Inter Simple Sequence Repeats (ISSRs) Fingerprinting, Phenotypic Variability and Trait Associations in Released and Elite Rice (Oryza sativa L.) Genotypes of Ethiopia

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Addis Ababa University


A study on the morphological and molecular characterization of rice (Oryza sativa L.) varieties and lines of Ethiopia was carried out in 2009/10 cropping season. A total of 18 released and elite rice varieties of Ethiopia were used. Inter simple sequence repeats (ISSR) was used as a molecular marker to assess genetic diversity within and among varieties using five ISSR primers (810, 824, 834, 873 and 878). A total of 75 clear and reproducible bands were amplified, out of which 62(82.67%) were observed to be polymorphic. The number of polymorphic loci ranged from 8 for primer-873 to 16 for primer-810. The lowland rice genotypes showed the highest polymorphism (74.67%), followed by upland (61.33%) and NERICA varieties (57.33%). In the same fashion, genetic diversity analysis indicated that lowland rice genotypes showed higher diversity (0.27) than both upland (0.25) and NERICA varieties (0.23). The over all genetic diversity of Ethiopian rice was found to be 0.29. The un-weighted pair group method using arithmetic mean (UPGMA) and neighbor joining trees clustered the genotypes in to their respective ecosystem Lack of purity in IREM-194, HO-04 and AD-12 was prevalent from the constructed trees and field observation. The principal coordinate analysis (PCO) also recovered the UPGMA and neighbor joining tree groups. Analysis of molecular variance (AMOVA) revealed that higher percentage of variation was attributed to variation within individuals (88.67) and the variation among groups was lower (11.33).In the morphological study, which was carried out in a randomized complete block design (RCBD) with three replications, 23 qualitative and 13 quantitative traits were evaluated based on the standard procedures given by International Rice Research Institute and Bioversity International. The result of all diversity parameters indicated that there exists a clear difference among the genotypes for all the traits considered. Analysis of variance (ANOVA) and Duncan’s multiple range test (DMRT) revealed the variability of the genotypes for each of the 13 quantitative traits. Phenotypic coefficient of variation (PCV) varied from 5.38% for number of days to heading to 20.49% for leaf length. Similarly, genotypic coefficient of variation (GCV) ranged from 5.36% for number of days to heading to 19.47% for leaf length. Higher heritability values were observed for all the 13 quantitative traits, out of which nine traits showed heritability percentage more than 90 %. It ranged from 98.98% for number of days to heading to 55.13% for grain yield. Correlation of traits showed that most of the traits were associated. Cluster analysis using morphological data grouped all the test materials in to two main clusters but failed to strictly cluster the genotypes in to their respective ecosystems. Principal component analysis (PCO) showed that the first three principal components explained about 86.81 % of the total variation. Generally, the study indicated the existence of narrower genetic diversity among the genotypes which calls for timely action to widen the genetic diversity of Ethiopian rice so as to combat the devastating outcome of having narrower genetic diversity in cultivated crops. Key words: Rice (Oryza Sativa L.), ISSR, genetic diversity, trait association



Rice (Oryza Sativa L.), ISSR, genetic diversity, trait association