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Impacts of nucleotide fixation during soybean domestication and improvement.

Zhao S, Zheng F, He W, Wu H, Pan S, Lam HM - BMC Plant Biol. (2015)

Bottom Line: Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans.Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm.Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time.

Results: Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases.

Conclusions: Our analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice.

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Related in: MedlinePlus

Analysis of genetic diversity and phylogenetic relationship among soybean accessions. (A) Reduction of genetic diversity from wild, to landrace and then to elite soybeans; (B) A neighbor-joining tree; (C) Principal component analysis of soybeans.
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Fig2: Analysis of genetic diversity and phylogenetic relationship among soybean accessions. (A) Reduction of genetic diversity from wild, to landrace and then to elite soybeans; (B) A neighbor-joining tree; (C) Principal component analysis of soybeans.

Mentions: Soybean has suffered several genetic bottlenecks, such as early domestication producing lots of Asian landrace, the introduction of few landraces to North America, and modern extensive breeding activities [20]. Subsequently, different level of genetic diversity was reduced during these human-mediated events. More SNVs were identified in wild than in cultivated accessions. Two common statistics used to measure nucleotide diversity are the pairwise divergence per nucleotide θπ [21] and Watterson estimator θw [22] that corrected for sample size. Whole-genome analysis using these parameters shows a higher level of genetic diversity in wild populations (Figure 2A). Estimated by θπ, the average diversity within wild, landrace and elite cultivars are 3.84 × 10-3, 2.40 × 10-3, and 2.08 × 10-3 per nucleotide, respectively. Considering the cultivars consist of landrace and elites, the average θπ is 2.25× 10-3 in cultivated population. It is notable that the cultivars have retained only 58.6% of the sequence diversity present in wild soybeans, which is lower than previous estimation [7,20]. The genetic diversity was reduced by 37.5% in early domestication and further reduced by 8.3% in genetic improvement.Figure 2


Impacts of nucleotide fixation during soybean domestication and improvement.

Zhao S, Zheng F, He W, Wu H, Pan S, Lam HM - BMC Plant Biol. (2015)

Analysis of genetic diversity and phylogenetic relationship among soybean accessions. (A) Reduction of genetic diversity from wild, to landrace and then to elite soybeans; (B) A neighbor-joining tree; (C) Principal component analysis of soybeans.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4358728&req=5

Fig2: Analysis of genetic diversity and phylogenetic relationship among soybean accessions. (A) Reduction of genetic diversity from wild, to landrace and then to elite soybeans; (B) A neighbor-joining tree; (C) Principal component analysis of soybeans.
Mentions: Soybean has suffered several genetic bottlenecks, such as early domestication producing lots of Asian landrace, the introduction of few landraces to North America, and modern extensive breeding activities [20]. Subsequently, different level of genetic diversity was reduced during these human-mediated events. More SNVs were identified in wild than in cultivated accessions. Two common statistics used to measure nucleotide diversity are the pairwise divergence per nucleotide θπ [21] and Watterson estimator θw [22] that corrected for sample size. Whole-genome analysis using these parameters shows a higher level of genetic diversity in wild populations (Figure 2A). Estimated by θπ, the average diversity within wild, landrace and elite cultivars are 3.84 × 10-3, 2.40 × 10-3, and 2.08 × 10-3 per nucleotide, respectively. Considering the cultivars consist of landrace and elites, the average θπ is 2.25× 10-3 in cultivated population. It is notable that the cultivars have retained only 58.6% of the sequence diversity present in wild soybeans, which is lower than previous estimation [7,20]. The genetic diversity was reduced by 37.5% in early domestication and further reduced by 8.3% in genetic improvement.Figure 2

Bottom Line: Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans.Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm.Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time.

Results: Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases.

Conclusions: Our analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice.

Show MeSH
Related in: MedlinePlus