Wang Yaping, Habekuß Antje, Jayakodi Murukarthick, Mascher Martin, Snowdon Rod J, Stahl Andreas, Fuß Janina, Ordon Frank, Perovic Dragan
Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany.
Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
Front Plant Sci. 2022 Jun 2;13:908170. doi: 10.3389/fpls.2022.908170. eCollection 2022.
(BaYMV) and (BaMMV), which are transmitted by the soil-borne plasmodiophorid , cause high yield losses in barley. In previous studies, the recessive BaMMV resistance gene , derived from the Japanese landrace Chikurin Ibaraki 1, was mapped on chromosome 6HS of . In this study, 423 F segmental recombinant inbred lines (RILs) were developed from crosses of Chikurin Ibaraki 1 with two BaMMV-susceptible cultivars, Igri (139 RILs) and Uschi (284 RILs). A set of 32 competitive allele-specific PCR (KASP) assays, designed using single nucleotide polymorphisms (SNPs) from the barley 50 K Illumina Infinium iSelect SNP chip, genotyping by sequencing (GBS) and whole-genome sequencing (WGS), was used as a backbone for construction of two high-resolution maps. Using this approach, the target locus was narrowed down to 0.161 cM and 0.036 cM in the Igri × Chikurin Ibaraki 1 (I × C) and Chikurin Ibaraki 1 × Uschi (C × U) populations, respectively. Corresponding physical intervals of 11.3 Mbp and 0.281 Mbp were calculated for I × C and C × U, respectively, according to the Morex v3 genome sequence. In the 0.281 Mbp target region, six high confidence (HC) and two low confidence (LC) genes were identified. Genome assemblies of BaMMV-susceptible cultivars Igri and Golden Promise from the barley pan-genome, and a HiFi assembly of Chikurin Ibaraki 1 together with re-sequencing data for the six HC and two LC genes in susceptible parental cultivar Uschi revealed functional SNPs between resistant and susceptible genotypes only in two of the HC genes. These SNPs are the most promising candidates for the development of functional markers and the two genes represent promising candidates for functional analysis.
由土壤传播的根肿菌传播的大麦黄花叶病毒（BaYMV）和大麦温和花叶病毒（BaMMV）会给大麦造成严重的产量损失。在之前的研究中，源自日本地方品种筑紫茨城1号的隐性BaMMV抗性基因被定位在大麦的6HS染色体上。在本研究中，通过筑紫茨城1号与两个对BaMMV敏感的品种Igri（139个重组自交系）和Uschi（284个重组自交系）杂交，培育出了423个F代染色体片段重组自交系（RIL）。利用从大麦50K Illumina Infinium iSelect SNP芯片、简化基因组测序（GBS）和全基因组测序（WGS）中获得的单核苷酸多态性（SNP）设计了一组32个竞争性等位基因特异性PCR（KASP）检测方法，以此作为构建两张高分辨率图谱的主干。采用这种方法，在Igri×筑紫茨城1号（I×C）群体和筑紫茨城1号×Uschi（C×U）群体中，目标基因座分别被缩小到0.161厘摩和0.036厘摩。根据Morex v3基因组序列，分别计算出I×C和C×U群体对应的物理区间为11.3兆碱基对和0.281兆碱基对。在0.281兆碱基对的目标区域内，鉴定出了6个高可信度（HC）基因和2个低可信度（LC）基因。大麦泛基因组中对BaMMV敏感的品种Igri和Golden Promise的基因组组装，以及筑紫茨城1号的高保真组装，再加上对敏感亲本品种Uschi中6个HC基因和2个LC基因的重测序数据，结果显示抗性和敏感基因型之间的功能性SNP仅存在于2个HC基因中。这些SNP是开发功能标记最有希望的候选者，而这两个基因是功能分析最有希望的候选者。
