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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: 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)).Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume.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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Phenotypic variations among the possible genotype combinations for lignin under multi-SNP additive models. (A) These eight allelic variants have significant additive effect with a small proportion of phenotypic variation (R2), ranging from 0.80 to 5.48%. Pairwise LD plots among multiple loci within each candidate genes were estimated using TASSEL Ver. 2.0.1(http://www.maizegenetics.net/). Genotype effect and the position/haplotype block of each allelic variant were shown for lignin content. (B) Twenty possible common combinations with a frequency ≥5% from the eight allelic variants were identified with various phenotypic variations on lignin content in the association population of Populus tomentosa. Some combinations were discarded, because the sample size was <10 individuals.
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DSU040F5: Phenotypic variations among the possible genotype combinations for lignin under multi-SNP additive models. (A) These eight allelic variants have significant additive effect with a small proportion of phenotypic variation (R2), ranging from 0.80 to 5.48%. Pairwise LD plots among multiple loci within each candidate genes were estimated using TASSEL Ver. 2.0.1(http://www.maizegenetics.net/). Genotype effect and the position/haplotype block of each allelic variant were shown for lignin content. (B) Twenty possible common combinations with a frequency ≥5% from the eight allelic variants were identified with various phenotypic variations on lignin content in the association population of Populus tomentosa. Some combinations were discarded, because the sample size was <10 individuals.

Mentions: On the basis of these additive SNPs simultaneously associated to each trait (Supplementary Table S6), we identified phenotypic variation among possible genotype combinations for the same trait and some genotype combinations that may be useful for selection breeding. An example of multi-genotype combinations for lignin is shown in Fig. 5. Eight SNPs from six different genes were significantly associated with lignin content, with two associated SNPs from PtoGH9A1 showing low LD and hence representing independent associations.Figure 5.


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)

Phenotypic variations among the possible genotype combinations for lignin under multi-SNP additive models. (A) These eight allelic variants have significant additive effect with a small proportion of phenotypic variation (R2), ranging from 0.80 to 5.48%. Pairwise LD plots among multiple loci within each candidate genes were estimated using TASSEL Ver. 2.0.1(http://www.maizegenetics.net/). Genotype effect and the position/haplotype block of each allelic variant were shown for lignin content. (B) Twenty possible common combinations with a frequency ≥5% from the eight allelic variants were identified with various phenotypic variations on lignin content in the association population of Populus tomentosa. Some combinations were discarded, because the sample size was <10 individuals.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSU040F5: Phenotypic variations among the possible genotype combinations for lignin under multi-SNP additive models. (A) These eight allelic variants have significant additive effect with a small proportion of phenotypic variation (R2), ranging from 0.80 to 5.48%. Pairwise LD plots among multiple loci within each candidate genes were estimated using TASSEL Ver. 2.0.1(http://www.maizegenetics.net/). Genotype effect and the position/haplotype block of each allelic variant were shown for lignin content. (B) Twenty possible common combinations with a frequency ≥5% from the eight allelic variants were identified with various phenotypic variations on lignin content in the association population of Populus tomentosa. Some combinations were discarded, because the sample size was <10 individuals.
Mentions: On the basis of these additive SNPs simultaneously associated to each trait (Supplementary Table S6), we identified phenotypic variation among possible genotype combinations for the same trait and some genotype combinations that may be useful for selection breeding. An example of multi-genotype combinations for lignin is shown in Fig. 5. Eight SNPs from six different genes were significantly associated with lignin content, with two associated SNPs from PtoGH9A1 showing low LD and hence representing independent associations.Figure 5.

Bottom Line: 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)).Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume.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