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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

Detection of single nucleotide variations in sequencing soybean accessions. (A) Accumulated SNV coverage in cultivars, wild and all accessions; (B) Distribution of missing SNVs in previous report by Lam et al.
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Fig1: Detection of single nucleotide variations in sequencing soybean accessions. (A) Accumulated SNV coverage in cultivars, wild and all accessions; (B) Distribution of missing SNVs in previous report by Lam et al.

Mentions: To estimate the coverage of these SNVs in the whole soybean germplasm, we employed a random sampling approach to investigate the accumulation of SNVs detected in different accessions (Figure 1A). The end of the SNV curve tends to be flat, which indicates that the SNVs identified here probably reach saturation in soybean germplasm. It is sufficient for as few as 48 accessions to detect 95% of all SNVs in different populations. For cultivated soybeans, only 30 individuals can achieve 95% of SNVs. Approximately 5.2 million SNVs would reach saturation in cultivars, which are far less than those in wild soybeans. In previous work [7], Lam et al reported 6.3 million SNVs in 31 soybeans, while we discovered 2,481,645 more in the same individuals by a larger population. A large number of rare SNVs and those with low allele frequency were missed in former analysis due to strict filtering conditions and a small number of individuals (Figure 1B). Although some very rare SNVs still remain to be discovered, we have identified a substantial majority of the common SNVs in soybeans.Figure 1


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)

Detection of single nucleotide variations in sequencing soybean accessions. (A) Accumulated SNV coverage in cultivars, wild and all accessions; (B) Distribution of missing SNVs in previous report by Lam et al.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Detection of single nucleotide variations in sequencing soybean accessions. (A) Accumulated SNV coverage in cultivars, wild and all accessions; (B) Distribution of missing SNVs in previous report by Lam et al.
Mentions: To estimate the coverage of these SNVs in the whole soybean germplasm, we employed a random sampling approach to investigate the accumulation of SNVs detected in different accessions (Figure 1A). The end of the SNV curve tends to be flat, which indicates that the SNVs identified here probably reach saturation in soybean germplasm. It is sufficient for as few as 48 accessions to detect 95% of all SNVs in different populations. For cultivated soybeans, only 30 individuals can achieve 95% of SNVs. Approximately 5.2 million SNVs would reach saturation in cultivars, which are far less than those in wild soybeans. In previous work [7], Lam et al reported 6.3 million SNVs in 31 soybeans, while we discovered 2,481,645 more in the same individuals by a larger population. A large number of rare SNVs and those with low allele frequency were missed in former analysis due to strict filtering conditions and a small number of individuals (Figure 1B). Although some very rare SNVs still remain to be discovered, we have identified a substantial majority of the common SNVs in soybeans.Figure 1

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