Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice (Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection.

Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L. ) using RAPD markers

The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. Information on genetic diversity and relationships among rice genotypes from Pakistan is currently very limited. The objective of this study was to evaluate the genetic polymorphisms and identities of 10 traditional, 28 improved and 2 Japanese cultivars of rice using the random amplified polymorphic DNA technique. Twenty-five decamer-primers could generate a total of 208 RAPD fragments, of which 186 or 89.4 percent were polymorphic. The number of amplification products produced by each primer varied from 4 to 16 with an average of 8.3 bands primer-1. The size of amplified fragments were ranged from 200 to 4000 bp. Pair-wise Nei and Li's similarity had estimated the range of 0.50 to 0.96 between rice cultivars. Based on analysis performed on a similarity matrix using UPGMA, 40 cultivars were grouped into 3 main clusters corresponding to aromatic, non-aromatic and japonica group. There were a few of independent cultivars. The cluster analysis had placed most of the aromatic cultivars into a close relation showing a high level of genetic relatedness. However, the clusters formed by the aromatic cultivars were distinct from those of non-aromatic and japonica types. Interestingly, a number of improved and traditional cultivars originating from diverse sources did not form well defined groups and were interspersed, indicating no association between the RAPD patterns and the geographic origin of the cultivars. The information generated from this study can be used to maximize selection of diverse parents and broaden the germplasm base in the future of rice breeding programs.