb1 for several complex morphological traits. The Teosinte introgressions separate into three distinct phenotypic classes, which correspond to the taxonomic origin of the alleles. The effects of the three allelic classes also correspond to known morphological differences between the Teosinte taxa. Our results suggest that tb1 contributed to the morphological diversification of Teosinte taxa as well as to the domestication of maize.
Richard M Clark - One of the best experts on this subject based on the ideXlab platform.
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major regulatory genes in maize contribute to standing variation in Teosinte zea mays ssp parviglumis
Genetics, 2007Co-Authors: Allison L Weber, Richard M Clark, Jose De Jesus Sanchezgonzalez, Peter J Bradbury, Laura Vaughn, Brian S Yandell, John DoebleyAbstract:In plants, many major regulatory genes that control plant growth and development have been identified and characterized. Despite a detailed knowledge of the function of these genes little is known about how they contribute to the natural variation for complex traits. To determine whether major regulatory genes of maize contribute to standing variation in Balsas Teosinte we conducted association mapping in 584 Balsas Teosinte individuals. We tested 48 markers from nine candidate regulatory genes against 13 traits for plant and inflorescence architecture. We identified significant associations using a mixed linear model that controls for multiple levels of relatedness. Ten associations involving five candidate genes were significant after correction for multiple testing, and two survive the conservative Bonferroni correction. zfl2, the maize homolog of FLORICAULA of Antirrhinum, was associated with plant height. zap1, the maize homolog of APETALA1 of Arabidopsis, was associated with inflorescence branching. Five SNPs in the maize domestication gene, Teosinte branched1, were significantly associated with either plant or inflorescence architecture. Our data suggest that major regulatory genes in maize do play a role in the natural variation for complex traits in Teosinte and that some of the minor variants we identified may have been targets of selection during domestication.
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a distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture
Nature Genetics, 2006Co-Authors: Tina Nussbaum Wagler, Richard M Clark, Pablo A Quijada, John DoebleyAbstract:Although quantitative trait locus (QTL) mapping has been successful in describing the genetic architecture of complex traits1,2,3,4, the molecular basis of quantitative variation is less well understood, especially in plants such as maize that have large genome sizes. Regulatory changes at the Teosinte branched1 (tb1) gene have been proposed to underlie QTLs of large effect for morphological differences that distinguish maize (Zea mays ssp. mays) from its wild ancestors, the Teosintes (Z. mays ssp. parviglumis and mexicana)1,5,6,7. We used a fine mapping approach to show that intergenic sequences ∼58–69 kb 5′ to the tb1 cDNA confer pleiotropic effects on Z. mays morphology. Moreover, using an allele-specific expression assay, we found that sequences >41 kb upstream of tb1 act in cis to alter tb1 transcription. Our findings show that the large stretches of noncoding DNA that comprise the majority of many plant genomes can be a source of variation affecting gene expression and quantitative phenotypes.
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a distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture
Nature Genetics, 2006Co-Authors: Richard M Clark, Tina Nussbaum Wagler, Pablo A Quijada, John DoebleyAbstract:Although quantitative trait locus (QTL) mapping has been successful in describing the genetic architecture of complex traits, the molecular basis of quantitative variation is less well understood, especially in plants such as maize that have large genome sizes. Regulatory changes at the Teosinte branched1 (tb1) gene have been proposed to underlie QTLs of large effect for morphological differences that distinguish maize (Zea mays ssp. mays) from its wild ancestors, the Teosintes (Z. mays ssp. parviglumis and mexicana). We used a fine mapping approach to show that intergenic sequences approximately 58-69 kb 5' to the tb1 cDNA confer pleiotropic effects on Z. mays morphology. Moreover, using an allele-specific expression assay, we found that sequences >41 kb upstream of tb1 act in cis to alter tb1 transcription. Our findings show that the large stretches of noncoding DNA that comprise the majority of many plant genomes can be a source of variation affecting gene expression and quantitative phenotypes.
