Molecular Characterization of Different Varieties of rice (Oryza sativa L.) using SSR Markers (original) (raw)
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Molecular marker based genetic diversity analysis in rice (Oryza sativa L.) using SSR markers
Assessment of genetic diversity is very important in rice breeding from the standpoint of selection, conservation and proper utilization. The role of a broad genetic base and systematically characterized germplasm in the crop improvement of cultivated plants has been well recognized. To meet the continuously expanding needs of varietal improvements, the evaluation and characterization of all existing germplasm are required. Genetic variability studies are important in selection of parents for hybridization as sound crop improvement depends upon the magnitude of variability in the base population. In the present investigation 36 rice genotypes were studied for diversity studies using polymorphic SSR markers. These rice genotypes were grouped into two main clusters that is cluster I and II with similarity coefficient (0.00). Cluster I can be sub divided into two minor sub-groups IA, IB, and with similarity coefficient (0.15). Cluster IA consisted of 12 genotypes, whereas cluster IB consisted of 13 genotypes. The second main cluster can be also sub divided into two minor sub-groups that is IIA and IIB (0.25). This indicated presence of considerable diversity in the genotypes studied. Through diversity analysis, highest similarity was observed between cultivar URG-5 and URG-8 followed by NDR-359 and Pusa-6-B. The most diverse cultivars were Akshaya dhan and URG-24.
Molecular diversity analysis in rice (Oryza sativa L.) using SSR markers
ELECTRONIC JOURNAL OF PLANT BREEDING
Rice is the most important staple food crop among the cereals and feeds more than half of the world's population. Assessment of genetic diversity is of utmost importance in rice breeding from the perspective of selection, conservation and proper utilization. The present study was undertaken with an objective to assess the genetic diversity among 27 rice cultivars with 12 SSR markers. The results revealed a total of 40 alleles were detected across 27 rice cultivars tested. PIC values varied widely among SSR loci tested and it ranged from 0.38 to 0.65, with an average of 0.56 per marker. The 27 rice cultivars were grouped into two major clusters i.e., cluster I and II with similarity coefficient 0.13. Cluster I was sub divided into two minor subgroups IA and IB having 5 and 8 genotypes respectively. These subgroups were further subdivided into minor groups. In similar way, the second main cluster i.e. Cluster II was also sub divided into two minor subgroups that is IIA and IIB having 5 and 9 genotypes respectively. These subgroups were further divided into minor groups. This indicated presence of considerable diversity in the genotypes studied and the most diverse cultivars were IR 98846-2-1-2-3 and IR 14D201.
Studies on genetic diversity in rice (Oryza sativa L.) using SSR markers
Journal of Pharmacognosy and Phytochemistry, 2019
Rice is the most important staple food grain of all cereal crops and feeds more than half of the world’s population. Assessment of genetic diversity is of utmost important in rice breeding from the perspective of selection, conservation and proper utilization. The present study was undertaken with an objective to assess the genetic diversity among 28 rice cultivars by use of 22 SSR markers. A total of 41 alleles were detected across 28 rice cultivars used. PIC values varied widely among SSR loci tested and it ranged from 0.753 to 0.067, with a mean value of 0.376. The 28 rice cultivars were grouped into two clusters i.e., cluster I and II with dissimilarity coefficient 0.42. Cluster I was sub divided into two minor sub-groups IA and IB having 6 and 11 genotypes respectively. IB was further subdivided into minor groups. In similar way, the second main cluster i.e. Cluster II was also sub divided into two minor sub-groups that is IIA and IIB having 3 and 8 genotypes respectively. IIB ...
2012
In order to study of genetic diversity in rice, Twenty-nine genotypes comprising land races, pure lines and breeding lines were evaluated using simple sequence repeat (SSR) markers. Out of 30 primers of SSR markers, The PIC value ranged from 0.07 (RM 340) to 0.71 (RM 7426) with an average of 0.45. A total 30 SSR primers were used to amplify some part of rice genome in germplasm used. The results showed that a total number of 106 amplified bands were detected on studying. Among the used primers, RM7426 showed the highest some alleles while, the lowest was observed for RM340 primer. Average numbers of observed alleles in total genotypes were 3.53. The lowest PIC value observed for RM445, RM466, RM3345, RM7424 primers and highest PIC value observed RM7426, RM1337, RM47 and RM5430 primers. Principle component explained 84.40% of variation. The clustering pattern the genotypes were grouped into 3 clusters based on their response to salinity and morpho-physiological characters. Cluster an...
Assessment of genetic diversity in a set of rice (Oryza sativa L.)genotypes using molecular markers
Journal of Cereal Research, 2020
The assessment of genetic diversity in the germplasm is an essential pre requisite for a breeding programme. In the present study genetic diversity was analysed in a set of 94 genotypes evaluated for various yield attributes under high temperature stress using 48 SSR primers. A total of 129 alleles were detected by 48 primers among 94 rice genotypes with an average of 2.7 alleles per primer. The number of alleles generated by each marker varied from 1 to 4. The Polymorphism Information Content values ranged from 0.19 to 0.60 with an average of 0.41. Twenty six SSR primers revealed PIC values higher than the average. The genetic dissimilarity index ranged from 0.04 to 0.92. The dendrogram generated using DAR with indicated that the 94 genotypes were clustered into three distinct clusters with two sub clusters in each cluster. The selected genotypes will be useful in the ongoing breeding programme and will help in broadening the genetic base of the breeding material.
