Rapid Identification of Soybean Resistance Genes to Soybean Mosaic Virus by SLAF-seq Bulked Segregant Analysis

Abstract

Soybean mosaic virus (SMV) is one of the most harmful pathogens in soybeans, causing large yield losses. Therefore, it is very important to breed resistant soybean cultivars, but first we need to understand the genetics of soybean. Genetic maps are efficient tools in plant genetics and molecular-assisted breeding. In this study, a large-scale survey of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique was used to construct the fine gene mapping for two soybean cultivars. The cultivar Tianlong No. 1 (TL1) is resistant to the SC9 strain, but Zhexiandou No. 4 (ZXD4) is susceptible to this strain. All F1 individuals showed the susceptible phenotype for strain SC9. Among the 425 F2 plants derived from F1 individuals, 309 had the susceptible phenotype and 116 were resistant (χ2 = 1.1929, P = 0.725). The results indicated that TL1 harbors a recessive gene underlying resistance to strain SC9. A total of 28.91 million sequencing reads were obtained, with average sequencing depths of over 17-fold for TL1 and ZXD4 and 63-fold for the F2 offspring. In summary, 144,754 high-quality SLAFs were obtained, of which 30,578 were polymorphic. In all, 8738 SNPs were selected to construct the fine gene mapping with an average genetic distance of 1.30 cM between adjacent markers. Approximately 148 target genes were mapped in the intervening genomic region of chromosome 2. The results of this study will not only provide a fine gene mapping for SMV resistance research but will also serve as a robust tool for the molecular breeding of soybean.