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      Archaeological Soybean ( Glycine max) in East Asia: Does Size Matter?

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          Abstract

          The recently acquired archaeological record for soybean from Japan, China and Korea is shedding light on the context in which this important economic plant became associated with people and was domesticated. This paper examines archaeological (charred) soybean seed size variation to determine what insight can be gained from a comprehensive comparison of 949 specimens from 22 sites. Seed length alone appears to represent seed size change through time, although the length×width×thickness product has the potential to provide better size change resolution. A widespread early association of small seeded soybean is as old as 9000–8600 cal BP in northern China and 7000 cal BP in Japan. Direct AMS radiocarbon dates on charred soybean seeds indicate selection resulted in large seed sizes in Japan by 5000 cal BP (Middle Jomon) and in Korea by 3000 cal BP (Early Mumun). Soybean seeds recovered in China from the Shang through Han periods are similar in length to the large Korean and Japanese specimens, but the overall size of the large Middle and Late Jomon, Early Mumun through Three Kingdom seeds is significantly larger than any of the Chinese specimens. The archaeological record appears to disconfirm the hypothesis of a single domestication of soybean and supports the view informed by recent phyologenetic research that soybean was domesticated in several locations in East Asia.

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          Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.

          We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.
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            Impacts of genetic bottlenecks on soybean genome diversity.

            Soybean has undergone several genetic bottlenecks. These include domestication in Asia to produce numerous Asian landraces, introduction of relatively few landraces to North America, and then selective breeding over the past 75 years. It is presumed that these three human-mediated events have reduced genetic diversity. We sequenced 111 fragments from 102 genes in four soybean populations representing the populations before and after genetic bottlenecks. We show that soybean has lost many rare sequence variants and has undergone numerous allele frequency changes throughout its history. Although soybean genetic diversity has been eroded by human selection after domestication, it is notable that modern cultivars have retained 72% of the sequence diversity present in the Asian landraces but lost 79% of rare alleles (frequency
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              Artificial selection for determinate growth habit in soybean.

              Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit, whereas Glycine soja, the wild progenitor of soybean, is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes, when mated, produce progeny that segregate in a monogenic pattern. Here, we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1), a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene, each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype, but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However, the GmTfl1 homeolog, despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1, appears to be sub- or neo-functionalized, as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                4 November 2011
                : 6
                : 11
                : e26720
                Affiliations
                [1 ]Department of Anthropology, University of Oregon, Eugene, Oregon, United States of America
                [2 ]Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada
                [3 ]East Asian Languages and Cultures, Stanford Archaeology Center, Stanford University, Stanford, California, United States of America
                [4 ]Paleo Labo Co., Ltd., Toda, Japan
                [5 ]Department of Archaeology, Shandong University, Jinan, China
                The Pennsylvania State University, United States of America
                Author notes

                Conceived and designed the experiments: GL GWC LL. Performed the experiments: GL GWC LL. Analyzed the data: GL GWC LL YS XC. Contributed reagents/materials/analysis tools: GL GWC LL YS XC. Wrote the paper: GL GWC LL. Data acquisition & excavation: GL GWC LL. Revised the draft critically for important intellectual content: GL GWC LL YS XC.

                Article
                PONE-D-11-06451
                10.1371/journal.pone.0026720
                3208558
                22073186
                b9249d74-b295-49cd-b37b-ccc5df3e08f2
                Lee et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 13 April 2011
                : 3 October 2011
                Page count
                Pages: 12
                Categories
                Research Article
                Agriculture
                Biology
                Ecology
                Plant Ecology
                Evolutionary Biology
                Paleontology
                Paleobotany
                Paleontology
                Paleobotany
                Plant Science
                Agronomy
                Plant Breeding
                Botany
                Ethnobotany
                Paleobotany
                Plant Ecology
                Plant Growth and Development
                Plants
                Earth Sciences
                Paleontology
                Paleobotany
                Social and Behavioral Sciences
                Archaeology
                Archaeological Excavation

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                Uncategorized

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