Assessment of allelic and genetic diversity, and population structure among farmers' rice varieties using microsatellite markers and morphological traits

Traditional rice varieties grown by the farmers serve as valuable genetic resources for future rice improvement. These varieties are highly adapted to varied agro-ecological conditions. However, they are rapidly lost because of the adoption of high-yielding varieties. The extent of allelic and genetic diversity present in the germplasm is a prerequisite for the improvement of any crop and conservation strategies under adverse impacts of climate. Farmers' rice varieties are usually poor yielders but are allelic treasurer for different traits, especially biotic and abiotic stresses, grain qualities, early seedling vigor, input use efficiency, etc. Therefore, the present study was aimed for a detailed understanding of allelic and genetic diversity, and population structure of 607 farmers' rice varieties using 36 fluorescently labeled microsatellite markers and 53 morphological traits. A total of 363 alleles was detected with an average of 10.33 alleles per locus and moderately high Nei's allelic/gene diversity (0.502) was detected. Polymorphic information content ranged from 0.685 to 0.987 with an average of 0.901. 34 unique, 236 rare, 84 low-frequency and 44 high-frequency alleles were detected. 53 morphological traits harbored a total of 195 variables with an average of 4.217 variables per trait. 50 out of 53 morphological traits showed poly-morphism and highly significant differences among varieties. High genetic diversity was observed among 607 farmers' rice varieties both at molecular (0.653) and phenotypic (0.656) levels. The dendrogram based on both microsatellite markers and morphological traits grouped the 607 farmers' rice varieties into three major groups. A moderate population structure was observed with two independent subpopulations SP1 and SP2, which have membership percentages of 82.6 % and 17.4 %, fixation index values of 0.19 and 0.194, respectively. The AMOVA could explain 63 % of the total variation among varieties and 34 % within varieties. Our results showed that the farmers' rice varieties of Odisha harbored higher levels of both allelic and genetic diversity. Hence, these varieties would be useful for the identification of novel and elite alleles, and serve as a source of donors for the development of climate-smart varieties with improved grain yield and qualities, and input use efficiency, which would be sustainable in changing climate scenario conditions and improve farmers' income.