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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

Comparisons of orders of shared markers between input maps and the MergeMap consensus genetic map of Pinus taeda and Pinus elliottii. Linkage group (LG) lengths were standardized to 100 units for comparison among maps.
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fig1: Comparisons of orders of shared markers between input maps and the MergeMap consensus genetic map of Pinus taeda and Pinus elliottii. Linkage group (LG) lengths were standardized to 100 units for comparison among maps.

Mentions: Strong colinearity was observed between the MergeMap consensus and the four input maps (Figure 1). The consensus map positioned 3353 SNPs discovered within ESTs, 175 restriction fragment length polymorphisms (RFLPs), 126 noncoding simple sequence repeats (SSRs), 114 expressed sequence tag polymorphisms (ESTPs), 71 SSRs within ESTs, and 17 presence/absence variants (PAVs) of ESTs (File S7). Of the 3856 markers mapped, 3639 (94%) aligned to P. taeda transcript assemblies with an average sequence identity of 98.8%. Predicted functions for 3082 mapped ESTs were obtained through alignment of the translated transcripts to 2385 unique Arabidopsis protein sequences in the TAIR10 database and to 1419 unique conserved domains in the NCBI CDD database. A total of 3762 mapped markers aligned to 3305 P. taeda version 1.01 genomic scaffolds (Neale et al. 2014; Zimin et al. 2014) with 99.0% average nucleotide sequence identity. Of the 357 genomic scaffolds that aligned with more than one marker, 168 scaffolds aligned with markers on different LGs and 189 scaffolds aligned with markers from the same LG. Most scaffolds were too short to span multiple markers precluding unbiased estimation of physical to genetic distance.


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)

Comparisons of orders of shared markers between input maps and the MergeMap consensus genetic map of Pinus taeda and Pinus elliottii. Linkage group (LG) lengths were standardized to 100 units for comparison among maps.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig1: Comparisons of orders of shared markers between input maps and the MergeMap consensus genetic map of Pinus taeda and Pinus elliottii. Linkage group (LG) lengths were standardized to 100 units for comparison among maps.
Mentions: Strong colinearity was observed between the MergeMap consensus and the four input maps (Figure 1). The consensus map positioned 3353 SNPs discovered within ESTs, 175 restriction fragment length polymorphisms (RFLPs), 126 noncoding simple sequence repeats (SSRs), 114 expressed sequence tag polymorphisms (ESTPs), 71 SSRs within ESTs, and 17 presence/absence variants (PAVs) of ESTs (File S7). Of the 3856 markers mapped, 3639 (94%) aligned to P. taeda transcript assemblies with an average sequence identity of 98.8%. Predicted functions for 3082 mapped ESTs were obtained through alignment of the translated transcripts to 2385 unique Arabidopsis protein sequences in the TAIR10 database and to 1419 unique conserved domains in the NCBI CDD database. A total of 3762 mapped markers aligned to 3305 P. taeda version 1.01 genomic scaffolds (Neale et al. 2014; Zimin et al. 2014) with 99.0% average nucleotide sequence identity. Of the 357 genomic scaffolds that aligned with more than one marker, 168 scaffolds aligned with markers on different LGs and 189 scaffolds aligned with markers from the same LG. Most scaffolds were too short to span multiple markers precluding unbiased estimation of physical to genetic distance.

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