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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.


Illustration of the selective sweep signal obtained from collection 2. (a) Nucleotide diversity of the whole rice genome from chromosome 1 to chromosome 12. (b) Nucleotide diversity of chromosome 2. (c) Nucleotide diversity ratio of the major QTL region (from RM6 to RM240 on chromosome 2). π, Nucleotide diversity (number of nucleotide differences per site between two randomly chosen sequences in this population). Sliding 500kb windows were used during the calculation with a 50kb sliding step. The x-axis indicates π values. Blue, green, and red lines indicates π values of the deep-rooting group, shallow-rooting group, and complete group, respectively. A clear selective sweep region is indicated by the black arrow. In (c), π ratio=πshallow/πdeep.
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Figure 4: Illustration of the selective sweep signal obtained from collection 2. (a) Nucleotide diversity of the whole rice genome from chromosome 1 to chromosome 12. (b) Nucleotide diversity of chromosome 2. (c) Nucleotide diversity ratio of the major QTL region (from RM6 to RM240 on chromosome 2). π, Nucleotide diversity (number of nucleotide differences per site between two randomly chosen sequences in this population). Sliding 500kb windows were used during the calculation with a 50kb sliding step. The x-axis indicates π values. Blue, green, and red lines indicates π values of the deep-rooting group, shallow-rooting group, and complete group, respectively. A clear selective sweep region is indicated by the black arrow. In (c), π ratio=πshallow/πdeep.

Mentions: Selective sweep is a powerful method to find strong selective zones in evolution and to identify important agronomic genes (Lyu et al., 2013). The whole-genome nucleotide diversity of collection 2 and the two extreme RDR groups (shallow-rooting and deep-rooting groups) was calculated using a 500kb sliding window and 50kb sliding step (Fig. 4). Each group consisted of 29 rice varieties with the highest or lowest RDR values from collection 2 (Supplementary Table S3, available at JXB online). The average RDR values of the highest and lowest groups were 44.2 and 14.1%, respectively. About 75% of the varieties from the deep-rooting group belonged to the japonica subspecies, while 75% of the varieties from the shallow-rooting group belonged to the indica subspecies. For the shallow-rooting and the whole collection, the π value (nucleotide diversity=number of nucleotide differences per site between two randomly chosen sequences in this population) distributions were very similar. However, the deep-rooting group had lower nucleotide diversity than the shallow-rooting and complete groups, especially in some regions of chromosomes 1 and 2. Fig. 4b presents the π values for chromosome 2, and there was an obvious selective sweep on its long arm, as indicated by the black arrow. The average π value of the deep-rooting group was 0.000448 in this selective sweep region, while the average π values in the shallow-rooting group and the whole collection were 0.000732 and 0.000685, respectively. Interestingly, the major QTL qRDR-2 flanked by RM6 and RM240 was located within this selective sweep region. Fig. 4c shows the signal for the πratio (=πshallow/πdeep) for this QTL region, and all values were greater than 1.2, with the mean of the πratio for this region being 1.6.


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)

Illustration of the selective sweep signal obtained from collection 2. (a) Nucleotide diversity of the whole rice genome from chromosome 1 to chromosome 12. (b) Nucleotide diversity of chromosome 2. (c) Nucleotide diversity ratio of the major QTL region (from RM6 to RM240 on chromosome 2). π, Nucleotide diversity (number of nucleotide differences per site between two randomly chosen sequences in this population). Sliding 500kb windows were used during the calculation with a 50kb sliding step. The x-axis indicates π values. Blue, green, and red lines indicates π values of the deep-rooting group, shallow-rooting group, and complete group, respectively. A clear selective sweep region is indicated by the black arrow. In (c), π ratio=πshallow/πdeep.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Illustration of the selective sweep signal obtained from collection 2. (a) Nucleotide diversity of the whole rice genome from chromosome 1 to chromosome 12. (b) Nucleotide diversity of chromosome 2. (c) Nucleotide diversity ratio of the major QTL region (from RM6 to RM240 on chromosome 2). π, Nucleotide diversity (number of nucleotide differences per site between two randomly chosen sequences in this population). Sliding 500kb windows were used during the calculation with a 50kb sliding step. The x-axis indicates π values. Blue, green, and red lines indicates π values of the deep-rooting group, shallow-rooting group, and complete group, respectively. A clear selective sweep region is indicated by the black arrow. In (c), π ratio=πshallow/πdeep.
Mentions: Selective sweep is a powerful method to find strong selective zones in evolution and to identify important agronomic genes (Lyu et al., 2013). The whole-genome nucleotide diversity of collection 2 and the two extreme RDR groups (shallow-rooting and deep-rooting groups) was calculated using a 500kb sliding window and 50kb sliding step (Fig. 4). Each group consisted of 29 rice varieties with the highest or lowest RDR values from collection 2 (Supplementary Table S3, available at JXB online). The average RDR values of the highest and lowest groups were 44.2 and 14.1%, respectively. About 75% of the varieties from the deep-rooting group belonged to the japonica subspecies, while 75% of the varieties from the shallow-rooting group belonged to the indica subspecies. For the shallow-rooting and the whole collection, the π value (nucleotide diversity=number of nucleotide differences per site between two randomly chosen sequences in this population) distributions were very similar. However, the deep-rooting group had lower nucleotide diversity than the shallow-rooting and complete groups, especially in some regions of chromosomes 1 and 2. Fig. 4b presents the π values for chromosome 2, and there was an obvious selective sweep on its long arm, as indicated by the black arrow. The average π value of the deep-rooting group was 0.000448 in this selective sweep region, while the average π values in the shallow-rooting group and the whole collection were 0.000732 and 0.000685, respectively. Interestingly, the major QTL qRDR-2 flanked by RM6 and RM240 was located within this selective sweep region. Fig. 4c shows the signal for the πratio (=πshallow/πdeep) for this QTL region, and all values were greater than 1.2, with the mean of the πratio for this region being 1.6.

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.