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Identification of brown planthopper resistance gene Bph32 in the progeny of a rice dominant genic male sterile recurrent population using genome-wide association study and RNA-seq analysis

Pan, Yi, Huang, Ling, Song, Shufeng, Hu, Meixia, Chang, Shuoqi, Lv, Qiming, Li, Yixing, Wang, Tiankang, Ouyang, Xiang, Xiao, Yinghui, Fu, Xiqin
Molecular breeding 2019 v.39 no.5 pp. 72
Nilaparvata lugens, biochemical pathways, chromosomes, field experimentation, gene expression regulation, gene ontology, genome-wide association study, insect infestations, male sterility, marker-assisted selection, pests, progeny, quantitative trait loci, recurrent selection, resistance genes, rice, sequence analysis, transcription (genetics)
Brown planthopper (BPH) is one of the most damaging pests of rice. Improving the resistance of rice varieties is considered a safe and effective way to control this pest. Here, a field experiment was conducted to test BPH resistance in a rice population developed by recurrent selection of a variety with dominant genic male sterility. Three high-resistance lines were identified and subjected to a genome-wide association study (GWAS), which mapped the BPH resistance gene to the short arm of chromosome 6. One highly resistant line (14CF2426) was further crossed with Taichuang Native 1 (TN1) to construct an F₂ segregating population. Artificial insect infestation identified three quantitative trait loci (QTLs), which were mapped to chromosomes 1, 6, and 10; the QTL on chromosome 6 of 14CF2426 contained a known resistance gene, Bph32. Near-isogenic lines NIL-Bph32 and NIL-bph32 of Bph32 were constructed using molecular marker-assisted selection. RNA sequencing (RNA-seq) detected 1268 differentially expressed genes (DEGs) between the two near-isogenic lines. Compared with NIL-Bph32, 1064 genes were upregulated and 204 were downregulated in NIL-bph32. Gene ontology (GO) enrichment analysis detected 46 significantly enriched terms, and KEGG analysis revealed four significantly enriched metabolic pathways. This robust multi-method strategy showed that combining GWAS analysis with a dominant genic male sterile recurrent rice population can significantly improve the efficiency of gene identification. RNA-seq revealed some candidate genes with a potential regulatory function in BPH resistance, thus providing insights into the transcriptional regulatory network and the molecular mechanisms of resistance.