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pattern of diversity in the genomic region near the maize domestication gene tb1
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Richard M Clark, Eric Linton, Joachim Messing, John DoebleyAbstract:Domesticated maize and its wild ancestor (Teosinte) differ strikingly in morphology and afford an opportunity to examine the connection between strong selection and diversity in a major crop species. The tb1 gene largely controls the increase in apical dominance in maize relative to Teosinte, and a region of the tb1 locus 5′ to the transcript sequence was a target of selection during maize domestication. To better characterize the impact of selection at a major “domestication” locus, we have sequenced the upstream tb1 genomic region and systematically sampled nucleotide diversity for sites located as far as 163 kb upstream to tb1. Our analyses define a selective sweep of ≈60–90 kb 5′ to the tb1 transcribed sequence. The selected region harbors a mixture of unique sequences and large repetitive elements, but it contains no predicted genes. Diversity at the nearest 5′ gene to tb1 is typical of that for neutral maize loci, indicating that selection at tb1 has had a minimal impact on the surrounding chromosomal region. Our data also show low intergenic linkage disequilibrium in the region and suggest that selection has had a minor role in shaping the pattern of linkage disequilibrium that is observed. Finally, our data raise the possibility that maize-like tb1 haplotypes are present in extant Teosinte populations, and our findings also suggest a model of tb1 gene regulation that differs from traditional views of how plant gene expression is controlled.
Jeffrey Rossibarra - One of the best experts on this subject based on the ideXlab platform.
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strengthened mutualistic adaptation between Teosinte and its rhizosphere biota in cold climates
bioRxiv, 2021Co-Authors: Anna M Obrien, Luis E Eguiarte, Jeffrey Rossibarra, Sawers Rjh, Jaime Gascapineda, Ivan Baxter, S Y StraussAbstract:O_LIWhile abiotic environments consistently shape local adaptation, the strength of local adaptation to biotic interactions may vary more. One theory, COCO (CO-evolutionary Outcomes across Conditionality), predicts it may be strongest where species experience greater stress, because stress increases fitness impacts of species interactions. For example, in plant interactions with rhizosphere biota, positive outcomes increase with stress from low soil fertility, drought and cold. C_LIO_LITo investigate the influence of abiotic stress gradients on adaptation between plants and rhizosphere biota, we used a greenhouse common garden experiment recombining Teosinte, Zea mays ssp. mexicana (wild relative of maize), and rhizosphere biota, collected across a stress gradient (elevational variation in temperature, precipitation, and nutrients). C_LIO_LIWe found stronger local adaptation between Teosinte and rhizosphere biota from colder, more stressful sites, as expected by COCO. However, biota from less stressful, warmer sites provided greater average benefits across Teosinte populations. Links between plant traits and 20-element profiles of plant leaves explained fitness variation, persisted in the field, were influenced by both plants and biota, and largely reflected patterns of local adaptation. C_LIO_LIIn sum, we uncovered greater local adaptation to biotic interactions in colder sites, and that both plants and rhizosphere biota affect the expression of plant phenotypes. C_LI
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adaptive phenotypic divergence in Teosinte differs across biotic contexts
bioRxiv, 2018Co-Authors: Anna M Obrien, Ruairidh J H Sawers, Sharon Y Strauss, Jeffrey RossibarraAbstract:Abstract Climate is a powerful force shaping adaptation within species, often creating dramatic phenotypic clines. Yet adaptation to climate does not occur in a vacuum: species interactions filter the fitness consequences of both climatic and phenotypic variation. In other words, the translation of genotype to phenotype may be altered by biotic context, influencing the variation upon which climatic selection can act. We investigate the role of such interactions in changing the phenotypes on which selection acts using ten populations of an annual grass species (Teosinte: Zea mays ssp. mexicana) sourced from along an elevational gradient, along with rhizosphere biota sourced from three of those populations. We grow Teosinte families in a half-sibling design in separate biota treatments to first test whether the divergence we see among traits in Teosinte populations exceeds what we would expect from genetic drift and then whether the source of rhizosphere biota affects the expression of divergent traits. We also assay the influence of these three rhizosphere biotas on contemporary additive genetic variation in Teosinte traits across populations. We find that expression of most measured traits in Teosinte is altered by rhizosphere biota, as well as the degree of variance and covariance among traits involved in root mass and flowering time. As a number of these traits are also found to underlie adaptive divergence across habitats, our data suggest that biota influence the expression of traits underlying local adaptation. Together, our results suggest that changes in trait expression and covariance elicited by interactor communities in root mass and flowering time may have played a historical role in local adaption of Teosinte to environments, and that they would play a contemporary role in responses to changing selection pressures.
