ABSTRACT
MOLECULAR VARIATION AND GENETIC DIVERGENCE IN T. AMAN RICE GENOTYPES USING SSR MARKERS
Journal: Malaysian Journal of Sustainable Agriculture (MJSA)
Author: Alkasim S.M., Ibrahim, M.I., Hafsat, S.M., Tswanya, M.N., Hasanuzzaman, Md., Arifuzzaman Md., Zahidul Islam Md., Suleiman H., Abubakar S
This is an open access article distributed under the Creative Commons Attribution License CC BY 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
DOI: 10.26480/mjsa.02.2024.72.79
Transplanted (T.) aman rice (Oryza sativa L.) covers the largest cultivated area in Bangladesh while very little information on molecular level characterization of T. aman genotypes persists. The major aim of this study was to dissect molecular characterization and genetic diversity of 25 T. aman rice genotypes using twelve simple sequences repeats (SSRs) markers. The rice genotypes comprised local landraces that were collected from twelve districts of Bangladesh. A total of twelve SSR primer pairs covering all 12 chromosomes of rice were selected for the study. The molecular characterization, genetic diversity, population structure and principal component analysis (PCA) were estimated and the results revealed a total of fifty alleles across 12 loci ranged from 2 (RM411) to 7 (RM252) per locus. The maximum gene diversity exhibited in RM252 (0.7) while the minimum was in RM320 (0.15). The polymorphism information content (PIC) values ranged from 0.14 to 0.67 while RM252 and RM206 identified as the most suitable markers. Clustering based on unweight pair group method with arithmetic mean (UPGMA) analysis clustered 25 genotypes into six major clusters (I-VI) with similarity coefficient value of 0.34. Cluster V contained a maximum seven genotypes with 5 sub- groups. Again, the population structure displayed 3 populations namely population 1, 2 and 3. These populations were clustered into the 3 major groups in the Principle Component Analysis (PCA) 2D plot. Here, PC1 and PC2 contributed 32.7% variations. However, the overall hybridization suggested between the genotypes of the population 1 and 3, specifically between clusters I and cluster VI, and between the diverse parents such as, genotypes Bohi Trimota and Ranga, Bohi Trimota and Purple Rice-2, Bohi Trimota and Purple Rice-3. These diverse clusters and genotypes identified through SSR makers are lay foundation of molecular characterization of T. aman rice genotypes in Bangladesh and further marker-assisted studies will be suggested.