Limits...
Genome-wide association mapping of salinity tolerance in rice (Oryza sativa).

Kumar V, Singh A, Mithra SV, Krishnamurthy SL, Parida SK, Jain S, Tiwari KK, Kumar P, Rao AR, Sharma SK, Khurana JP, Singh NK, Mohapatra T - DNA Res. (2015)

Bottom Line: It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS).In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7.The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

View Article: PubMed Central - PubMed

Affiliation: National Research Centre on Plant Biotechnology, New Delhi 110012, India.

Show MeSH

Related in: MedlinePlus

Population structure of current association panel which consisted mostly of the indica accessions. (A) Scree plot from GAPIT showing the selection of PCs for association study. (B) PCA plot of first two components. (C) Bayesian clustering of 220 rice accessions using STRUCTURE program.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4401324&req=5

DSU046F3: Population structure of current association panel which consisted mostly of the indica accessions. (A) Scree plot from GAPIT showing the selection of PCs for association study. (B) PCA plot of first two components. (C) Bayesian clustering of 220 rice accessions using STRUCTURE program.

Mentions: Using PCA, most of the genetic variation (66%) in the accessions was explained by first two PCs. Based on 4,191 SNPs, the first PC explained almost 52% of genetic variation, whereas PC II explained 14%. The scree plot generated through GAPIT recommended the first three components as informative, where descent changes gradually (Fig. 3A). When we plotted the first two components against each other, three subpopulations were identified. A total of 130 accessions were clustered as a single large subpopulation (I) (Fig. 3B). For inferring the most likely number of populations among 220 accessions in STRUCTURE, the transformation method51 was used, and similar to PCA, three subpopulations were identified (Fig. 3C). Forty-four per cent of the accessions (97/220) did not show any admixture, 46% accessions (101/220) showed up to 20% admixture, while the remaining 10% (22/220) were found to be highly admixed.Figure 3.


Genome-wide association mapping of salinity tolerance in rice (Oryza sativa).

Kumar V, Singh A, Mithra SV, Krishnamurthy SL, Parida SK, Jain S, Tiwari KK, Kumar P, Rao AR, Sharma SK, Khurana JP, Singh NK, Mohapatra T - DNA Res. (2015)

Population structure of current association panel which consisted mostly of the indica accessions. (A) Scree plot from GAPIT showing the selection of PCs for association study. (B) PCA plot of first two components. (C) Bayesian clustering of 220 rice accessions using STRUCTURE program.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401324&req=5

DSU046F3: Population structure of current association panel which consisted mostly of the indica accessions. (A) Scree plot from GAPIT showing the selection of PCs for association study. (B) PCA plot of first two components. (C) Bayesian clustering of 220 rice accessions using STRUCTURE program.
Mentions: Using PCA, most of the genetic variation (66%) in the accessions was explained by first two PCs. Based on 4,191 SNPs, the first PC explained almost 52% of genetic variation, whereas PC II explained 14%. The scree plot generated through GAPIT recommended the first three components as informative, where descent changes gradually (Fig. 3A). When we plotted the first two components against each other, three subpopulations were identified. A total of 130 accessions were clustered as a single large subpopulation (I) (Fig. 3B). For inferring the most likely number of populations among 220 accessions in STRUCTURE, the transformation method51 was used, and similar to PCA, three subpopulations were identified (Fig. 3C). Forty-four per cent of the accessions (97/220) did not show any admixture, 46% accessions (101/220) showed up to 20% admixture, while the remaining 10% (22/220) were found to be highly admixed.Figure 3.

Bottom Line: It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS).In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7.The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

View Article: PubMed Central - PubMed

Affiliation: National Research Centre on Plant Biotechnology, New Delhi 110012, India.

Show MeSH
Related in: MedlinePlus