Towards isolation of the BaMMV resistance gene rym15 derived from the Japanese cultivar Chikurin Ibaraki 1

Abstract

Barley mild mosaic virus (BaMMV) and Barley yellow mosaic virus (BaYMV), members of the genus Bymovirus in the family Potyviridae, are the causal agents for barley yellow mosaic disease in winter barley in Europe and Asia. Due to transmission of BaMMV and BaYMV via the soil-borne plasmodiophorid Polymyxa graminis, which can survive in the soil for many years, can reinfect the roots of barley plants given the suitable environmental conditions, thus breeding of resistant cultivars is the only efficient and environmentally friendly way to prevent high yield losses caused by this disease. In 2004, it was shown that the BaMMV resistance of Chikurin Ibaraki 1 is imparted by a single recessive gene named rym15 that is located on chromosome 6HS. This resistance gene was previously localized in a genetic map of Chikurin Ibaraki 1 × Plaisant, however the order of flanking markers EBmac0874 and Bmag0173 was found to be inverted compared to the previous genetic map of Hordeum vulgare Lina × Hordeum spontaneum Canada Park. Therefore, in the present study, the first step towards identifying the causal gene was to construct a medium-resolution map of the chromosome segment containing rym15. This was achieved using a set of 522 F2 plants derived from the two F2 populations Igri × Chikurin Ibaraki 1 (I×C, 180 plants) and Chikurin Ibaraki 1 × Uschi (C×U, 342 plants), respectively, derived from crosses of different susceptible parents with the resistance donor. The phenotypic results revealed segregation ratios of 250s:92r (I×C, χ2=0.659) and 140s:40r (C×U, χ2=0.741), suggesting the presence of a single recessive resistance gene against BaMMV in Chikurin Ibaraki 1. The order of all markers was the same in both F2 populations and in accordance with the physical map (Morex v2 genome assembly). Two single nucleotide polymorphisms (SNPs)-based competitive allele specific PCR (KASP) markers designated rym15_1 and rym15_8 were selected as new flanking markers for the target locus rym15. Using these two flanking markers, two sets of 139 (I×C) and 284 (C×U) segmental recombinant inbred lines (RILs) were selected from 2174 (I×C) and 5728 (C×U) F2-plants, respectively. Subsequently, a total of 32 KASP markers were used for marker saturation of the target locus rym15 in these RILs. High-resolution maps were constructed and the target interval was downsized to 0.161 cM and 0.036 cM in the two respective crosses, corresponding to a physical interval of 11.3 Mbp in the I×C RILs and 0.281 Mbp in the CxU RILs according to the Morex v3 genome sequence. In the target region of 0.281 Mbp, a set of six high confidence (HC) and two low confidence (LC) genes was identified. Blast analysis revealed functional SNPs in two HC genes. This work lays the foundation for gene identification of the target locus rym15.