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

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.