Zhang Guorong, Hua Zhihua
Agricultural Research Center-Hays, Kansas State University, Hays, KS, United States of America.
Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States of America.
PeerJ. 2018 Apr 23;6:e4678. doi: 10.7717/peerj.4678. eCollection 2018.
(WSMV) causes streak mosaic disease in wheat ( L.) and has been an important constraint limiting wheat production in many regions around the world. is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. However, the sequence nature and the biological function of remain unknown due to the difficulty of genetic manipulation in wheat. In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice () and . Based on the phenotypic result and previous genomic studies, we developed a novel bioinformatics pipeline for interpreting a potential biological function of and its ancestor locus in wheat. In the WSMV resistance tests, we found that rice has a WMSV resistance gene while does not, which allowed us to hypothesize the presence of a ortholog in rice. Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and discovered 4,035 OrthoMCL groups as preliminary candidates of orthologs. Given that is likely duplicated through an intrachromosomal illegitimate recombination and that is dominant, we inferred that this new WSMV-resistance gene acquired an activation domain, lost an inhibition domain, or gained high expression compared to its ancestor locus. Through comparison, we identified that 67, 16, and 10 out of 4,035 OrthoMCL orthologous groups contain a rice member with 25% shorter or longer in length, or 10 fold more expression, respectively, than those from wheat and Taken together, we predicted a total of 93 good candidates for a ancestor locus. All of these 93 candidates are not tightly linked with , indicative of the role of illegitimate recombination in the birth of . Further sequence analysis suggests that the protein products of may combat WSMV disease through a molecular mechanism involving protein degradation and/or membrane trafficking. The 93 putative ancestor loci discovered in this study could serve as good candidates for future genetic isolation of the true locus.
小麦条纹花叶病毒（WSMV）会引发小麦（Triticum aestivum L.）的条纹花叶病，并且一直是限制世界许多地区小麦产量的重要制约因素。Wsm1是在小麦基因组中发现的唯一抗性基因，已定位在其3B染色体的一个短基因组区域。然而，由于小麦遗传操作的困难，Wsm1的序列性质和生物学功能仍然未知。在本研究中，我们测试了WSMV在小麦及其两个近缘禾本科物种水稻（Oryza sativa）和节节麦（Aegilops tauschii）中的感染性。基于表型结果和先前的基因组研究，我们开发了一种新颖的生物信息学流程，用于解释Wsm1及其在小麦中的祖先基因座的潜在生物学功能。在WSMV抗性测试中，我们发现水稻具有WMSV抗性基因，而节节麦没有，这使我们推测水稻中存在Wsm1的直系同源基因。我们对小麦3B染色体及其在水稻和节节麦中的同源染色体上的蛋白质编码基因进行的OrthoMCL分析发现了4035个OrthoMCL组作为Wsm1直系同源基因的初步候选者。鉴于Wsm1可能通过染色体内非法重组而复制，并且Wsm1是显性的，我们推断这个新的WSMV抗性基因与其祖先基因座相比获得了一个激活域，失去了一个抑制域，或者获得了高表达。通过比较，我们确定在4035个OrthoMCL直系同源组中，分别有67个、16个和10个组包含一个水稻成员，其长度比来自小麦和节节麦的成员短25%或长25%，或者表达量高10倍。综合起来，我们预测了总共93个Wsm1祖先基因座的良好候选者。所有这93个候选者都与Wsm1没有紧密连锁，这表明非法重组在Wsm1产生中的作用。进一步的序列分析表明，Wsm1的蛋白质产物可能通过涉及蛋白质降解和/或膜运输的分子机制对抗WSMV疾病。本研究中发现的93个推定的Wsm1祖先基因座可以作为未来真正Wsm1基因座遗传分离的良好候选者。
