Genetic Diversity Analysis in Rice (<i>Oryza sativa</i> L.) Accessions using SSR Markers

Rashmi, Deep; Bisen, Prashant; Saha, Shoumik; Loitongbam, Bapsila; Singh, Sakshi; Pallavi, .; Singh, Prashant Kumar

doi:10.5958/2230-732x.2017.00057.2

Cited by 26 publications

(22 citation statements)

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“…The mean PIC value of the microsatellite markers used to assess the diversity of rice genetic resources was 0.3, which was much higher than the PIC values of microsatellite markers used in other studies (Aljumailiet al, 2018;Suviet al, 2020). Marker RM231 linked to QBph3.1 was considered as best for the tested germplasm lines with the highest PIC value (0.621) which was in agreement with Rashmi et al (2017), who reported RM231 as the most appropriate marker to discriminate among 65 rice genotypes owing to the highest PIC value of 0.588. These results indicated that the microsatellite markers selected for use in this study are very suitable and efficient for assessing the genetic diversity.…”

Section: Resultssupporting

confidence: 83%

Molecular diversity assessment of rice genotypes for brown planthopper resistance using microsatellite markers

Lakshmi

Sreedhar²,

Lakshmi³

et al. 2021

EJPB

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The brown planthopper (Nilaparvata lugens (Stål) is a major insect pest that is primarily present in Asia causing a significant impact on rice crop. Seventy-three rice genotypes were evaluated for molecular diversity based on known BPH resistance loci. A total number of 108 alleles were detected by 39 polymorphic markers with an average of 2.37 alleles per locus. The allele frequency which is useful in estimating the frequency of alleles, ranged from 0.054 to 0.9726, while the expected heterozygosity varied between 0.054 (RM494) and 0.688 (RM231) with an average of 0.431.The Polymorphic Information Content (PIC) values provided an estimation of the marker's discriminating power by ranged from 0.066 (RM496) to 0.621 (RM231) suggesting moderate level of polymorphism for the selected BPH specific SSR markers among the germplasm lines. Accounting the major allele frequency, heterozygosity and PIC content, the marker RM231 associated with QBph3.1 and regarded as the most informative one along with RM19291, RM335, RM469, RM518, RM8213, RM228, RH078 and RM589 for dissecting the molecular diversity of germplasm lines with respect to BPH resistance. Based on the marker data, the genotypes were classified into seven clusters that distinguished the lines clustering as resistant and susceptible separately. The information about the genetic diversity of these lines will be extremely useful for proper selection of parents related to BPH reaction, especially for gene mapping and for marker assisted selection.

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Section: Resultssupporting

confidence: 83%

Molecular diversity assessment of rice genotypes for brown planthopper resistance using microsatellite markers

Lakshmi

Sreedhar²,

Lakshmi³

et al. 2021

EJPB

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“…PIC is the value of a marker for distinguishing polymorphism within a population based on the number of detectable alleles and major allelic frequency. The higher the PIC value of a locus, the higher the number of alleles detected which indicates higher diversity of germplasm and thus PIC values unveil allelic frequency and the diversity among rice germplasm could be assorted from one to another SSR locus [23]. The mean PIC value (0.658) explored from the current study is higher than the reported PIC value in a previous work [24].…”

Section: Discussioncontrasting

confidence: 62%

“…Polymorphism of microsatellite markers Allelic variation among SSR markers was high enough to categorize rice landraces [23]. The number of alleles per locus (6.416), observed in the current study, was high compared with some earlier reports, which reported 2.274 [19], 5.79 [20].…”

Section: Discussioncontrasting

confidence: 57%

SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces

Vasumathy

Manickavelu

2021

Mol Biol Rep

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I. Background: As rice is the staple food for more than half of the world population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many of the traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement. II. Methods and Results: The present study disclosed high level of genetic diversity among the unexploited rice landraces cultivated by farmers of Kerala. Twelve polymorphic markers detected a total of seventy-seven alleles with an average of 6.416 alleles per locus. PIC value ranged from 0.459 to 0.809 and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with the highest value of 0.809. The current study indicated that the rice landraces were highly diverse with higher values of the effective number of alleles, PIC, and Shannon information index and utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome that are inherited together and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study. III. Conclusions:The present investigation revealed genetic diversity of rice landraces and the haplotype analysis will open the way for genome wide association studies, QTL identi cation, and marker assisted selection in the unexplored rice landraces collected from Kerala.

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“…Use of molecular markers is the chromosomal landmark through which an organism can be recognized and has gained popularity as a genetic diversity tool (Ishii et al, 2001). Evaluation of genetic diversity using DNA marker technology is non-destructive, not affected by environmental factors, requires small number of samples, and does not require large experimental setup (Rashmi et al, 2017;Kanawapee et al, 2011).…”

Section: Issn: 2319-7706 Volume 9 Number 5 (2020)mentioning

confidence: 99%

“…Rice is the life and the prince among cereals as this unique grain helps to sustain two thirds of the world's population (Bisen et al, 2019). The rice accessions are a rich reservoir of useful genes that rice breeder can harness for rice improvement programme and the genetic variability exists among rice accessions leaving a wide scope for crop improvements (Rashmi et al, 2017;Singh et al, 2015). Genetic diversity is a pre-requisite for any…”

Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Diversity in Rice Germplasm (Oryza sativa L.) using SSR Markers

Pratap¹,

Bisen²,

Loitongbam³

et al. 2020

Int.J.Curr.Microbiol.App.Sci

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Genetic Diversity Analysis in Rice (Oryza sativa L.) Accessions using SSR Markers

Cited by 26 publications

References 0 publications

Molecular diversity assessment of rice genotypes for brown planthopper resistance using microsatellite markers

Molecular diversity assessment of rice genotypes for brown planthopper resistance using microsatellite markers

SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces

Assessment of Genetic Diversity in Rice Germplasm (Oryza sativa L.) using SSR Markers

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