Analysis of genetic diversity, population structure and phylogenetic relationships of rice (Oryza sativa L.) cultivars using simple sequence repeat (SSR) markers

The genetic diversity of Egyptian rice has received diminished attention recently, resulting in a weakened genetic foundation that renders it more vulnerable to environmental fluctuations. Developing durable rice cultivars necessitates the ongoing exploration of genetic resources and the utilization of diverse germplasm. The examination of rice diversity was conducted by researchers utilizing 27 rice genotypes and 23 polymorphic microsatellite markers. The microsatellite comprises 106 alleles that have been observed (Na), with an effective allele count of 67.36 (Ne). The average number of alleles per locus is 4.61, with a standard deviation of 2.93. On average, the values of polymorphism information content (PIC) were found to be 0.580. A noteworthy correlation was observed between the number of alleles and both gene diversity (r = 0.713) and polymorphic information content (PIC) (r = 0.785). The results of our study provide empirical evidence supporting the existence of both the P1 and P2 subgroups; P1 comprises twelve distinct rice genotypes, while P2 encompasses fifteen different rice genotypes. The analysis of molecular variance determined that individual variations contributed to 34.22% of the observed variance, while population differences accounted for the remaining 65.78%. The gene flow coefficient was determined to be 0.481, whereas the fixation index exhibited a statistically significant value of 0.342. The presence of admixtures within the population suggests a significant likelihood of gene transfer between different genotypes. The principal component analysis (PCA) encompassed 27 components, with only the initial four components (PC1, PC2, PC3, and PC4) regarded as variation representatives. In that order, the initial four components exhibited the highest eigenvalues, specifically 18.413, 10.759, 7.618, and 7.031. The findings underscore the importance of investigating and establishing connections between genetic diversity and developing Egyptian rice breeding and enhancement strategies. Selecting genotypes as possible donors in a crop breeding approach to improve rice quality requires examining genetic diversity within populations. The distribution of alleles within subpopulations reveals valuable loci for genetic diversity research. This study contributes to developing environmentally sustainable cultivars by providing insights into the mechanisms of gene flow and genetic structure in Egyptian rice.