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extending the stress gradient hypothesis increased local adaptation between Teosinte and soil biota at the stressful end of a climate gradient
bioRxiv, 2015Co-Authors: Anna M Obrien, Ruairidh J H Sawers, Jeffrey Rossibarra, Sharon Y StraussAbstract:In order to predict plant responses to rapid climate change, we will need to understand the role of biotic interactions in plant climate adaptation. We extend the stress-gradient (SG) hypothesis to posit that, as interactions become more mutualistic at stressful ends of environmental gradients, so does selection for mutualistic co-adaptation. We call this the stress-gradient evolution hypothesis (SGE). We test our SGE hypothesis in the interactions of Teosinte (Zea mays ssp. mexicana) with its rhizosphere soil biota in populations across a climate gradient. In support of SGE predictions, we find local adaptation of Teosinte to soil biota at the stressful (cold) end of our climatic gradient but not at the benign (warm) end: sympatric combinations of plants and biota from stressful sites both increase plant fitness and generate more locally adapted plant phenotypes. Our results suggest that co-adaptation of interacting partners may be a means of ameliorating stressful environments.
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natural variation in Teosinte at the domestication locus Teosinte branched1 tb1
PeerJ, 2015Co-Authors: Laura Vann, Tanja Pyhajarvi, Matthew B Hufford, Thomas J Y Kono, Jeffrey RossibarraAbstract:The Teosinte branched1(tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, Teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maize tb1 allele in Teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in Teosinte. We assessed the prevalence of the Hopscotch element across an Americas-wide sample of 837 maize and Teosinte individuals using a co-dominant PCR assay. Additionally, we calculated population genetic summaries using sequence data from a subset of individuals from four Teosinte populations and collected phenotypic data using seed from a single Teosinte population where Hopscotch was found segregating at high frequency. Genotyping results indicate the Hopscotch element is found in a number of Teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on the tb1 locus, revealing a potential ecological role, but a greenhouse experiment does not detect a strong association between the Hopscotch and tillering in Teosinte. Our findings suggest the role of Hopscotch differs between maize and Teosinte. Future work should assess tb1 expression levels in Teosinte with and without the Hopscotch and more comprehensively phenotype Teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in Teosinte.
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natural variation in Teosinte at the domestication locus Teosinte branched1 tb1
bioRxiv, 2014Co-Authors: Laura Vann, Tanja Pyhajarvi, Matthew B Hufford, Thomas J Y Kono, Jeffrey RossibarraAbstract:Premise of the study: The Teosinte branched1 (tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, Teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene's expression, causing reduced tillering in maize. Observations of the maize tb1 allele in Teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in Teosinte. Methods: Prevalence of the Hopscotch element was assessed across an Americas-wide sample of 837 maize and Teosinte individuals using a codominant PCR assay. Population genetic summaries were calculated for a subset of individuals from four Teosinte populations in central Mexico. Phenotypic data were also collected using seed from a single Teosinte population where Hopscotch was found segregating at high frequency. Key results: Genotyping results indicate the Hopscotch element is found in a number of Teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on this locus revealing a potential ecological role for Hopscotch in Teosinte, but a greenhouse experiment does not detect a strong association between tb1 and tillering in Teosinte. Conclusions: Our findings suggest the role of Hopscotch differs between maize and Teosinte. Future work should assess tb1 expression levels in Teosinte with and without the Hopscotch and more comprehensively phenotype Teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in Teosinte.
Chin Jian Yang - One of the best experts on this subject based on the ideXlab platform.
