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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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Functional annotation of selective genes with nucleotide fixation introduced in early domestication and modern improvement.
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Fig5: Functional annotation of selective genes with nucleotide fixation introduced in early domestication and modern improvement.

Mentions: Domestication caused complex morphological and physiological changes in soybeans. Annotated by the KEGG and agriGO database, selective genes were associated with different biological functions, among which, plant-pathogen interaction, sequence-specific DNA binding, phenylpropanoid biosynthesis, starch and sucrose metabolism are over-represented categories (FigureĀ 5; Additional file 6: Figure S5). Plant-pathogen interactions are conducted between a pathogen and the host plant. In nature, plants are generally resistant to most invading pathogens due to innate ability to recognize them through successful defenses. When an exception happens, a pathogen would cause diseases in its host [59]. However, pathogens could also cause diseases if they have evolved to evade detection or suppress host defense mechanisms, or both. The effects of plant-pathogen interactions are of particular relevance during early domestication events on agricultural systems [60]. Thus, understanding the genetic basis of why a certain pathogen causes disease in its host plant instead of others has long intrigued and motivated plant pathologists.Figure 5


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)

Functional annotation of selective genes with nucleotide fixation introduced in early domestication and modern improvement.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Functional annotation of selective genes with nucleotide fixation introduced in early domestication and modern improvement.
Mentions: Domestication caused complex morphological and physiological changes in soybeans. Annotated by the KEGG and agriGO database, selective genes were associated with different biological functions, among which, plant-pathogen interaction, sequence-specific DNA binding, phenylpropanoid biosynthesis, starch and sucrose metabolism are over-represented categories (FigureĀ 5; Additional file 6: Figure S5). Plant-pathogen interactions are conducted between a pathogen and the host plant. In nature, plants are generally resistant to most invading pathogens due to innate ability to recognize them through successful defenses. When an exception happens, a pathogen would cause diseases in its host [59]. However, pathogens could also cause diseases if they have evolved to evade detection or suppress host defense mechanisms, or both. The effects of plant-pathogen interactions are of particular relevance during early domestication events on agricultural systems [60]. Thus, understanding the genetic basis of why a certain pathogen causes disease in its host plant instead of others has long intrigued and motivated plant pathologists.Figure 5

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