Soybean (Glycine max(L.) Merrill) is an important crop in the world. In this study, a Chinese local soybean cultivar, Hedou 12, was re-sequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for geneticmapping.49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms (SNP) were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5 to 50 bp in length were chosen for PCR validation, and 165 (68%) of them revealed polymorphisms between Hedou 12 and Williams 82. The validated INDEL markers were also tested in 12 other soybean cultivars. The number of polymorphisms in the pairwise comparisons of 14 soybean cultivars varied from 27 to 165. To test the utility of these INDEL markers, they were used to perform a genetic mapping of a crinkly leaf mutant, and the CRINKLY LEAF locus was successfully mapped to a 360 Kb region on chromosome 7. This research shows that high-throughput sequencing technologies can facilitate the development of genome-wide molecular markers for genetic mapping in soybean.
Cultivated soybean (Glycine max(L.) Merrill) is an economically crop that provides a large amount of plant protein and oil in the world. Most soybean important agronomic traits are usually quantitative traits, including yield, quality and resistance to environmental stresses (Bolonet al. 2010; Leeet al 2004; Lianget al. 2010; Xinget al 2012; Zhanget al 2004). Soybean has more than 46,430 protein-coding genes, nearly 75% of which exist as multiple homologs (Schmutzet al 2010). The complexity of the soybean genome makes it difficult to perform studies on gene functions. It is crucial to develop adequate molecular markers for the genotypes of interest, that can be used for mapping and marker assisted selection (MAS). However, most of the available soybean molecular markers are based on polymorphisms among popular studied cultivars. Thescreening for polymorphisms between new local cultivars and the studied cultivars can expand the scope of molecular marker resource which can facilitate the soybean genetic studies.
Xiaofeng Song, Haichao Wei, Wen Cheng, Suxin Yang, Yanxiu Zhao, Xuan Li, Da Luo, Hui Zhang, Xianzhong Feng . Development of INDEL Markers for Genetic Mapping Based on Whole-Genome Re-sequencing in Soybean.
Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences
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