Data_Sheet_2_Genomic and Molecular Characterization of Wheat Streak Mosaic Virus Resistance Locus 2 (Wsm2) in Common Wheat (Triticum aestivum L.).xlsx

Wheat streak mosaic virus (WSMV) is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains of the United States. The Wsm2 locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in wheat and aid the development of perfect markers for breeding. In this study, linkage mapping in a doubled-haploid (DH) mapping population confirmed Wsm2 as a major locus conferring WSMV resistance in wheat. The Wsm2 flanking markers were mapped to a 4.0 Mbp region at the distal end of chromosome 3BS containing 142 candidate genes. Eight haplotypes were identified from seventeen wheat genotypes collected from different agroecological zones, indicating that Wsm2 lies in a dynamic region of the genome with extensive structural variation and that it is likely a rare allele in most available genome assemblies of common wheat varieties. Exome sequencing of the variety “Snowmass”, which carries Wsm2, revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the Wsm2 interval. Six of these genes are differentially expressed in “Snowmass” compared to “Antero,” a variety lacking Wsm2, including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A de novo assembly of unmapped RNA-seq reads identified nine transcripts expressed only in “Snowmass,” three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying Wsm2 and provides a list of candidate genes for subsequent validation.

小麦线条花叶病毒（Wheat streak mosaic virus, WSMV）是一种具有重要经济价值的病毒病原，对全球小麦生产构成威胁，尤以美国大平原地区最为严重。Wsm2位点可赋予小麦对WSMV的抗性，且已在适配该区域的普通小麦品种中广泛部署。解析该位点背后的因果遗传变异，有助于深化对小麦抗病毒机制的理解，并助力育种用完美标记的开发。本研究通过双单倍体（doubled-haploid, DH）作图群体开展连锁作图，证实Wsm2是赋予小麦WSMV抗性的主效位点。Wsm2的侧翼标记被定位在3BS染色体远端的4.0 Mbp区域内，该区域共包含142个候选基因。从不同农业生态区收集的17份小麦种质中，共鉴定出8种单倍型，这表明Wsm2所在的基因组区域属于动态区域，存在广泛的结构变异，且在多数现有普通小麦基因组组装中，该位点大概率为稀有等位基因。对携带Wsm2的品种"Snowmass"进行外显子组测序，在Wsm2区间内的142个候选基因中，发现了若干功能丧失突变与拷贝数变异。与不含Wsm2的品种"Antero"相比，"Snowmass"中有6个基因呈现差异表达，其中包括一个编码与RPM1同源的核苷酸结合位点亮氨酸重复（nucleotide-binding site leucine-rich repeat, NBS-LRR）型蛋白的基因。对未比对至参考基因组的RNA测序（RNA-seq）读段进行从头组装，鉴定出9份仅在"Snowmass"中表达的转录本，其中3份同样在WSMV接种后被诱导表达。本研究阐明了Wsm2的遗传变异基础，并为后续验证工作提供了候选基因列表。