栽培大豆和野生大豆的Glyma13g21630基因多样性分析

doi:10.3724/SP.J.1006.2011.01724

摘要/Abstract

摘要： 利用Sanger方法对49份野生大豆，46份地方品种和38份选育品种的Glyma13g21630基因测序，采用DNAStar、Mega、DNAsp和Tassel软件分析Glyma13g21630的单核苷酸多态性(SNP)位点在不同类型大豆群体的分布规律。结果表明，在133份供试种质中检测到多态性位点29个，包括22个SNP和7个InDel，多态性频率分别为1SNP/138 bp和1InDel/434 bp。Glyma13g21630基因序列中多态性位点的分布不均匀，其中内含子3和5为变异富集区，其他区域变异较小。单倍型分析表明，Glyma13g21630在野生大豆和栽培大豆中的多态性位点数目逐渐减少，分布范围也越来越窄；连锁不平衡分析表明，野生大豆的7个高频SNP位点中有42.86%处于极显著的连锁不平衡状态；Ka/Ks>1，说明野生大豆在向栽培大豆的进化中，某些位点受到正向选择，多态性显著降低。Glyma13g21630基因在大豆由野生向栽培驯化的过程中因正向选择作用而固定了有益变异，表现出瓶颈效应。

关键词: 大豆, Glyma13g21630, 单核苷酸多态性, 单倍型

Abstract: Glyma13g21630 from soybean is homologous with a gene related to leaf size from Arabidopisis thaliana, and it experienced man-made selection during domestication in small sample test. This paper aims at analyzing single nucleotide polymorphism of Glyma13g21630 in large sample test and providing the foundation for tracing back to soybean domestication and analyzing the genetic basis of domesticated traits. According to Sanger method, PCR products of Glyma13g21630 from 49 wild soybean and 84 cultivars (including 46 landraces and 38 cultivars) were sequenced. The distribution patterns of single nucleotide polymorphism (SNP) for Glyma13g21630 were summarized. Using DNAStar, Mega, DNAsp and Tassel software tools, a total of 29 polymorphism sites were identified, which included 22 SNPs and seven InDels with frequencies of 1SNP/138 bp and 1InDel/434 bp, respectively. There were rich regions for nucleotide variation in intron three and intron five and less variations in other regions. Haplotype analysis indicated that the number of polymorphic loci was reducing from wild soybean to cultivated soybean, and the distribution range was correspondingly narrowed. Linkage disequilibrium analysis demonstrated that 42.86% of SNP sites in wild soybean were at significant linkage disequilibrium levels. The high ratio of Ka/Ks illustrated that some sites suffered strong positive selection pressure, which resulted in the reduction of polymorphism. The favored variation of Glyma13g21630 has been fixed in cultivated soybean, showing a bottleneck effect simultaneously.

Key words: Soybean, Glyma13g21630, Single nucleotide polymorphism, Haplotype

张乐, 李英慧, 刘章雄, 邱丽娟. 栽培大豆和野生大豆的Glyma13g21630基因多样性分析[J]. 作物学报, 2011, 37(10): 1724-1734.

ZHANG Le, LI Yang-Hui, LIU Zhang-Xiong, QIU Li-Juan. Analysis of Gene Glyma13g21630 Diversity in Cultivated (G. max) and Wild (G. soja) Soybeans[J]. Acta Agron Sin, 2011, 37(10): 1724-1734.

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