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Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†.

Du Q, Tian J, Yang X, Pan W, Xu B, Li B, Ingvarsson PK, Zhang D - DNA Res. (2014)

Bottom Line: The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined.We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)).Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China.

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Decay pattern of LD in all Populus tomentosa samples and each climatic region. Decay of LD for all common SNP (minor allele frequency ≥ 5%) sites pooled across all analysed genes. Pairwise correlations between SNPs are plotted against the physical distance between the SNPs in base pairs. The curves describe the non-linear regressions of r2 (Er2) onto the physical distance in base pairs. The details of three climatic regions are shown in Supplementary Table S1.
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DSU040F2: Decay pattern of LD in all Populus tomentosa samples and each climatic region. Decay of LD for all common SNP (minor allele frequency ≥ 5%) sites pooled across all analysed genes. Pairwise correlations between SNPs are plotted against the physical distance between the SNPs in base pairs. The curves describe the non-linear regressions of r2 (Er2) onto the physical distance in base pairs. The details of three climatic regions are shown in Supplementary Table S1.

Mentions: Estimates of r2 values for all pairwise combinations of SNPs were pooled to assess the overall pattern of LD with physical distance (Fig. 2). The non-linear regression shows a clear and rapid decline of LD from 0.60 to 0.10 at a distance of ∼1,100 bp in the whole population (Fig. 2). Nevertheless, LD analyses within each geographical climatic region showed a much higher level of LD with the r2 values declining to 0.1 within c. 2,300 bp (Southern and Northeastern regions) and c. 3,400 bp (Northwestern region) (Fig. 2). We found a clear and rapid decline of LD with distance within each gene in the whole population, respectively (r2 ≥ 0.1, within c. 500–1,800 bp, Supplementary Fig. S2), indicating that LD does not extend over entire gene in the species.Figure 2.


Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†.

Du Q, Tian J, Yang X, Pan W, Xu B, Li B, Ingvarsson PK, Zhang D - DNA Res. (2014)

Decay pattern of LD in all Populus tomentosa samples and each climatic region. Decay of LD for all common SNP (minor allele frequency ≥ 5%) sites pooled across all analysed genes. Pairwise correlations between SNPs are plotted against the physical distance between the SNPs in base pairs. The curves describe the non-linear regressions of r2 (Er2) onto the physical distance in base pairs. The details of three climatic regions are shown in Supplementary Table S1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379978&req=5

DSU040F2: Decay pattern of LD in all Populus tomentosa samples and each climatic region. Decay of LD for all common SNP (minor allele frequency ≥ 5%) sites pooled across all analysed genes. Pairwise correlations between SNPs are plotted against the physical distance between the SNPs in base pairs. The curves describe the non-linear regressions of r2 (Er2) onto the physical distance in base pairs. The details of three climatic regions are shown in Supplementary Table S1.
Mentions: Estimates of r2 values for all pairwise combinations of SNPs were pooled to assess the overall pattern of LD with physical distance (Fig. 2). The non-linear regression shows a clear and rapid decline of LD from 0.60 to 0.10 at a distance of ∼1,100 bp in the whole population (Fig. 2). Nevertheless, LD analyses within each geographical climatic region showed a much higher level of LD with the r2 values declining to 0.1 within c. 2,300 bp (Southern and Northeastern regions) and c. 3,400 bp (Northwestern region) (Fig. 2). We found a clear and rapid decline of LD with distance within each gene in the whole population, respectively (r2 ≥ 0.1, within c. 500–1,800 bp, Supplementary Fig. S2), indicating that LD does not extend over entire gene in the species.Figure 2.

Bottom Line: The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined.We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)).Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China.

Show MeSH
Related in: MedlinePlus