Chen Szu-Yu, Lai Ming-Hsin, Tung Chih-Wei, Wu Dong-Hong, Chang Fang-Yu, Lin Tsung-Chun, Chung Chia-Lin
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan.
Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist., Taichung City, 41362, Taiwan.
Rice (N Y). 2019 Nov 21;12(1):85. doi: 10.1186/s12284-019-0337-3.
Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of bakanae resistance in rice. The lack of large-scale screens for bakanae resistance in rice germplasm has also limited the development and deployment of resistant varieties.
A genome-wide association study (GWAS) was conducted to identify genes/loci conferring bakanae resistance in rice. A total of 231 diverse accessions from Rice Diversity Panel 1 (RDP1) were inoculated with a highly virulent Taiwanese Fusarium fujikuroi isolate and assessed for resistance using two parameters: (1) disease severity index based on visual rating and (2) colonization rate determined by reisolation of F. fujikuroi from the basal stems of infected rice seedlings. We identified 14 quantitative trait loci (QTLs) (10 for disease severity and 4 for colonization rate), including 1 mapped for both parameters. A total of 206 candidate genes were identified within the 14 QTLs, including genes encoding leucine-rich repeat (LRR)-containing and NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) proteins, hormone-related genes, transcription factor genes, ubiquitination-related genes, and oxidase/oxidoreductase genes. In addition, a candidate QTL (qBK1.7) that co-localized with the previously identified QTLs qBK1 and qFfR1, was verified by linkage analysis using a population of 132 recombinant inbred lines derived from IR64 x Nipponbare. GWAS delineated qBK1.7 to a region of 8239 bp containing three genes. Full-length sequencing across qBK1.7 in 20 rice accessions revealed that the coding regions of two LRR-containing genes Os01g0601625 and Os01g0601675 may be associated with bakanae resistance.
This study facilitates the exploitation of bakanae resistance resources in RDP1. The information on the resistance performance of 231 rice accessions and 14 candidate QTLs will aid efforts to breed resistance to bakanae and uncover resistance mechanisms. Quantification of the level of F. fujikuroi colonization in addition to the conventional rating of visual symptoms offers new insights into the genetics of bakanae resistance.
水稻恶苗病已成为水稻生产的新威胁。近年来，亚洲多个地区报道了恶苗病发生频率和严重程度的增加。尽管恶苗病会影响水稻产量和品质，但对水稻抗恶苗病的遗传学了解甚少。水稻种质中缺乏大规模的抗恶苗病筛选也限制了抗性品种的开发和应用。
进行了全基因组关联研究（GWAS）以鉴定赋予水稻抗恶苗病的基因/位点。用一种高毒力的台湾藤仓镰刀菌分离株接种了来自水稻多样性面板1（RDP1）的总共231个不同种质，并使用两个参数评估抗性：（1）基于视觉评分的病情严重指数，以及（2）通过从受感染水稻幼苗的基部茎中重新分离藤仓镰刀菌确定的定殖率。我们鉴定出14个数量性状位点（QTL）（10个与病情严重程度相关，4个与定殖率相关），其中1个在两个参数中均被定位。在这14个QTL内共鉴定出206个候选基因，包括编码富含亮氨酸重复序列（LRR）和NB-ARC（由APAF-1、R蛋白和CED-4共享的核苷酸结合衔接子）蛋白的基因、激素相关基因、转录因子基因、泛素化相关基因以及氧化酶/氧化还原酶基因。此外，通过使用由IR64×日本晴衍生的132个重组自交系群体进行连锁分析，验证了一个与先前鉴定的QTL qBK1和qFfR1共定位的候选QTL（qBK1.7）。GWAS将qBK1.7定位到一个包含三个基因的8239 bp区域内。对20个水稻种质的qBK1.7进行全长测序表明，两个富含LRR的基因Os01g0601625和Os01g0601675的编码区可能与抗恶苗病有关。
本研究有助于利用RDP1中的抗恶苗病资源。关于231个水稻种质和14个候选QTL抗性表现的信息将有助于培育抗恶苗病品种并揭示抗性机制。除了传统的视觉症状评级外，对藤仓镰刀菌定殖水平的量化为恶苗病抗性遗传学提供了新的见解。
