Nucleotide diversity patterns of three divergent soybean populations: evidences for population‐dependent linkage disequilibrium and taxonomic status of Glycine gracilis

Ecology and Evolution

Yunsheng Wang¹  Muhammad Qasim Shahid²  Hongwen Huang¹ 

[1] Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, China;College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China

关键词: Evolution;    linkage disequilibrium;    nucleotide polymorphism;    population genetics;    semi‐wild soybean;   

DOI  :  10.1002/ece3.1550

来源: Wiley

【 摘 要 】

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 r² = 0.2426) was found in intragene in G. max and G. gracilis populations, but unexpected low level of LD (r² ≤ 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.

【 授权许可】

CC BY   
© 2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

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