Genetic diversity in rice (Oryza sativa L.) landraces of Sikkim-Himalaya and early insight into their use in genome-wide association analysis

The Sikkim-Himalaya represents one of the unique reservoirs of rice genetic resources in India owing to the presence of a large number of landraces adapted to extreme climatic and edaphic conditions. This valuable gene pool is now under threat due to the introduction of high-yielding varieties, wanting suitable genetic intervention for enhancing their productivity, and thus economic viability. Development of lodging resistant, high-yielding varieties tolerant to soil acidity through association mapping aided marker-assisted breeding programmes can help achieve this in a fast and efficient manner. But this requires information on genetic diversity, population structure, etc., of the germplasm collection, which is strikingly lacking. We, therefore, characterized a set of 53 rice landraces from Sikkim to address the above issues. The results revealed moderate diversity, poor divergence and high gene flow in our germplasm collection attesting its utility as an association mapping panel. Further, a total of 115 putative marker-trait associations (P < 0.05, R2 ≥ 10%) were obtained using the general linear model and mixed linear models of which 25 were identical in both. Some of the associated markers were positioned in those regions where Qualitative Trait Loci have been previously identified in rice, providing credence to our results. The resources generated from this study will benefit the rice breeders from this region and elsewhere for targeting the yield and related traits, in addition to conservation efforts by the interested researchers.