RNA-seq of bulked segregants to identify resistant gene of barley yellow mosaice virus disease

The soil-borne yellow mosaic virus disease is a major threat to winter barley (Hordeum vulgare) production in Europe and East Asia. However, the exploration of resistant germplasm or casual genes used for barley breeding was rather limited in relative to the rapid diversification of viral strains. Here we identified an Iranian barley landrace ‘HOR3298’, which represented complete resistance to the bymovirus disease of barley. In contrast to the resistance donor rym4 and rym5, which act as predominant source in Europe and East Asia breeding over decades and which has been overcome by several virulent isolates, this landrace showed broad-spectrum resistance to multiple isolates of BaYMV/BaMMV in the disease prevalent fields of Germany and China. By employment of bulked segregant RNA sequencing (BSR-seq), test for allelism and haplotype analysis, a single recessive resistance gene in ‘HOR3298’ was genetically mapped coincident with the host factor eukaryotic translation initiation factor 4E (eIF4E, causal gene of rym4 and rym5). The eIF4EHOR3298 allele encoded for a novel haplotype that contained an exclusive nucleotide mutation (G565A) in the coding sequence. An easily handled marker was developed based on the exclusively rare variation, providing precise selection of this allele. Thus, this work provided a novel reliable resistance source and a feasible marker assisted selection assay that can be used in breeding for the yellow mosaic virus disease resistance in cultivated barley.