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A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda.

Westbrook JW, Chhatre VE, Wu LS, Chamala S, Neves LG, Muñoz P, Martínez-García PJ, Neale DB, Kirst M, Mockaitis K, Nelson CD, Peter GF, Davis JM, Echt CS - G3 (Bethesda) (2015)

Bottom Line: The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations.The average squared correlations, r(2), between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r(2) did not decay substantially with genetic distance.The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii.

View Article: PubMed Central - PubMed

Affiliation: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410.

No MeSH data available.


Related in: MedlinePlus

Linkage disequilibrium between SNPs on different linkage groups in the ADEPT2 (unrelated association) and CCLONES (multiple-family pedigree) populations of P. taeda. Distributions of r2 were plotted for SNP pairs on different LGs with r2 > 0.1. The distributions were compared (A) before and (B) after adjusting r2 values for subpopulation structure in ADEPT2 and kinship in CCLONES.
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fig7: Linkage disequilibrium between SNPs on different linkage groups in the ADEPT2 (unrelated association) and CCLONES (multiple-family pedigree) populations of P. taeda. Distributions of r2 were plotted for SNP pairs on different LGs with r2 > 0.1. The distributions were compared (A) before and (B) after adjusting r2 values for subpopulation structure in ADEPT2 and kinship in CCLONES.

Mentions: Adjusting r2 for structure in ADEPT2 or kinship in CCLONES reduced number of locus pairs with r2 > 0.1 in both populations (Table 3). Larger reductions in the extent of LD within LGs (Figure 6) and the percentages of SNPs in LD between LGs (Figure 7) were observed after adjusting for kinship in CCLONES as compared to adjusting for structure in ADEPT2. Some cases of extended LD within LGs may have been attributable to error in the estimation of marker positions or spurious effects due to low minor allele frequency (Plomion et al. 2014). Considering only pairs of SNPs where both loci were separated by more than 5 cM within a single input map, and considering that both SNPs had MAF >0.1, 135 SNP pairs in CCLONES and seven SNP pairs in ADEPT2 had adjusted r2 > 0.1. No SNP pairs on different LGs had adjusted r2 > 0.1 in ADEPT2, and 558 SNP pairs had adjusted r2 > 0.1 in CCLONES (MAF >0.1) (Table 3). To test for possible epistatic LD between SNPs on different LGs in CCLONES, the distribution of adjusted r2 values from 135 SNP pairs with strong evidence for extended LD within LGs was used to estimate a critical value of r2 > 0.82 that exceeded the Bonferroni significance threshold (α = 0.05/558 tests). No locus pairs on different LGs had adjusted r2 that exceeded the 0.82 significance threshold in CCLONES (Figure 7).


A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda.

Westbrook JW, Chhatre VE, Wu LS, Chamala S, Neves LG, Muñoz P, Martínez-García PJ, Neale DB, Kirst M, Mockaitis K, Nelson CD, Peter GF, Davis JM, Echt CS - G3 (Bethesda) (2015)

Linkage disequilibrium between SNPs on different linkage groups in the ADEPT2 (unrelated association) and CCLONES (multiple-family pedigree) populations of P. taeda. Distributions of r2 were plotted for SNP pairs on different LGs with r2 > 0.1. The distributions were compared (A) before and (B) after adjusting r2 values for subpopulation structure in ADEPT2 and kinship in CCLONES.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528325&req=5

fig7: Linkage disequilibrium between SNPs on different linkage groups in the ADEPT2 (unrelated association) and CCLONES (multiple-family pedigree) populations of P. taeda. Distributions of r2 were plotted for SNP pairs on different LGs with r2 > 0.1. The distributions were compared (A) before and (B) after adjusting r2 values for subpopulation structure in ADEPT2 and kinship in CCLONES.
Mentions: Adjusting r2 for structure in ADEPT2 or kinship in CCLONES reduced number of locus pairs with r2 > 0.1 in both populations (Table 3). Larger reductions in the extent of LD within LGs (Figure 6) and the percentages of SNPs in LD between LGs (Figure 7) were observed after adjusting for kinship in CCLONES as compared to adjusting for structure in ADEPT2. Some cases of extended LD within LGs may have been attributable to error in the estimation of marker positions or spurious effects due to low minor allele frequency (Plomion et al. 2014). Considering only pairs of SNPs where both loci were separated by more than 5 cM within a single input map, and considering that both SNPs had MAF >0.1, 135 SNP pairs in CCLONES and seven SNP pairs in ADEPT2 had adjusted r2 > 0.1. No SNP pairs on different LGs had adjusted r2 > 0.1 in ADEPT2, and 558 SNP pairs had adjusted r2 > 0.1 in CCLONES (MAF >0.1) (Table 3). To test for possible epistatic LD between SNPs on different LGs in CCLONES, the distribution of adjusted r2 values from 135 SNP pairs with strong evidence for extended LD within LGs was used to estimate a critical value of r2 > 0.82 that exceeded the Bonferroni significance threshold (α = 0.05/558 tests). No locus pairs on different LGs had adjusted r2 that exceeded the 0.82 significance threshold in CCLONES (Figure 7).

Bottom Line: The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations.The average squared correlations, r(2), between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r(2) did not decay substantially with genetic distance.The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii.

View Article: PubMed Central - PubMed

Affiliation: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410.

No MeSH data available.


Related in: MedlinePlus