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Kate E. Guill - One of the best experts on this subject based on the ideXlab platform.
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comparative population genomics of maize Domestication and improvement
Nature Genetics, 2012Co-Authors: Matthew B. Hufford, Tanja Pyhäjärvi, Jer Ming Chia, Robert J. Elshire, Kate E. Guill, Jeffery C. Glaubitz, Reed A Cartwright, Xun Xu, Joost Van HeerwaardenAbstract:Jeff Ross-Ibarra and colleagues report a population genomic analysis of maize evolution. They analyze genome-wide evidence for selection during the initial Domestication of wild maize and during the improvement of landraces to modern inbred breeds. Their findings suggest stronger selection during Domestication compared to improvement.
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Comparative population genomics of maize Domestication and improvement
Nature Genetics, 2012Co-Authors: Matthew B. Hufford, Joost Van Heerwaarden, Tanja Pyhäjärvi, Jer Ming Chia, Robert J. Elshire, Kate E. Guill, Jeffery C. Glaubitz, Reed A Cartwright, Xun Xu, Shawn M. KaepplerAbstract:Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after Domestication, likely introgression from wild relatives, and evidence for stronger selection during Domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize Domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.
Michael D. Purugganan - One of the best experts on this subject based on the ideXlab platform.
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Copy Number Variation in Domestication.
Trends in Plant Science, 2019Co-Authors: Michael D. PuruggananAbstract:Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important Domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of Domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during Domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying Domestication, and review examples of Domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the Domestication process.
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Multiple origin but single Domestication led to domesticated Asian rice
bioRxiv, 2017Co-Authors: Jae Young Choi, Michael D. PuruggananAbstract:The Domestication scenario that led to Asian rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated rice dataset, which were also analyzed by two studies but resulted in two contrasting Domestication scenario. Our result indicates Asian rice originated from multiple wild progenitor subpopulations, however, Domestication occurred only once and the Domestication alleles were transferred between rice subpopulation through introgression.
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current perspectives and the future of Domestication studies
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Greger Larson, Loukas Barton, Michael D. Purugganan, Dolores R Piperno, Robin G Allaby, Leif Andersson, Manuel Arroyokalin, Cynthia C Vigueira, Tim DenhamAbstract:It is difficult to overstate the cultural and biological impacts that the Domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times Domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of Domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in Domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent Domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of Domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the Domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how Domestication took place, but also when and where it did, and where and why it did not.
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convergent evolution and parallelism in plant Domestication revealed by an expanding archaeological record
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Dorian Q Fuller, Michael D. Purugganan, Robin G Allaby, Manuel Arroyokalin, Tim Denham, Leilani Lucas, Chris J StevensAbstract:Recent increases in archaeobotanical evidence offer insights into the processes of plant Domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired Domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during Domestication. Among Domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most Domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological Domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant Domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter–gatherers whereas more often it was initiated by mobile societies of hunter–gatherers or herder–gatherers.
Susan Mccouch - One of the best experts on this subject based on the ideXlab platform.
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new insights into the history of rice Domestication
Trends in Genetics, 2007Co-Authors: Michael J. Kovach, Megan Sweeney, Susan MccouchAbstract:The history of rice Domestication has long been a subject of debate. Recently obtained genetic evidence provides new insights into this complex story. Genome-wide studies of variation demonstrate that the two varietal groups in Oryza sativa (indica and japonica) arose from genetically distinct gene pools within a common wild ancestor, Oryza rufipogon, suggesting multiple Domestications of O. sativa. However, the evolutionary history of recently cloned Domestication genes adds another layer of complexity to the Domestication of rice. Although some alleles exist only within specific subpopulations, as would be expected if the Domestications occurred independently, other major Domestication alleles are common to all cultivated O. sativa varieties. Our current view of rice Domestication supports multiple Domestications coupled with limited introgression that transferred key Domestication alleles between divergent rice gene pools.
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the complex history of the Domestication of rice
Annals of Botany, 2007Co-Authors: Megan Sweeney, Susan MccouchAbstract:†Background Rice has been found in archaeological sites dating to 8000 BC, although the date of rice Domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. †Scope Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes Domestication, supporting independent Domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for Domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous Domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several Domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the Domestication process and the relationship between the subspecies. †Conclusions The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.
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The complex history of the Domestication of rice
Annals of Botany, 2007Co-Authors: Megan Sweeney, Susan MccouchAbstract:BACKGROUND Rice has been found in archaeological sites dating to 8000 bc, although the date of rice Domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes Domestication, supporting independent Domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for Domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous Domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several Domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the Domestication process and the relationship between the subspecies. CONCLUSIONS The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.
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New insights into the history of rice Domestication
Trends in Genetics, 2007Co-Authors: Michael J. Kovach, Megan T. Sweeney, Susan MccouchAbstract:The history of rice Domestication has long been a subject of debate. Recently obtained genetic evidence provides new insights into this complex story. Genome-wide studies of variation demonstrate that the two varietal groups in Oryza sativa (indica and japonica) arose from genetically distinct gene pools within a common wild ancestor, Oryza rufipogon, suggesting multiple Domestications of O. sativa. However, the evolutionary history of recently cloned Domestication genes adds another layer of complexity to the Domestication of rice. Although some alleles exist only within specific subpopulations, as would be expected if the Domestications occurred independently, other major Domestication alleles are common to all cultivated O. sativa varieties. Our current view of rice Domestication supports multiple Domestications coupled with limited introgression that transferred key Domestication alleles between divergent rice gene pools. © 2007 Elsevier Ltd. All rights reserved.
