Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): Use of random versus trait-linked microsatellite markers (original) (raw)
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Analysis of Genetic Diversity using Molecular Markers among Some Elite Rice Genotypes
Current Journal of Applied Science and Technology
Microsatellites, also known as SSRs, are one of the most commonly utilised DNA marker types for a variety of applications, including genotypic differences, genetic relationships, QTLs, association mapping, genome mapping, and varietal identification. With the goal of assessing genetic diversity analysis of different varieties to measure the extent of genotypic differences, genetic relationship, and also to broaden the germplasm base of future rice breeding programmes, 40 rice genotypes were analysed for genetic variation using 20 SSR markers in the current study. These markers were discovered to produce polymorphic bands among the population, revealing the population's variability. Several alleles were found using microsatellite markers in this study, ranging from 2 to 5, with an average of 3.75 and 0.71 of average genetic diversity. The average PIC value for the current study was 0.62, indicating that the germplasm included in the study is diversified. This study exhibited that...
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.
Genetic diversity among 35 rice accessions, which included 19 landraces, 9 cultivars and 7 wild relatives, was investigated by using microsatellite (SSR) markers distributed across the rice genome. The mean number of alleles per locus was 4.86, showing 95.2% polymorphism and an average polymorphism information content of 0.707. Cluster analysis based on microsatellite allelic diversity clearly demarcated the landraces, cultivars and wild relatives into different groups. The allelic richness computed for the clusters indicated that genetic diversity was the highest among wild relatives (0.436), followed by landraces (0.356), and the lowest for cultivars. Allelic variability among the SSR markers was high enough to categorize cultivars, landraces and wild relatives of the rice germplasm, and to catalogue the genetic variability observed for future use. The results also suggested the necessity to introgress genes from landraces and wild relatives into cultivars, for cultivar improvement.
Indian Journal of Genetics and Plant Breeding (The), 2016
Approximately 11% of the Indian rice varieties notified from 1969 to 2012 have IR-8 in their parentage. More than 30% notified varieties during this period are derived from germplasm with 'IR' in their parentage. India is one of the centers of diversity in rice and broadening of genetic base of cultivated rice can be successfully performed using indigenous germplasms. Genetic diversity among 42 Indian rice varieties (Oryza sativa L.), including landraces, aus cultivars and modern varieties of India were investigated for phenotype as well as genotype diversity. Genetic diversity analysis using genome-wide SNP panel suggested that aus cultivars, landraces and indica rice germplasm are genetically very close. The SNP panel was based on single copy genes thereby reflecting functional diversity of the germplasm set. The dendrogram based on molecular marker analysis grouped the 42 rice cultivars into 4 diverse groups. Further, population structure analysis also resulted to 4 sub populations. These sub population differentiated aus germplasm set from other accessions. Further, principal component analysis based on phenotype also suggested the closeness of aus cultivars, landraces and indica rice germplasm sets. Information generated through genetic, phenotypic and comprehensive diversity profiles in the present study can be efficiently utilized in breeding high yielding rice varieties.
2022
Background: Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. Methods and results: This study entails the agro-morphological, cooking quality and molecular characterization of 51 genotypes / advance breeding lines of rice from Kashmir Himalayas. Signi cant variability was observed for all agromorphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles per locus and an average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. Conclusion: The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing and also the analysis was useful to generate information on indica-japonica classi cation of our germplasm.
Scientific Reports, 2020
To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly simi...
AFRICAN JOURNAL OF BIOTECHNOLOGY
Rice is an emerging food and cash crop in Eastern Africa. Thousands of germplasm accessions have been introduced from major rice breeding centers, such as the International Rice Research Institute (IRRI), and Africa Rice but the genetic variability among the introduced rice germplasm is unknown. Knowledge on genetic diversity would be useful in designing measures for comprehensive breeding and conservation. To address this knowledge gap, 10 highly polymorphic rice simple sequence repeat (SSR) markers were used to characterize 99 rice genotypes to determine their diversity and place them in their different population groups. The SSR markers were multiplexed in 3 panels to increase their throughput. An average of 15.9 alleles was detected, ranging from 6 alleles detected by marker RM7 to 30 by marker RM333. The UPGMA dendogram based on Nei’s genetic distance cluster analysis, revealed 5 genetic groups among the genotypes tested. Analysis of molecular variance indicated that 97% of the...
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...