Allelic distribution and association of key gene-specific markers with rice (Oryza sativa L.) yield under acidic soil

Rice blast disease and soil acidity-related phosphorus deficiency are the major issues observed in rice-growing ecosystems across the world, especially in the North Eastern Hill (NEH) region of India. The present study aimed to check the allelic distribution of major genes for blast resistance, low P tolerance, grain yield and their association with increasing yield under acidic soils in NEH region. A set of 75 genotypes, including parental lines, advanced breeding lines and landraces, were evaluated and a significant association of SPIKE allele (Type-5) with spikelets per panicle, grain yield per panicle and plot yield was recorded. Gn1a-InDel3 allele was significantly associated with increased spikelets and grain number per panicle. The gene PSTOL1 showed a significant association with tiller number at 30 and 60 days after transplanting but not with plot yield. The genotypes carrying desirable alleles for Pi9, Pi2 and Pi-ta recorded lower disease scores but none of them were significantly associated with blast resistance. The study also identified advanced breeding lines ULRC24-48-5-1, ULRC24-57-1-1-1, ULRC24-49-5-1-1, ULRC24-99-3-1-1, ULRC26-11-2-1-1 and ULRC26-1-1-1 carrying six to eight favorable allelic combinations with high plot yield under acidic soil conditions. These lines can be used as potential donors for enhancing genetic gain under low input acidic soil conditions.