Molecular Evidence for Soybean Domestication

Van, Kyujung; Kim, Moon Young; Shin, Jin Hee; Kim, Kyung Do; Lee, Yeong-Ho; Lee, Suk-Ha

doi:10.1007/978-94-007-7572-5_19

Cited by 9 publications

(17 citation statements)

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“…and Zucc. ), an undomesticated form of the current soybean, is distributed in East Asia, including China, Taiwan, Russian Far East, the Korean Peninsula, and Japan, the origin or domestication site of soybean is still in controversy (Boerma and Specht, 2004; Van et al, in press). After soybean is introduced into Central and South America in the mid-1900's via North America in 1765, soybean becomes one of the major economically valuable crops in terms of the world's total production (Vuong et al, 2007; Stupar and Specht, 2013).…”

Section: Introductionmentioning

confidence: 99%

Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Lestari¹,

Van²,

Lee³

et al. 2013

Front. Plant Sci.

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Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL) for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr) 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both Chrs. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

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Section: Introductionmentioning

confidence: 99%

Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Lestari¹,

Van²,

Lee³

et al. 2013

Front. Plant Sci.

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“…As shown in the plot of EHH versus distance, the areas under the EHH curve were much greater for the four selected alleles than for the corresponding neutral alleles (Figure ). To quantitatively capture this effect, a commonly used statistic, iHS, which is calculated from the ratio of haplotype homozygosity for the haplotypes carrying the derived iHH D and ancestral allele iHH A (Voight et al., ), was calculated for all of the available SNPs of Dt1 (Figure ). iHS values were calculated in both the G. max population and the subpopulation of determinate landraces, which were considered as the results of incomplete and complete selective sweeps, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…The statistic iHS proposed by Voight et al. () is an analytical method for scanning SNP data for signals of recent selection. It is the natural logarithm of a ratio of integrated EHH (iHH) for the haplotypes carrying the derived core allele (iHH D ) and the ancestral allele (iHH A ), that is iHS = ln(iHH D /iHH A ).…”

Section: Methodsmentioning

confidence: 99%

“…The integrated EHH is the observed decay of EHH summed over both directions away from a specified core allele until EHH reaches 0.05. Large negative values of iHS indicate unusually long haplotypes carrying the derived allele, and large positive values indicate long haplotypes carrying the ancestral allele (Voight et al., ). The statistics of H1, H2 and H12 were recently developed by Garud et al.…”

Section: Methodsmentioning

confidence: 99%

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Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]

et al. 2017

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Determinate growth habit is an agronomically important trait associated with domestication in soya bean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four nonsynonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb, were identified, which constitute the soft sweeps for the adaptation. These variable-sized sweeps substantially reflected the strength and timing of selection and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures of extensive long-range LD and haplotype homozygosity, and multiple frequent adaptive haplotypes. A haplotype network constructed for Dt1 and a phylogenetic tree based on its extended haplotype block implied independent sources of the adaptive alleles through de novo mutations or rare standing variation in quick succession during the selective phase, strongly supporting multiple origins of the determinacy. We propose that the adaptation of soya bean determinacy is guided by a model of soft sweeps and that this model might be indispensable during crop domestication or evolution.

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“…(Hyten et al, 2006;Jun et al, 2011;Li et al, 2013, Van et al, 2014. (Hyten et al, 2006;Jun et al, 2011;Li et al, 2013, Van et al, 2014.…”

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Method for Early Generation Soybean Population Selection Using F₂ High‐Parent Heterosis Testing

2019

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The germplasm pool for North American soybean [Glycine max (L.) Merr.] is narrow, and identifying novel and useful genetic diversity is time consuming and expensive. The objective of this research was to develop an early‐generation population screening method to select diversity × elite populations. The F2 high‐parent heterosis (F2 heterosis) was used as a tool to identify populations with the greatest potential for producing high‐yielding lines in subsequent generations. For Set 1 populations, six populations were selected for significantly positive F2 heterosis, and six were selected for significantly negative F2 heterosis. When these populations were advanced into plant row yield trials, five out of six populations with positive F2 heterosis had the highest average yield for the top 5% of the lines, and five out of six populations with negative F2 heterosis had the lowest average yield for the top 5% of the lines. For Set 2, two populations with the highest positive F2 heterosis value had significantly higher average population yield and average top 5% selection yield compared with two populations with negative F2 heterosis. Differences in combining ability were evident in both sets of populations, as two populations with one parent in common may have opposite classifications for F2 heterosis. Using F2 heterosis as an early‐generation population selection tool may enable the focus of resources to identify which populations have the best opportunity to develop high‐yielding lines with unique diversity. These data will need to be verified in replicated yield testing over multiple years and locations.

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Molecular Evidence for Soybean Domestication

Cited by 9 publications

References 84 publications

Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]

Method for Early Generation Soybean Population Selection Using F₂ High‐Parent Heterosis Testing

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Molecular Evidence for Soybean Domestication

Cited by 9 publications

References 84 publications

Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]

Method for Early Generation Soybean Population Selection Using F2 High‐Parent Heterosis Testing

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Method for Early Generation Soybean Population Selection Using F₂ High‐Parent Heterosis Testing