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Acta Agron Sin ›› 2011, Vol. 37 ›› Issue (10): 1724-1734.doi: 10.3724/SP.J.1006.2011.01724

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of Gene Glyma13g21630 Diversity in Cultivated (G. max) and Wild (G. soja) Soybeans

ZHANG Le,Li Ying-Hui**,LIU Zhang-Xiong,QIU Li-Juan*   

  1. National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Germplasm Utilization, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2011-03-15 Revised:2011-06-25 Online:2011-10-12 Published:2011-07-28
  • Contact: 邱丽娟, E-mail: qiu_lijuan@263.net, Tel: 010-82105841

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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

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