Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae)
Myounghai Kwak,Paul Gepts +1 more
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The Andean domesticated race Nueva Granada had the highest FST value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.Abstract:
Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F(ST), and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F(ST) value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.read more
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A reference genome for common bean and genome-wide analysis of dual domestications
Jeremy Schmutz,Phillip E. McClean,Sujan Mamidi,G Albert Wu,Steven B. Cannon,Jane Grimwood,Jerry Jenkins,Shengqiang Shu,Qijian Song,Carolina Chavarro,Mirayda Torres-Torres,Valérie Geffroy,Samira Mafi Moghaddam,Dongying Gao,Brian Abernathy,Kerrie Barry,Matthew W. Blair,Mark A. Brick,Mansi Chovatia,Paul Gepts,David Goodstein,Michael D. Gonzales,Uffe Hellsten,David L. Hyten,Gaofeng Jia,James D. Kelly,Dave Kudrna,Rian Lee,Manon M.S. Richard,Phillip N. Miklas,Juan M. Osorno,Josiane Rodrigues,Vincent Thareau,Carlos A. Urrea,Mei Wang,Yeisoo Yu,Ming Zhang,Rod A. Wing,Perry B. Cregan,Daniel S. Rokhsar,Scott A. Jackson +40 more
TL;DR: 2 independent domestications from genetic pools that diverged before human colonization are confirmed and a set of genes linked with increased leaf and seed size are identified and combined with quantitative trait locus data from Mesoamerican cultivars.
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Current perspectives and the future of domestication studies
Greger Larson,Dolores R. Piperno,Robin G. Allaby,Michael D. Purugganan,Leif Andersson,Leif Andersson,Manuel Arroyo-Kalin,Loukas Barton,Cynthia C. Vigueira,Tim Denham,Keith Dobney,Andrew N. Doust,Paul Gepts,M. Thomas P. Gilbert,Kristen J. Gremillion,Leilani Lucas,Lewis Lukens,Fiona Marshall,Kenneth M. Olsen,J. Chris Pires,Peter J. Richerson,Rafael Rubio de Casas,Oris I. Sanjur,Mark G. Thomas,Dorian Q. Fuller +24 more
TL;DR: It is argued 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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Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity.
Stéphanie Klaedtke,Leonardo Caproni,Julia Klauck,Paul De La Chevardière De La Grandville,Martin Dutartre,Pierre-Marie Stassart,Véronique Chable,Valeria Negri,Lorenzo Raggi +8 more
TL;DR: Results indicate that three years of multiplication suffice for local adaptation to occur, and the microevolution of bean populations within networks of gardens and farms emerges as a research perspective.
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