Genetic diversity analysis of rice germplasm (oryza sativa, oryza glaberrima) using morphological and molecular markers

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This experiment was carried out to determine the genotypic variation among rice accessions using phenotypic traits and SSR markers and the relationship between phenotypic traits and yield of rice accessions. A total of 87 accessions from six countries were laid out in a completely randomised design with 3 replications. Seventeen quantitative and 11 qualitative traits were recorded based on the internationally accepted standard evaluation system for rice. Genstat, NTSYS-pc and PowerMarker were the software’s used for data analysis. Highly significant (P < 0.001) differences were observed among the accessions for all the quantitative traits. Differences were also observed among the accessions regarding the 11 qualitative traits. First five principal components accounted for 75.01 % of the total genetic variance among the accessions. Significant positive correlation with grain yield was noticed for some of the morphological traits. At 21 % similarity coefficient, the 87 accessions from six countries were grouped into seven clusters based on the morphological traits. Accessions from these seven clusters have tiller number 10-20, erect culm angle, no awn, 90-120 days to 50 % flowering, semi erect flag leaf, well exserted panicle and grain width 2-3.5 mm respectively. Following successful field experiment, the genetic diversity were again examined using 12 SSR markers. Six primers out of these 12 primers showed DNA amplification and polymorphism among the 87 rice accessions. The number of alleles detected by these six primers ranged from 2-9 with an average of 6.83 while PIC ranged from 0.34-0.79 with an average of 0.55. The UPGMA cluster dendrogram generated based on the 6 SSR markers grouped the accessions into 4 clusters at 41 % similarity coefficient. Accessions from these four clusters have late maturity, green basal leaf sheath colour, no awn and fewer tillers respectively. This experiment has proven that both morphological and SSR markers are effective tools in assessing genetic diversity in rice accessions. The genetic diversity revealed by the morphological and SSR markers in this study would be very important to select potentially good genotypes for future rice improvement programmes.
A thesis submitted to the School of Graduate Studies in partial fulfillment of the requirement for the degree of MPhil. Agronomy (plant breeding),