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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

Footprints of artificial selection during (A) early domestication and (B) modern improvement.
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Fig3: Footprints of artificial selection during (A) early domestication and (B) modern improvement.

Mentions: The signal of artificial selection could be detected by the loss of genetic diversity, which shaped selective sweeps around beneficial alleles on the genomes [24-26]. To further elucidate the effects of domestication, we detected the genomic regions showing artificial selection signals by genetic bottleneck model [18,19] and population branch statistics [27]. The sequenced accessions except C12 and C16 were grouped into wild and cultivated population to detect selection signals in early domestication process. Using a sliding window approach, we calculated the distribution of θπ and Tajima’s D [28] in wild and cultivated populations along the genome. Regions with significantly lower θπ (Z test, P < 0.05) and lower Tajima’s D (Z test, P < 0.05) in cultivars than that in wild accessions were treated as putative candidates that were affected by early domestication (Figure 3A). However, signals of very recent natural selection could be easily omitted using the above bottleneck model. To detect signatures that shaped in modern crop improvement, we employed an effective method known as population branch statistics. Taking wild soybeans as control, we recalculated the divergence index Fst [29] in a sliding window along the genome, based on which we detected significant signals (P < 0.001 after Bonferroni correction) to infer selective footprints from landraces to elite cultivars (Figure 3B). This approach had been shown to be effective in identifying recent artificial selection considering the very short time of modern breeding practice [18]. A total of 598 regions comprising 27.9 Mb genome sequences and 286 regions with a length of 12.7 Mb were affected by early domestication and genetic improvement, respectively. Based on the latest annotation, 2,255 genes with 3,100 transcripts were involved in early domestication, whereas 1,051 genes with 1,462 transcripts were affected in subsequent improvement.Figure 3


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)

Footprints of artificial selection during (A) early domestication and (B) modern improvement.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Footprints of artificial selection during (A) early domestication and (B) modern improvement.
Mentions: The signal of artificial selection could be detected by the loss of genetic diversity, which shaped selective sweeps around beneficial alleles on the genomes [24-26]. To further elucidate the effects of domestication, we detected the genomic regions showing artificial selection signals by genetic bottleneck model [18,19] and population branch statistics [27]. The sequenced accessions except C12 and C16 were grouped into wild and cultivated population to detect selection signals in early domestication process. Using a sliding window approach, we calculated the distribution of θπ and Tajima’s D [28] in wild and cultivated populations along the genome. Regions with significantly lower θπ (Z test, P < 0.05) and lower Tajima’s D (Z test, P < 0.05) in cultivars than that in wild accessions were treated as putative candidates that were affected by early domestication (Figure 3A). However, signals of very recent natural selection could be easily omitted using the above bottleneck model. To detect signatures that shaped in modern crop improvement, we employed an effective method known as population branch statistics. Taking wild soybeans as control, we recalculated the divergence index Fst [29] in a sliding window along the genome, based on which we detected significant signals (P < 0.001 after Bonferroni correction) to infer selective footprints from landraces to elite cultivars (Figure 3B). This approach had been shown to be effective in identifying recent artificial selection considering the very short time of modern breeding practice [18]. A total of 598 regions comprising 27.9 Mb genome sequences and 286 regions with a length of 12.7 Mb were affected by early domestication and genetic improvement, respectively. Based on the latest annotation, 2,255 genes with 3,100 transcripts were involved in early domestication, whereas 1,051 genes with 1,462 transcripts were affected in subsequent improvement.Figure 3

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