title: Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci.
abstract: • The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. • In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. • The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. • G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China.
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China.
authors.forename: Ying-Hui
authors.initials: YH
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Chen
authors.initials: C
authors.lastname: Zhang
authors.forename: Liang
authors.initials: L
authors.lastname: Yang
authors.forename: Ru-Zhen
authors.initials: RZ
authors.lastname: Chang
authors.forename: Brandon S
authors.initials: BS
authors.lastname: Gaut
authors.forename: Li-Juan
authors.initials: LJ
authors.lastname: Qiu
mesh_terms: D000383:Agriculture; D000483:Alleles; D001499:Bayes Theorem; D016000:Cluster Analysis; D056426:Genetic Loci / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D005843:Geography; D018598:Minisatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011157:Population Dynamics; D013025:Glycine max / Q000235:genetics*