Identification of quantitative trait loci underlying resistance and tolerance to the rice root-knot nematode, Meloidogyne graminicola, in Asian rice (Oryza sativa)

Meloidogyne graminicola is one of the most important plant-parasitic nematodes in rice. Breeding for natural resistance and tolerance is considered one of the most economical and sustainable approaches to control this damaging pathogen. Quantitative trait loci (QTL) mapping was carried out in a recombinant inbred line (RIL) population derived from a cross between the Asian rice genotypes IR78877-208-B-1-2 and Dinorado. IR78877-208-B-1-2 is an aerobic rice genotype that is resistant and tolerant to M. graminicola. Dinorado is a traditional upland rice genotype from the Philippines that is characterized by its aroma and prized for its cooking quality. The host response of 300 F4 lines derived from this cross was evaluated in both nematode infested and non-infested concrete beds in the dry seasons of 2013 and 2014. Five genotypes were found consistently resistant while 13 genotypes were consistently partially resistant to M. graminicola. QTL mapping for M. graminicola resistance/tolerance, yield-contributing traits, and yield revealed four main effect QTLs (qJ2RS2.1, qJ2GRT2.1, qJ2RS3.1, and qJ2GRT3.1) associated with reduced nematode reproduction on chromosomes 2 and 3 and two QTLs (qGR3.1 and qGR5.1) associated with reduced root galling on chromosomes 3 and 5. Twenty main effect QTLs associated with yield-contributing traits and yield were also found. Our study further identified co-locating QTLs associated with nematode resistance, yield-contributing traits, and yield on chromosomes 3 and 5. QTLs harboring candidate genes, such as OsBAK1, OsDST, OsIPT4, and DUF26, for higher grain yield and tolerance to abiotic and biotic stress, were identified. These QTLs and the RILs that are consistently resistant and tolerant to M. graminicola, and which are high-yielding in nematode-infested fields, can be utilized in breeding programs to improve the resistance and tolerance of Asian rice to this important pathogen.