SSR Marker-based Genetic Diversity Analysis of Tidal and Flood Prone Areas in Rice (Oryza sativa L.)

Masuduzzaman, Asm; Haque, M.E.; Ahmed, MM Emam; Mohapatra, Chandan Kumar

doi:10.4172/2155-952x.1000241

Cited by 4 publications

(5 citation statements)

References 33 publications

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“…This observation corresponds to the previous observations of other rice germplasm studies [42, 43]. In another rice diversity study, 42 colored rice varieties were reported to have clustered according to their country and region of origin [25].…”

Section: Resultssupporting

confidence: 90%

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

Aljumaili

Rafii

Latif

et al. 2018

BioMed Research International

104

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Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

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Section: Resultssupporting

confidence: 90%

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

Aljumaili

Rafii

Latif

et al. 2018

BioMed Research International

104

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“…All these points to the accuracy and usefulness of the SSR markers in tracing the phylogency or pedigree of a germplasm or breeding materials. These observations, corresponds to the previous observations of other rice germplasm studies (Bonny et al, 2015 andMasuduzzaman et al, 2016). Similarly, a clustering pattern has also been reported by Pachauri et al (2013) based on allelic and morphological data along with the location in rice varieties using SSR markers.…”

Section: Fig 2 Dendrogram Showing the Genetic Dissimilarity Among The Rice Genotypessupporting

confidence: 91%

Investigation of population structure and molecular genetic diversity under coastal agro-ecosystem in rice (Oryza sativa L.)

2021

EJPB

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Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. Thirty nine simple sequence repeat (SSR) markers were selected in order to evaluate the genetic diversity in 88 genotypes. A total of 115 alleles were detected in 39 SSR polymorphic markers. The number of alleles per marker ranged from 1 to 5, with an average of 3 alleles per locus. An average polymorphism information content value of 0.5615 was recorded. It ranged from zero (RM431, RM379 and RM262) to 0.6476 (RM324), indicating significant genetic diversity among and within the rice accessions of the present study. The average observed heterozygosity was 0.1136, while the average expected genetic diversity was 0.6105. A dendrogram constructed using the Unweighted Pair Group Method with Arithmetic means (UPGMA), grouped the 88 rice genotypes into three well differentiated major clusters. The structured program without prior information provided support for the existence of three genetically distinct clusters (K=3).

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“…Eleven varieties from different haplotypes (Masuduzzaman et al, 2016), differing in tolerance (Table 4) were examined. For assaying Sub1A and Sub1C expression, 4 sets of seedlings of 11 varieties were raised in separate plastic trays, containing grinded soils.…”

Section: Plant Materials and Submergence Treatmentmentioning

confidence: 99%

“…Recent study of Masuduzzaman et al (2016) identified few more tolerant genotypes, those are distinct from 'FR13A' (non-Sub1 type of tolerant, Madabaru, Kottamali). Efforts are needed to investigate strengths of transcriptional interactions of alleles related to tolerance.…”

Section: Introductionmentioning

confidence: 99%

Variation in expression of Sub1 gene confers differential response to submergence tolerance in rice (Oryza sativa L.)

Masuduzzaman¹,

Haque²,

Shamsuddin³

et al. 2017

Aust J Crop Sci

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A cluster of three ethylene response factor (ERF) like genes at the Sub1 locus has been identified from rice variety FR13A that confers tolerance to submergence for about 14 days. Restriction digestion-based haplotype variations among 11 rice accessions were analyzed to generate polymorphisms at Sub1C and Sub1A loci. Considering different combinations of SNPs (haplotype), four haplotypes: A1C1, A1C2, A2C2 and A0C2 were detected. Further, using semi-quantitative RT-PCR-Sub1A and Sub1C transcripts in different haplotypes were interpreted in respect with stem elongation and survival for understanding mechanism of submergence tolerance. Expression variations in Sub1 genes in relation with duration of submergence, haplotype diversity and an interaction of loci were found. Differential expression of Sub1A and Sub1C affected the stem elongation and survival of different haplotypes differentially. In tolerant varieties (A1C1 haplotype, IR40931), the highest expressed gene was Sub1A; while expression of Sub1C was lower. Over-expression of Sub1A gene in tolerant varieties, suppressed the stem elongation under submergence, which improved the level of submergence tolerance. In susceptible cultivar (Fulkari), the highest-expressed gene was Sub1C, while the Sub1A was not expressed which showed higher susceptibility. In moderately tolerant varieties (Kottamali), both Sub1A and Sub1C gene transcripts were up-regulated by submergence and higher level of both Sub1A and Sub1C genes transcripts. The varieties in A2C2 haplotype showed moderate level of tolerance without the Sub1A1 allele and a distinct novel mechanism favored the expression of both the Sub1A and Sub1C alleles that confer higher tolerance under complete submergence.

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SSR Marker-based Genetic Diversity Analysis of Tidal and Flood Prone Areas in Rice (Oryza sativa L.)

Cited by 4 publications

References 33 publications

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

Investigation of population structure and molecular genetic diversity under coastal agro-ecosystem in rice (Oryza sativa L.)

Variation in expression of Sub1 gene confers differential response to submergence tolerance in rice (Oryza sativa L.)

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