Journal of Experimental Biology and Agricultural Sciences, 2020
Current study was conducted to estimate the genetic diversity of 29 local rice cultivars including 3 checks at both morphological and molecular level during Kharif 2017 in an augmented design. Significant results obtained from ANOVA of 29 genotypes for 16 quantitative traits; Mahalanobis' D 2 grouped the total genotypes into 6 clusters. Highest inter-cluster distance was found between clusters III and VI indicating the genotypes in these clusters are most diverse. The SSR banding pattern revealed a total of 65 alleles from 21 polymorphic markers across 29 rice genotypes with an average of 3.09 alleles. The polymorphism information content (PIC) values ranged from 0.701 (RM 277) to 0.346 (RM237) with a mean value of 0.571 showing the marker RM277 as best based on the above study. The dendrogram analysis revealed all the 29 genotypes were grouped into two main clusters i.e. cluster I and cluster II with dissimilarity coefficient 0.36. Both the clusters were further divided into two groups each of which are further divide into two subgroups each. Based on the genetic distances and the dissimilarity coefficient obtained from both morphological and molecular analysis, genotypes like Bahubali, Golden 105, Pusa 1121, HUR-1301, RK-2 Lal kasturi and Pan 815 can be selected and used as parents due to their greater diversity. Knowledge of genetic diversity available within a population at both morphological and molecular level helps the breeder to formulate a successful hybridization programme and gain good results.
Wheat and Barley Research
The genetic diversity of 30 rice accessions both of basmati and non-basmati including 2 red rices collected from Rice and Wheat Research Centre, Malan was performed on the basis of 36 genome wide SSR markers with the objectives to quantify the genetic divergence and to identify the potential accessions. Molecular characterization grouped them according to their varietal affiliations into five major clusters. Majority of basmati genotypes were clustered together. SSR markers detected a total of 83 alleles ranging from 2-4. The pairwise genetic similarity values among different genotypes ranged from 0.17 to 0.92 with an average of 0.48 indicating the presence of moderate genetic diversity among the genotypes analysed. The PIC values reflected the level of diversity and allelic frequency among the varieties which varied widely among SSR loci from 0.062 to 0.664. Two SSR markers namely, RM7173 and RM101 were identified as genotype specific, for genotype HPR 2761 and Vasumati, respectively. Two advanced breeding lines of basmati HPR 2852 and HPR 2855 were clustered together with their basmati parents in dendrogram indicating maximum recovery of basmati genotypes. The polymorphism detected among the genotypes will be helpful in selecting genetically diverse parents in the future breeding programme. The information generated will be used for advanced studies in germplasm, pureline selection and rice breeding in the future breeding programme.
Assessment of Genetic Biodiversity of Some Traits Using SSR Markers in Rice (Oryza sativa L.)
Atlas journal of plant biology, 2019
Eight primers (RM 315, RM 318, RM 166, RM 302, RM 201, RM 234, RM 526 and RM 144) revealed different levels of polymorphism to tag the related traits of interest as tolerant to abiotic stress, resistant to biotic stress and yield-related traits. Two primers (RM 190 and RM 278) were monomorphic. The percentage of the polymorphism was nearly 80 %. The size of detected fragments ranged from 105-325 bp. A total of 186 bands were scored from the amplification products with the ten SSR primers. Genetic diversity analyses were conducted on the basis of the scores with 176 unique bands. Phylogenic tree for the fifteen rice accessions from each group were established according to the molecular data and based on ten SSRs. A marked genetic diversity was observed in these innovative accessions (Sakha 101, IR 03N137, IR 83142-12, IR 87856-10-AJY-1-B, HHZ 12-Y4-DT1-Y2 and IR 1552), which revealed higher levels of diversity and hence can be used as donors for the effective conservation, utilization and providing favorable genes in rice breeding programs.
2016
Genetic diversity among thirty two accessions of rice representing landraces, released varieties, cultivars and breeding lines was analysed using simple sequence repeat (SSR), inter-simple sequence repeat (ISSR) and three dwarfing trait based markers. A total of 81 polymorphic bands were detected with 20 primer combinations. The genetic similarity among the accessions ranged from (0.60) to (0.97) with a mean of 0.737. All 32 accessions were clustered into 5 major groups. Of the 32 pair wise combinations generated by rice genotypes, the lowest coefficient of similarity 0.505 was observed between Sarbati-A and Sathi, Bagni and VB24 genotypes. The highest coefficient of similarity 0.964 was obtained between VD 62 and VLD86, which appear as the most similar and closely related accessions. Results illustrated the high-level polymorphism obtained by SSR and ISSR, especially trait-linked markers used in this study. These markers will applicable in discriminating different germplasm, and ut...