title: Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status of Glycine gracilis.
abstract: The level of linkage disequilibrium (LD) is a major factor to determine DNA polymorphism pattern of a population and to construct high-resolution maps useful in localizing and gene cloning of complicated traits. Here, we investigated LD level of three soybean populations with different genetic backgrounds and taxonomic status of G. gracilis by comparing the DNA polymorphism patterns of four high-diversity single-copy nuclear genes. A total of 152, 22, and 77 accessions of G. soja, G. gracilis, and G. max were observed. The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja. Four gene loci evolved according to neutrality in both G. max and G. gracilis populations, and three gene loci evolved according to neutrality in G. soja population by Tajima's and Fu and Li's test. However, one gene locus deviated from neutrality by Fu and Li's test in the G. soja population. Further, medial level of LD (average r (2) = 0.2426) was found in intragene in G. max and G. gracilis populations, but unexpected low level of LD (r (2) ≤ 0.0539) was found in G. soja population. Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations. The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Science Wuhan Hubei 430074 China ; College of Environment and Life Science Kaili University Kaili Guizhou 556011 China.
authors.forename: Yunsheng
authors.initials: Y
authors.lastname: Wang
authors.affiliation: College of Agriculture South China Agricultural University Guangzhou Guangdong 510642 China.
authors.forename: Muhammad Qasim
authors.initials: MQ
authors.lastname: Shahid
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Science Wuhan Hubei 430074 China ; Key Laboratory of Plant Resources Conservation and Sustainable Utilization Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden Chinese Academy of Science Guangzhou Guangdong 510642 China.
authors.forename: Hongwen
authors.initials: H
authors.lastname: Huang
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Science Wuhan Hubei 430074 China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
keywords: Evolution; linkage disequilibrium; nucleotide polymorphism; population genetics; semi‐wild soybean