Genetic variation and association analysis of some important traits related to grain in rice (Oryza sativa L.) germplasm

The identification of genomic loci involved in control of quantitative traits receives growing attention in plant molecular breeding. The present study was carried out to evaluate the genetic variability among 48 rice genotypes and determine the genomic regions associated with ten grain related important traits. A total number of 63 alleles were detected by 18 selected SSR markers from different chromosomes with an average of 3.5 alleles per marker. A model-based Bayesian approach subdivided 48 evaluated rice genotypes into three major subgroups with the consideration of the highest value of ΔK. The mean r2 value for all loci pairs on the same chromosome was 0.053. A total of 38 significant marker-trait associations were identified (P< 0.05) that explaining more than 32% of the total variation. RM315, RM3428, RM289, RM16, RM574 and RM156 markers had highest R2 and most association with assayed traits, respectively. The findings of this study revealed association of grain properties in rice with some SSR markers that could serve as target genomic regions for further research such as MAS, fine mapping and candidate gene discovery in rice breeding programs.