Genome-wide identification of genetic determinants for gall midge resistance in rice using genic markers

Abstract

The Asian rice gall midge poses a severe threat to rice yields, making the development of resistant rice cultivars the most cost-effective and efficient strategy to manage the gall midge. A diverse panel of 115 rice accessions was phenotyped, revealing varying resistance to the gall midge biotype 2. The panel's diversity and familial relatedness were assessed before conducting a genome-wide association study to identify marker-trait associations (MTAs) for gall midge resistance. Newly developed candidate gene-derived markers were used along with random microsatellite markers in genotyping. A total of 50 significant MTAs with P < 0.05 were found. Except for chromosome 11, all of the rice chromosomes had significant MTAs. The QTL identified on chromosomes 6, 8, and 9 has been associated with 66F 67R, 54F 55R, and RM107, explaining maximum phenotypic variation. The allele effects of the associated markers differentiated susceptible and highly resistant genotypes, confirming their association with gall midge resistance. Seven genes associated with the general response to stress tolerance were found in the gall midge resistance QTL region. On chromosome 9, one putative gene for gall midge resistance was identified, which is associated with marker RM23914. These candidate genes identified have a significant impact on the gall midge resistance response. This investigation contributes to a better understanding of the rice gall midge resistance mechanism and provides essential genetic information for the breeding and functional verification of resistant cultivars.

Keywords: Candidate genes; Efficient mixed-model associations; Gall midge; Marker-assisted breeding; Resistance response.