Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean.
Soybean [Glycine max (L.) Merrill] is an important crop worldwide. In this study, a Chinese local soybean cultivar, Hedou 12, was resequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for genetic mapping. 49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5-50 bp in length were chosen for 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 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.
Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China.
Xiaofeng
X
Song
Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 130102 Changchun, China.
Haichao
H
Wei
Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China.
Wen
W
Cheng
Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 130102 Changchun, China.
Suxin
S
Yang
Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China.
Yanxiu
Y
Zhao
Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, China.
Xuan
X
Li
School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China.
Da
D
Luo
Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China fengxianzhong@iga.ac.cn laohanzhang@hotmail.com.
Hui
H
Zhang
Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 130102 Changchun, China fengxianzhong@iga.ac.cn laohanzhang@hotmail.com.
Xianzhong
X
Feng
D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D010641:Phenotype; D010802:Phylogeny; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D013025:Glycine max / Q000145:classification / Q000235:genetics*
D005819:Genetic Markers
INDEL markers; crinkly leaf mutant; genetic mapping; soybean; whole genome resequencing