Population Structure and Marker-Trait Association in Indigenous Aromatic Rice

Talukdar, P.; Rathi, S. S.; Pathak, Khanin; Chetia, S. K.; Sarma, R. N.

doi:10.1016/j.rsci.2016.08.009

Cited by 28 publications

(18 citation statements)

References 38 publications

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“…al. [6], which has been validated by the present investigation. In this study the additive effect for the major QTL showed that the aroma was contributed from the parent Kola Joha.…”

Section: Qtl Mappingsupporting

confidence: 81%

“…The QTL on chromosome 6 has been identified between at 77.4 cM explains minor variation of 0.7%, since there is a major gap in between the RM541 and RM340. Through Association mapping in Joha rice of Assam, Talukdar et al [6] identified eight QTLs to be associated with the time of heading on chromosomes 3, 5, 7, 8, 10 and 12, and among which the QTL linked to chromosome 3 explained the highest variation. Using F 2 and BIL populations of cross Nipponbare/Kasalath (NK), eight QTLs for heading date, Hd1-Hd5, Hd7, Hd8 and Hd11, were detected [56].…”

Section: Qtl Mappingmentioning

confidence: 99%

“…Fine mapping and sequence analysis identified a betaine aldehyde dehydrogenase gene (BADH2) associated with the fragrant phenotype [5]. Though Talukdar et al [6] reported the presence of similar gene for aroma in Joha rice based on association study using SSR markers, this results need confirmation to facilitate the breeders to deploy markers linked to aroma in a Joha rice improvement programme. There is complicacy in formulating the breeding programme for genetic manipulation of aroma in Joha rice due to limited knowledge in genetics of aroma and difficulty in objective assessment of aroma during selection programme.…”

Section: Introductionmentioning

confidence: 97%

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QTL Analysis in Aromatic Rice of Assam, India

Sarma¹,

Talukdar²,

Rathi³

et al. 2017

J Rice Res

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The study was carried out to identify quantitative trait loci (QTLs) controlling 12 morphological traits in rice using a F 2 derived from Ranjit and Kola Joha cross. A framework linkage map of 1387.9cM was developed using 102 SSR markers and other few markers linked to aroma. QTL analysis based on composite interval mapping identified 24 QTLs was for 12 traits. Among them two QTLs were identified for grain aroma each on chromosome 5 and chromosome 8, out of which the QTLs between Aro1-BAD2 is in similar position with aroma gene of Basmati rice. Most of the QTLs identified in the current study, showed a range of partial to over-dominance effects, indicating complexity of the traits under consideration. Some genomic regions were associated with more than one trait, indicating linkage and/or pleiotropic effects. Marker linked to the QTLs can be considered for use in marker assisted breeding as being confirmatory to other reports.

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“…al. [6], which has been validated by the present investigation. In this study the additive effect for the major QTL showed that the aroma was contributed from the parent Kola Joha.…”

Section: Qtl Mappingsupporting

confidence: 81%

Section: Qtl Mappingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

See 1 more Smart Citation

QTL Analysis in Aromatic Rice of Assam, India

Sarma¹,

Talukdar²,

Rathi³

et al. 2017

J Rice Res

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“…In this study, genetic diversity among the tested germplasm was also evaluated by a model-based structure using the SSR genotypic data. The genetic architecture of diverse germplasm can be estimated by determining the STRUCTURE of the population using molecular markers such as, but not limited to, SSRs or SNPs 16 , 21 , 30 , 40 , 59 , 60 . In STRUCTURE, LnP(D) denotes the highest optimal number of subsets (K) 61 – 63 for an optimal number of divisions 64 .…”

Section: Discussionmentioning

confidence: 99%

Variability Assessment of Aromatic Rice Germplasm by Pheno-Genomic traits and Population Structure Analysis

Islam

Khalequzzaman

Bashar³

et al. 2018

Sci Rep

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While the pleasant scent of aromatic rice is making it more popular, with demand for aromatic rice expected to rise in future, varieties of this have low yield potential. Genetic diversity and population structure of aromatic germplasm provide valuable information for yield improvement which has potential market value and farm profit. Here, we show diversity and population structure of 113 rice germplasm based on phenotypic and genotypic traits. Phenotypic traits showed that considerable variation existed across the germplasm. Based on Shannon–Weaver index, the most variable phenotypic trait was lemma-palea color. Detecting 140 alleles, 11 were unique and suitable as a germplasm diagnostic tool. Phylogenetic cluster analysis using genotypic traits classified germplasm into three major groups. Moreover, model-based population structure analysis divided all germplasm into three groups, confirmed by principal component and neighbors joining tree analyses. An analysis of molecular variance (AMOVA) and pairwise FST test showed significant differentiation among all population pairs, ranging from 0.023 to 0.068, suggesting that all three groups differed. Significant correlation coefficient was detected between phenotypic and genotypic traits which could be valuable to select further improvement of germplasm. Findings from this study have the potential for future use in aromatic rice molecular breeding programs.

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“…Among various molecular markers, SSR markers are simple, easy scoring ability, reliability, codominant and multi-allelic nature. These markers have become important tools for characterization of genotypes, marker-assisted selection breeding, genetic diversity and population structure analysis in several rice genetic studies (Thomson et al 2007;Das et al 2013;Singh et al 2013;Travis et al 2015;Ahmed et al 2016;Talukdar et al 2017;Islam et al 2018a,b). If the parental lines of hybrid rice are selected on the basis of diversity, highly diverse parents can be found that will help in developing heterotic hybrid combinations.…”

Section: Cereal Research Communications 47 2019mentioning

confidence: 99%

Morpho-molecular Divergence of Restorer Lines for Hybrid Rice (Oryza sativa L.) Development

Islam

Siddique

Akter

et al. 2019

Cereal Research Communications

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Genetic diversity of 28 restorer lines of rice was studied under irrigated condition through Mahalanobis D 2 statistics and simple sequence repeat (SSR) banding patterns. The cluster analysis grouped the lines into five clusters. The principal component analysis showed that the first four components with vector values > 1 contributed 76.32% of the total variations. The intra-and inter-cluster distances were the maximum in cluster V (0.86) and between clusters II and V (15.14), respectively. Flag leaf area, plant height, panicle length, five panicle weight, primary branches per panicle and secondary branches per panicle had maximum contribution towards genetic divergence. A total of 24 alleles varied from 2 to 5 with an average of 2.67 alleles per locus were detected for the nine microsatellite markers across 28 lines. The polymorphism information content (PIC) values ranged from 0.12 to 0.71 with an average of 0.29. RM229 was considered as the best markers on the basis of the highest PIC value. Phylogenetic cluster analysis of the SSR data based on distance divided all lines into three groups (A, B and C), whereas the cluster analysis divided these lines into five groups (I, II, III, IV and V). Besides, evaluation of yield contributing traits demonstrated that the restorer lines under the current study possessed a considerable genetic diversity. Potential lines such as BU1IR, China2R, China1R, BHD3R, IR509R and Heera5R can be used as pollen parent in developing new commercial hybrid varieties. Therefore, potential restorer lines need to be conserved in Genebank for future hybrid rice breeding programs.

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Population Structure and Marker-Trait Association in Indigenous Aromatic Rice

Cited by 28 publications

References 38 publications

QTL Analysis in Aromatic Rice of Assam, India

QTL Analysis in Aromatic Rice of Assam, India

Variability Assessment of Aromatic Rice Germplasm by Pheno-Genomic traits and Population Structure Analysis

Morpho-molecular Divergence of Restorer Lines for Hybrid Rice (Oryza sativa L.) Development

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