Genome-Wide Association Study Reveals a New Quantitative Trait Locus in Rice Related to Resistance to Brown Planthopper <i>Nilaparvata lugens</i> (Stål)
Longqing Shi,
Meng Dong,
Ling Lian,
Junian Zhang,
Yongsheng Zhu,
Weilong Kong,
Liangmiao Qiu,
Dawei Liu,
Zhenxing Xie,
Zhixiong Zhan,
Zhaowei Jiang
Affiliations
Longqing Shi
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Meng Dong
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Ling Lian
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Junian Zhang
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Yongsheng Zhu
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Weilong Kong
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Liangmiao Qiu
Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
Dawei Liu
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Zhenxing Xie
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Zhixiong Zhan
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
Zhaowei Jiang
Rice Research Institute, Fujian Academy of Agricultural Sciences, Cangshan, Fuzhou 350018, China
The brown planthopper (BPH) is one of the main pests endangering rice yields. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. To identify new BPH resistance-related genes, a total of 123 rice varieties were assessed for resistance and durable resistance. Three varieties were immune, and nine were highly resistant to BPH. After whole-genome resequencing of all 123 varieties, 1,897,845 single nucleotide polymorphisms (SNPs) were identified. Linkage disequilibrium (LD) decay analysis showed that the average LD of the SNPs at 20 kb was 0.30 (r2) and attenuated to half value (~0.30) at a distance of about 233 kb. A genome-wide association study (GWAS) of durable resistance to BPH was conducted using the Fast-MLM model. One quantitative trait locus, identified on chromosome 2, included 13 candidate genes. Two candidate genes contained a leucine-rich repeat and CC-NBS-LRR or NB-ARC domains, which might confer resistance to pests or diseases. Interestingly, LOC_Os02g27540 was highly expressed and was induced by BPH; GWAS identified potential rice genes coding for durable resistance to BPH. This study helps to elucidate the mechanism of durable resistance to BPH in rice and provides essential genetic information for breeding and functional verification of resistant varieties.
