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Abstract
BackgroundArtificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.ResultsA total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified.ConclusionsGiven the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.
Highlights
Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja
After calibrating the Single nucleotide polymorphisms (SNPs) calling quality by all the 55 accessions and discarding singletons and most doubletons according to rigorous filtering criteria [17,18], we identified 5,102,244 high quality SNPs in our sequenced accessions (Additional file 4, http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi? handle=NFCRI_MOA_CAAS), which was slightly lower than that discovered previously in the 31 soybean accessions
Taking wild soybeans as a control in the Population branch statistics (PBS) approach, we found that 306 regions were associated with significant signs (P < 0.001) of artificial selection by the modern breeding practice (Figure 4c, Figure 4d)
Summary
Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed. The modern cultivated soybean [Glycine max (L.) Merr.], which contains high protein and oil content, is an important crop worldwide. Soybean was domesticated from its wild progenitor, Glycine soja Sieb. The emergence of cultivated crops from their wild progenitors was achieved primarily by artificial selection for a wide range of desirable traits to meet human needs a Elite Landrace Wild Landrace Wild b S1 S2 S3 S4 S5 S6 S7 S8
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