Linkage Disequilibrium Based Association and Inheritance of Blast Resistance in Improved Varieties and Landraces of Aromatic Rice

Abstract

Aromatic rice (Oryza sativa L.), belongs to a genetically distinct subgroup of rice, is differentiated into two subgroups, viz. basmati and small grained non-basmati. It upholds unique and most accepted quality traits. Unfortunately, aromatic rice is highly susceptible to rice blast, one of the most devastating diseases over the world that is caused by Magnaporthe oryzae. In the present study, a set of aromatic rice accessions were screened for blast disease at blast hotspot and rice microsatellite markers were surveyed. Genetic diversity analysis measured a range of variations and genetic fingerprinting identified markers RM144, RM208, RM6836, MRG5836, RM266 and RM7102, which were important for differentiation of aromatic rice genotypic classes. Similarity matrix revealed about 30 % similarity between major clusters while more than 80 % of genetic similarity was found among subclusters. Pairwise Fst ranged from 0.001 to 0.397. Analysis of population structure revealed three genetic structures (K = 3). Association analysis proved significant association of markers RM3330 and RM224 (P < 0.05) with blast resistance. Furthermore, Chi-square analysis of F2 progenies fitted into 3:1 ratio and bulk segregation analysis indicated the presence of linked Piz and Pi-k h genes in two different segregated F2 populations. Genetic diversity and population structure analysis revealed three sub-populations among aromatic rice and proved that even parallel evolutionary decent has attained a considerable level of genetic variations. This study also clarifies the relationship between resistant and susceptible genotypes and offers some key genetic markers and genotypes (3131 and 3327) for aromatic rice improvement against blast disease.