Mapping and functional analysis of candidate genes involved in resistance to soybean (Glycine max) mosaic virus strain SC3

Soybean mosaic virus (SMV) infections can cause significant reduction in soybean yield and seed quality. Identifying SMV resistance genes in soybean and accordingly breeding resistant soybean varieties is an important approach to control soybean loss caused by SMV. Here, whole genome resequencing was performed on a pair of near-isogenic line (NIL), one resistant (R) line and one susceptible (S) line to SC3, from Qihuang-1 (resistant to SC3, R-SC3Q) x Nannong 1138-2 (susceptible to SC3, r(SC3Q)). Based on the distribution of single nucleotide polymorphisms (SNPs) and InDels in each chromosome, the R-SC3Q was mapped to a region between 27.4 and 29.8 Mbp in chromosome 13. Comparing the sequence and transcriptome data between R line and susceptible lines (S line and Willams82) to SC3, three R-SC3Q candidate genes (Glyma13g25950, Glyma13g25970 and Glyma13g26380) were identified. Silencing Glyma13g26380 in Qihuang-1 increased the accumulation of SMV at 6 and 24 hpi. Subsequently, the SMV concentration in silenced plants decreased to the same level as that of the control. Thus, Glyma13g26380 is involved in the early resistance response of Qihuang No. 1 to SC3. These results provide a basis for elucidating the soybean resistance mechanism against SMV and breeding more resistant soybean varieties against SMV.