Genome-wide association analysis of resistance to wheat spindle streak mosaic virus in bread wheat

Wheat spindle streak mosaic virus (WSSMV) is a major concern for cereal crops in Europe and North America. A strong increase in the occurrence of WSSMV has been observed in each French region where susceptible cultivars are cultivated. Most European bread wheat cultivars are resistant, but assessing the status of newly registered cultivars or breeding lines regarding WSSMV resistance is of importance. This paper describes a genome-wide association study carried out on a panel of 163 cultivars and tested for their resistance to WSSMV. Two regions on chromosomes 5B and 7D showed minor effects on WSSMV resistance. More importantly, a large genomic region on chromosome 2D explained most of the resistance to WSSMV. More than 99% of the cultivars carrying the AA genotype at the most associated marker (Excalibur_c15426_661) were resistant to WSSMV, while 100% of the cultivars showing the GG genotype were susceptible. This large genomic region of 45.8 Mb was found distal to the centromere and showed very high linkage disequilibrium. It is hypothesized that this region may be an alien introgression originating from a wild related species. This region contains a total of 2605 predicted genes based on the Chinese Spring IWGSC RefSeq v. 1.0 including genes potentially involved in plant disease resistance. A kompetitive allele-specific PCR (KASP) single-nucleotide polymorphism (SNP) marker was designed in order to identify breeding lines or registered cultivars resistant to WSSMV.