Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus

Abstract

Discovery of new germplasm sources and identification of haplotypes for the durable Soybean mosaic virus resistance gene, Rsv 4, provide novel resources for map-based cloning and genetic improvement efforts in soybean. The Soybean mosaic virus (SMV) resistance locus Rsv4 is of interest because it provides a durable type of resistance in soybean [Glycine max (L.) Merr.]. To better understand its molecular basis, we used a population of 309 BC3F2 individuals to fine-map Rsv4 to a ~120 kb interval and leveraged this genetic information in a second study to identify accessions 'Haman' and 'Ilpumgeomjeong' as new sources of Rsv4. These two accessions along with three other Rsv4 and 14 rsv4 accessions were used to examine the patterns of nucleotide diversity at the Rsv4 region based on high-depth resequencing data. Through a targeted association analysis of these 19 accessions within the ~120 kb interval, a cluster of four intergenic single-nucleotide polymorphisms (SNPs) was found to perfectly associate with SMV resistance. Interestingly, this ~120 kb interval did not contain any genes similar to previously characterized dominant disease resistance genes. Therefore, a haplotype analysis was used to further resolve the association signal to a ~94 kb region, which also resulted in the identification of at least two Rsv4 haplotypes. A haplotype phylogenetic analysis of this region suggests that the Rsv4 locus in G. max is recently introgressed from G. soja. This integrated study provides a strong foundation for efforts focused on the cloning of this durable virus resistance gene and marker-assisted selection of Rsv4-mediated SMV resistance in soybean breeding programs.

The Current Status of the Soybean-Soybean Mosaic Virus (SMV) Pathosystem

“…It was identified in soybean cultivars V94-5152 and mapped to a 0.4 cM interval between the proximal marker Rat2 and the distal marker S6ac, in a ∼94 kb haplotype block on soybean chromosome 2 (MLG D1b++W) (Hayes et al, 2000; Saghai Maroof et al, 2010; Ilut et al, 2016). A haplotype phylogenetic analysis of this region suggests that the Rsv4 locus in G. max is recently introgressed from G. soja (Ilut et al, 2016). Interestingly, this interval did not contain any NB-LRR type R genes.…”

“…Interestingly, this interval did not contain any NB-LRR type R genes. Instead, several genes encoding predicted transcription factors and unknown proteins are present within the region, suggesting that Rsv4 most likely belongs to a novel class of resistance gene (Hwang et al, 2006; Ilut et al, 2016). …”

Characterization of broad‐spectrum resistance to Soybean mosaic virus in soybean [Glycine max (L.) Merr.] cultivar ‘RN‐9’

“…Moreover, linkage analysis revealed that the Rsc10‐r was mapped on chromosome 6 (Figure b), while that of in KF ( Rsc10 ) was located in the vicinity of Rsv4 on chromosome 2 (Li et al., ) (Figure d), of which resistance was probably attributed to an original class of disease resistance genes (Ilut et al. ; Maroof et al., ; Wang, Ma, Yang et al., ; Zhao et al. ).…”

Fine mapping of the RSC8 locus and expression analysis of candidate SMV resistance genes in soybean

“…According to Ilut et al. (), R SC8 and Rsv4 may be two different dominant resistance genes that are tightly linked in a region on chromosome 2. Analysis of Williams 82 soybean genome sequences in the 30.8‐kb region believed to represent the location of R SC8 revealed the presence of two possible transcription factor genes, Glyma.02G121500 and Glyma.02G121600.…”

“…Ilut et al. () further narrowed the likely location of the Rsv4 locus to an approximately 94‐kb haplotype block.…”