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the genetic architecture of the maize progenitor Teosinte and how it was altered during maize domestication
PLOS Genetics, 2020Co-Authors: Qiuyue Chen, Chin Jian Yang, Luis Fernando Samayoa, Peter J Bradbury, Bode A Olukolu, Michael A Neumeyer, Maria Cinta Romay, Qi Sun, Anne Lorant, Edward S BucklerAbstract:The genetics of domestication has been extensively studied ever since the rediscovery of Mendel'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 FST) 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 "missing" 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.
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teonam a nested association mapping population for domestication and agronomic trait analysis in maize
Genetics, 2019Co-Authors: Qiuyue Chen, Chin Jian Yang, Alessandra M York, Wei Xue, Lora L Daskalska, Craig A Devalk, Kyle W Krueger, Samuel B Lawton, Bailey G SpiegelbergAbstract:Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple Teosinte inbred lines as parents has been lacking. Here, we report a Teosinte nested association mapping (TeoNAM) population, derived from crossing five Teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous Teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and a genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTL from JLM were identified, with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from Teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in Teosinte and maize. We detected multiple QTL for flowering time and other traits for which the Teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.
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teonam a nested association mapping population for domestication and agronomic trait analysis in maize
bioRxiv, 2019Co-Authors: Qiuyue Chen, Chin Jian Yang, Alessandra M York, Wei Xue, Lora L Daskalska, Craig A Devalk, Kyle W Krueger, Samuel B Lawton, Bailey G SpiegelbergAbstract:Abstract Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple Teosinte inbred lines as parents has been lacking. Here, we report a Teosinte nested association mapping population (TeoNAM), derived from crossing five Teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous Teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTLs from JLM were identified with many of these mapping to known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from Teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in Teosinte and maize. We detected multiple QTLs for flowering time and other traits for which the Teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.
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the genetic architecture of Teosinte catalyzed and constrained maize domestication
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Chin Jian Yang, Alessandra M York, Wei Xue, Lora L Daskalska, Luis Fernando Samayoa, Peter J Bradbury, Bode A Olukolu, Michael R Tuholski, Weidong Wang, Michael A NeumeyerAbstract:The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in Teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern Teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to Teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between Teosinte and maize landrace genetic variance–covariance matrices (G-matrices). While the structure of G-matrix in Teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.
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a gene for genetic background in zea mays fine mapping enhancer of Teosinte branched1 2 to a yabby class transcription factor
Genetics, 2016Co-Authors: Chin Jian Yang, Anthony J Studer, Lisa E Kursel, Madelaine E Bartlett, Clinton J Whipple, John DoebleyAbstract:The effects of an allelic substitution at a gene often depend critically on genetic background, i.e., the genotypes at other genes in the genome. During the domestication of maize from its wild ancestor (Teosinte), an allelic substitution at Teosinte branched (tb1) caused changes in both plant and ear architecture. The effects of tb1 on phenotype were shown to depend on multiple background loci, including one called enhancer of tb1.2 (etb1.2). We mapped etb1.2 to a YABBY class transcription factor (ZmYAB2.1) and showed that the maize alleles of ZmYAB2.1 are either expressed at a lower level than Teosinte alleles or disrupted by insertions in the sequences. tb1 and etb1.2 interact epistatically to control the length of internodes within the maize ear, which affects how densely the kernels are packed on the ear. The interaction effect is also observed at the level of gene expression, with tb1 acting as a repressor of ZmYAB2.1 expression. Curiously, ZmYAB2.1 was previously identified as a candidate gene for another domestication trait in maize, nonshattering ears. Consistent with this proposed role, ZmYAB2.1 is expressed in a narrow band of cells in immature ears that appears to represent a vestigial abscission (shattering) zone. Expression in this band of cells may also underlie the effect on internode elongation. The identification of ZmYAB2.1 as a background factor interacting with tb1 is a first step toward a gene-level understanding of how tb1 and the background within which it works evolved in concert during maize domestication.
Matthew B Hufford - One of the best experts on this subject based on the ideXlab platform.
