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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.

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Comparison of LD patterns and LD decay in the whole panel and subgroups. The whole genome r2 values from PLINK are first sorted considering distance, and then divided into 100 blocks of 20 kb. The r2 values in each block are averaged and plotted against the genetic distance for different subgroups.
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DSU046F4: Comparison of LD patterns and LD decay in the whole panel and subgroups. The whole genome r2 values from PLINK are first sorted considering distance, and then divided into 100 blocks of 20 kb. The r2 values in each block are averaged and plotted against the genetic distance for different subgroups.

Mentions: The LD decay rate was measured as the chromosomal distance (kb) at which the average pairwise correlation coefficient (r2) dropped to half its maximum value.36 The binned r2 values were mapped against the physical distance (kb) across the genome. Overall, the LD for SNPs at 20 kb distance from each other was 0.50 (r2), which decayed to its half value (∼0.25) at around 300 kb. However, further decay in r2 was found very slow and paralleled at 0.15 up to 2 Mb (Fig. 4). Out of total pairwise LD events, only 14% pairs showed r2 above 0.5. When LD was calculated population-wise, the maximum average (r2 < 0.70) was observed for Subpopulation I, which was maintained at r2 > 0.21 up to 2 Mb. The average LD for Subpopulation III was observed comparatively low (0.44), and decayed half to its initial value at 240 kb. The average minimum LD was also found very low (0.12) for Subpopulation III. The maximum and minimum LD for Subpopulation II were 0.50 and 0.15, respectively. PLINK was also used to calculate chromosome-wise LD between SNP pairs, which was found maximum (0.40) for chromosomes 3 and 7, and minimum (r2 < 0.23) for chromosome 11. Except chromosomes 8, 10 and 11, all other chromosomes showed LD above 0.30. On an average, 84 kb distance was observed between SNP pairs before applying MAF < 0.02, which increased to 95 kb after correcting for MAF. The average maximum distance (∼125 kb) was observed for chromosomes 8 and 12 while minimum distance (∼69 kb) was observed for chromosome 3. When LD heatmap generated through TASSEL was studied, the regions of high LD with significant P-values were found to be interspersed between the low LD regions throughout the genome.Figure 4.


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)

Comparison of LD patterns and LD decay in the whole panel and subgroups. The whole genome r2 values from PLINK are first sorted considering distance, and then divided into 100 blocks of 20 kb. The r2 values in each block are averaged and plotted against the genetic distance for different subgroups.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSU046F4: Comparison of LD patterns and LD decay in the whole panel and subgroups. The whole genome r2 values from PLINK are first sorted considering distance, and then divided into 100 blocks of 20 kb. The r2 values in each block are averaged and plotted against the genetic distance for different subgroups.
Mentions: The LD decay rate was measured as the chromosomal distance (kb) at which the average pairwise correlation coefficient (r2) dropped to half its maximum value.36 The binned r2 values were mapped against the physical distance (kb) across the genome. Overall, the LD for SNPs at 20 kb distance from each other was 0.50 (r2), which decayed to its half value (∼0.25) at around 300 kb. However, further decay in r2 was found very slow and paralleled at 0.15 up to 2 Mb (Fig. 4). Out of total pairwise LD events, only 14% pairs showed r2 above 0.5. When LD was calculated population-wise, the maximum average (r2 < 0.70) was observed for Subpopulation I, which was maintained at r2 > 0.21 up to 2 Mb. The average LD for Subpopulation III was observed comparatively low (0.44), and decayed half to its initial value at 240 kb. The average minimum LD was also found very low (0.12) for Subpopulation III. The maximum and minimum LD for Subpopulation II were 0.50 and 0.15, respectively. PLINK was also used to calculate chromosome-wise LD between SNP pairs, which was found maximum (0.40) for chromosomes 3 and 7, and minimum (r2 < 0.23) for chromosome 11. Except chromosomes 8, 10 and 11, all other chromosomes showed LD above 0.30. On an average, 84 kb distance was observed between SNP pairs before applying MAF < 0.02, which increased to 95 kb after correcting for MAF. The average maximum distance (∼125 kb) was observed for chromosomes 8 and 12 while minimum distance (∼69 kb) was observed for chromosome 3. When LD heatmap generated through TASSEL was studied, the regions of high LD with significant P-values were found to be interspersed between the low LD regions throughout the genome.Figure 4.

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