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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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The distribution of nucleotide fixation over the genome versus in the selective regions. The window size was set to be 20 kb.
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Fig4: The distribution of nucleotide fixation over the genome versus in the selective regions. The window size was set to be 20 kb.

Mentions: Compared with the genome-wide distribution, nucleotide fixations happened more frequently in the candidate regions of artificial selection (Figure 4). Nucleotide fixation accumulated substantially in cultivars and happened unevenly along chromosomes (Additional file 2: Figure S1), indicating that some chromosomes were more susceptible to be affected by artificial selection. Nucleotide fixation also explains the reduction of genetic diversity in cultivated crops compared with their wild ancestors. We analyzed the allele frequency of SNVs in wild soybeans that were fixed in cultivars, as it represents the initial status of these nucleotide fixations before domestication. The frequency spectrum shows that these SNVs were almost neutral at the beginning of domestication (Additional file 3: Figure S2). Since non-synonymous substitutions may result in a change in functions, they are subject to natural or artificial selection [32]. Of the nucleotide fixation happened in early domestication, 24,316 located in coding sequences and 2,162 of them caused non-synonymous substitutions in 1,188 genes, which altered the amino acid sequences of the proteins. For those loci fixed in modern improvement, 8,065 located in coding sequences with 756 non-synonymous in 489 genes. Apparently, more nucleotide fixations were introduced to cultivars during domestication than those during improvement.Figure 4


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)

The distribution of nucleotide fixation over the genome versus in the selective regions. The window size was set to be 20 kb.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: The distribution of nucleotide fixation over the genome versus in the selective regions. The window size was set to be 20 kb.
Mentions: Compared with the genome-wide distribution, nucleotide fixations happened more frequently in the candidate regions of artificial selection (Figure 4). Nucleotide fixation accumulated substantially in cultivars and happened unevenly along chromosomes (Additional file 2: Figure S1), indicating that some chromosomes were more susceptible to be affected by artificial selection. Nucleotide fixation also explains the reduction of genetic diversity in cultivated crops compared with their wild ancestors. We analyzed the allele frequency of SNVs in wild soybeans that were fixed in cultivars, as it represents the initial status of these nucleotide fixations before domestication. The frequency spectrum shows that these SNVs were almost neutral at the beginning of domestication (Additional file 3: Figure S2). Since non-synonymous substitutions may result in a change in functions, they are subject to natural or artificial selection [32]. Of the nucleotide fixation happened in early domestication, 24,316 located in coding sequences and 2,162 of them caused non-synonymous substitutions in 1,188 genes, which altered the amino acid sequences of the proteins. For those loci fixed in modern improvement, 8,065 located in coding sequences with 756 non-synonymous in 489 genes. Apparently, more nucleotide fixations were introduced to cultivars during domestication than those during improvement.Figure 4

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