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natural variation in Teosinte at the domestication locus Teosinte branched1 tb1
PeerJ, 2015Co-Authors: Laura Vann, Tanja Pyhajarvi, Matthew B Hufford, Thomas J Y Kono, Jeffrey RossibarraAbstract:The Teosinte branched1(tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, Teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maize tb1 allele in Teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in Teosinte. We assessed the prevalence of the Hopscotch element across an Americas-wide sample of 837 maize and Teosinte individuals using a co-dominant PCR assay. Additionally, we calculated population genetic summaries using sequence data from a subset of individuals from four Teosinte populations and collected phenotypic data using seed from a single Teosinte population where Hopscotch was found segregating at high frequency. Genotyping results indicate the Hopscotch element is found in a number of Teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on the tb1 locus, revealing a potential ecological role, but a greenhouse experiment does not detect a strong association between the Hopscotch and tillering in Teosinte. Our findings suggest the role of Hopscotch differs between maize and Teosinte. Future work should assess tb1 expression levels in Teosinte with and without the Hopscotch and more comprehensively phenotype Teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in Teosinte.
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natural variation in Teosinte at the domestication locus Teosinte branched1 tb1
bioRxiv, 2014Co-Authors: Laura Vann, Tanja Pyhajarvi, Matthew B Hufford, Thomas J Y Kono, Jeffrey RossibarraAbstract:Premise of the study: The Teosinte branched1 (tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, Teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene's expression, causing reduced tillering in maize. Observations of the maize tb1 allele in Teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in Teosinte. Methods: Prevalence of the Hopscotch element was assessed across an Americas-wide sample of 837 maize and Teosinte individuals using a codominant PCR assay. Population genetic summaries were calculated for a subset of individuals from four Teosinte populations in central Mexico. Phenotypic data were also collected using seed from a single Teosinte population where Hopscotch was found segregating at high frequency. Key results: Genotyping results indicate the Hopscotch element is found in a number of Teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on this locus revealing a potential ecological role for Hopscotch in Teosinte, but a greenhouse experiment does not detect a strong association between tb1 and tillering in Teosinte. Conclusions: Our findings suggest the role of Hopscotch differs between maize and Teosinte. Future work should assess tb1 expression levels in Teosinte with and without the Hopscotch and more comprehensively phenotype Teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in Teosinte.
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Teosinte as a model system for population and ecological genomics
Trends in Genetics, 2012Co-Authors: Matthew B Hufford, Paul Bilinski, Tanja Pyhajarvi, Jeffrey RossibarraAbstract:As the cost of next-generation sequencing diminishes and genomic resources improve, crop wild relatives are well positioned to make major contributions to the field of ecological genomics via full-genome resequencing and reference-assisted de novo assembly of genomes of plants from natural populations. The wild relatives of maize, collectively known as Teosinte, are a more varied and representative study system than many other model flowering plants. In this review of the population and ecological genomics of the Teosintes we highlight recent advances in the study of maize domestication, introgressive hybridization, and local adaptation, and discuss future prospects for applying the genomic resources of maize to this intriguing group of species. The maize/Teosinte study system is an excellent example of how crops and their wild relatives can bridge the model/non-model gap.
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complex patterns of local adaptation in Teosinte
arXiv: Populations and Evolution, 2012Co-Authors: Tanja Pyhajarvi, Matthew B Hufford, Sofiane Mezmouk, Jeffrey RossibarraAbstract:Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and a good understanding of population structure. We have used environmental and high-density genotype data to describe the genetic basis of local adaptation in 21 populations of Teosinte, the wild ancestor of maize. We found that altitude, dispersal events and admixture among subspecies formed a complex hierarchical genetic structure within Teosinte. Patterns of linkage disequilibrium revealed four mega-base scale inversions that segregated among populations and had altitudinal clines. Based on patterns of differentiation and correlation with environmental variation, inversions and nongenic regions play an important role in local adaptation of Teosinte. Further, we note that strongly differentiated individual populations can bias the identification of adaptive loci. The role of inversions in local adaptation has been predicted by theory and requires attention as genome-wide data become available for additional plant species. These results also suggest a potentially important role for noncoding variation, especially in large plant genomes in which the gene space represents a fraction of the entire genome.
