Identification of novel QTL for bakanae disease resistance in non-basmati indica rice

Bakanae disease in non-basmati indica rice is emerging as a major threat owing to climate change. Our objective was to identify quantitative trait loci (QTL)/gene(s) in Thavalakannan, responsible for bakanae disease resistance. A bi-parental population was developed between a resistant variety, Thavalakannan, and a susceptible variety, Pooja, to identify QTL for bakanae disease resistance. The population was challenged with a highly virulent Gerua F3 strain of the Fusarium fujikuroi pathogen in three different experiments. The percent disease incidence calculated over three experiments and the genotypic information of the population were used to identify the QTL. A main effect QTL was identified on chromosome 5 with 8.97% phenotypic variation explained. In the interval of the main effect QTL, the genes controlling gibberellic acid biosynthesis pathways were identified, indicating the significance of the QTL identified. Furthermore, seven di-QTL interactions favoring resistance were identified on different chromosomes. The main effect QTL has scope for utilization in marker-assisted introgression breeding, and interactive QTL may be utilized in genomic selection to improve disease resistance.