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Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.

Lou Q, Chen L, Mei H, Wei H, Feng F, Wang P, Xia H, Li T, Luo L - J. Exp. Bot. (2015)

Bottom Line: Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot.Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups.The findings from this study will be beneficial to rice drought-resistance research and breeding.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China Fudan University, No. 220, Handan Road, Yangpu District, Shanghai 200433, PR China.

No MeSH data available.


Related in: MedlinePlus

Genome-wide Manhattan plot of the association loci for RDR in collection 2. Association mapping in all 237 rice samples (a), in the indica subpopulation (b), and in the japonica subpopulation (c). P values (–log10 transformed) of each test were plotted against the SNP position from whole genome. The horizontal dotted line is the significant level for identification of RDR-associated SNPs.
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Figure 3: Genome-wide Manhattan plot of the association loci for RDR in collection 2. Association mapping in all 237 rice samples (a), in the indica subpopulation (b), and in the japonica subpopulation (c). P values (–log10 transformed) of each test were plotted against the SNP position from whole genome. The horizontal dotted line is the significant level for identification of RDR-associated SNPs.

Mentions: Using the 1 019 883 SNPs and phenotyping information of 237 varieties, a GWAS analysis of the RDR in collection 2 was performed by GAPIT (MAF>5%). Figure 3 shows the association mapping results in the whole collection (Fig. 3a), in the indica subpopulation (Fig. 3b), and in the japonica subpopulation (Fig. 3c), respectively. At the end of the short arm of chromosome 1, there was a significant peak in all three groups, and the P value of this region calculated from the whole collection was significantly lower than the values calculated from the two subpopulations. In collection 2, 48 associated SNPs (P<10–5) were identified that clustered into seven regions, which were located on chromosomes 1, 3, 4, 6, and 7. In the indica subpopulation, unlike the japonica subpopulation or the whole collection, there was a peak (P=7.41E–06) on the long arm of chromosome 2, which overlapped with the major QTL qRDR-2 identified by linakge-based mapping. In total from the indica subpopulation, 28 SNPs (P<10–4) were identified, with most of them being located on chromosomes 1 and 2. Additionally, 24 SNPs (P<10–4) were found to be related to RDR from the japonica subpopulation, and all were located on the short arm of chromosome 1.


Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.

Lou Q, Chen L, Mei H, Wei H, Feng F, Wang P, Xia H, Li T, Luo L - J. Exp. Bot. (2015)

Genome-wide Manhattan plot of the association loci for RDR in collection 2. Association mapping in all 237 rice samples (a), in the indica subpopulation (b), and in the japonica subpopulation (c). P values (–log10 transformed) of each test were plotted against the SNP position from whole genome. The horizontal dotted line is the significant level for identification of RDR-associated SNPs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4507776&req=5

Figure 3: Genome-wide Manhattan plot of the association loci for RDR in collection 2. Association mapping in all 237 rice samples (a), in the indica subpopulation (b), and in the japonica subpopulation (c). P values (–log10 transformed) of each test were plotted against the SNP position from whole genome. The horizontal dotted line is the significant level for identification of RDR-associated SNPs.
Mentions: Using the 1 019 883 SNPs and phenotyping information of 237 varieties, a GWAS analysis of the RDR in collection 2 was performed by GAPIT (MAF>5%). Figure 3 shows the association mapping results in the whole collection (Fig. 3a), in the indica subpopulation (Fig. 3b), and in the japonica subpopulation (Fig. 3c), respectively. At the end of the short arm of chromosome 1, there was a significant peak in all three groups, and the P value of this region calculated from the whole collection was significantly lower than the values calculated from the two subpopulations. In collection 2, 48 associated SNPs (P<10–5) were identified that clustered into seven regions, which were located on chromosomes 1, 3, 4, 6, and 7. In the indica subpopulation, unlike the japonica subpopulation or the whole collection, there was a peak (P=7.41E–06) on the long arm of chromosome 2, which overlapped with the major QTL qRDR-2 identified by linakge-based mapping. In total from the indica subpopulation, 28 SNPs (P<10–4) were identified, with most of them being located on chromosomes 1 and 2. Additionally, 24 SNPs (P<10–4) were found to be related to RDR from the japonica subpopulation, and all were located on the short arm of chromosome 1.

Bottom Line: Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot.Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups.The findings from this study will be beneficial to rice drought-resistance research and breeding.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China Fudan University, No. 220, Handan Road, Yangpu District, Shanghai 200433, PR China.

No MeSH data available.


Related in: MedlinePlus