Tao Sang - One of the best experts on this subject based on the ideXlab platform.
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The puzzle of rice Domestication
Journal of Integrative Plant Biology, 2007Co-Authors: Tao Sang, Song GeAbstract:The origin of cultivated rice has puzzled plant biologists for decades. This is due, at least in part, to the complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. The long-standing controversy over single versus multiple and annual versus perennial origins of cultivated rice has been brought into shaper focus with the rapid accumulation of genetic and phylogenetic data. Molecular phylogenetic analyses revealed ancient genomic differentiation between rice cultivars, suggesting that they were domesticated from divergent wild populations. However, the recently cloned Domestication gene sh4, responsible for the reduction of grain shattering from wild to cultivated rice, seems to have originated only once. Herein, we propose two models to reconcile apparently conflicting evidence regarding rice Domestication. The snow-balling model considers a single origin of cultivated rice. In this model, a core of critical Domestication alleles was fixed in the founding cultivar and then acted to increase the genetic diversity of cultivars through hybridization with wild populations. The combination model considers multiple origins of cultivated rice. In this model, initial cultivars were domesticated from divergent wild populations and fixed different sets of Domestication alleles. Subsequent crosses among these semi-domesticated cultivars resulted in the fixation of a similar set of critical Domestication alleles in the contemporary cultivars. In both models, introgression has played an important role in rice Domestication. Recent and future introgression of beneficial genes from the wild gene pool through conventional and molecular breeding programs can be viewed as the continuation of Domestication.
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genetic analysis of rice Domestication syndrome with the wild annual species oryza nivara
New Phytologist, 2006Co-Authors: Changbao Li, Ailing Zhou, Tao SangAbstract:Summary • With a small and sequenced genome, rice provides an excellent system for studying the genetics of cereal Domestication. • We conducted a quantitative trait locus (QTL) analysis of key Domestication traits using an F2 population derived from a cross between the cultivated rice, Oryza sativa, and the annual wild species, O. nivara. • We found that the QTL of large phenotypic effects were targeted by Domestication selection for effective harvest and planting, including a reduction in seed shattering and seed dormancy and the synchronization of seed maturation. Selection for higher yield was probably responsible for the fixation of mutations at a cluster of QTL on chromosome 7 and a few other chromosomal locations that could have substantially improved plant architecture and panicle structure, resulting in fewer erect tillers and longer and more highly branched panicles in cultivated rice. • In comparison with the wild perennial species, O. rufipogon, rice Domestication from O. nivara would have involved QTL with a greater degree of chromosomal co-localization and required little genetic change associated with life history or mating system transitions. The genetic analyses of Domestication traits with both wild relatives will open opportunities for the improvement of rice cultivars utilizing natural germplasm.
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Rice Domestication by reducing shattering
Science, 2006Co-Authors: Changbao Li, Ailing Zhou, Tao SangAbstract:Crop Domestication frequently began with the selection of plants that did not naturally shed ripe fruits or seeds. The reduction in grain shattering that led to cereal Domestication involved genetic loci of large effect. The molecular basis of this key Domestication transition, however, remains unknown. Here we show that human selection of an amino acid substitution in the predicted DNA binding domain encoded by a gene of previously unknown function was primarily responsible for the reduction of grain shattering in rice Domestication. The substitution undermined the gene function necessary for the normal development of an abscission layer that controls the separation of a grain from the pedicel.
John Doebley - One of the best experts on this subject based on the ideXlab platform.
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identification of a functional transposon insertion in the maize Domestication gene tb1
Nature Genetics, 2011Co-Authors: Anthony J Studer, Qiong Zhao, Jeffrey Rossibarra, John DoebleyAbstract:John Doebley and colleagues have identified a transposon insertion in the maize Domestication gene, tb1, that acts as a regulatory enhancer. The transposon insertion appears to be a causative variant that partially explains major changes in plant architecture during maize Domestication.
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A single Domestication for maize shown by multilocus microsatellite genotyping
Proceedings of the National Academy of Sciences, 2002Co-Authors: Y. Matsuoka, Yves Vigouroux, M. M. Goodman, Edward S. Buckler, J. Sanchez, John DoebleyAbstract:There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent Domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single Domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postDomestication gene flow from teosinte into maize.
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the limits of selection during maize Domestication
Nature, 1999Co-Authors: Ronglin Wang, Adrian O Stec, Lewis Lukens, John DoebleyAbstract:The Domestication of all major crop plants occurred during a brief period in human history about 10,000 years ago1. During this time, ancient agriculturalists selected seed of preferred forms and culled out seed of undesirable types to produce each subsequent generation. Consequently, favoured alleles at genes controlling traits of interest increased in frequency, ultimately reaching fixation. When selection is strong, Domestication has the potential to drastically reduce genetic diversity in a crop. To understand the impact of selection during maize Domestication, we examined nucleotide polymorphism in teosinte branched1, a gene involved in maize evolution2. Here we show that the effects of selection were limited to the gene's regulatory region and cannot be detected in the protein-coding region. Although selection was apparently strong, high rates of recombination and a prolonged Domestication period probably limited its effects. Our results help to explain why maize is such a variable crop. They also suggest that maize Domestication required hundreds of years, and confirm previous evidence that maize was domesticated from Balsas teosinte of southwestern Mexico.
