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Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish.

Li Y, Liu S, Qin Z, Waldbieser G, Wang R, Sun L, Bao L, Danzmann RG, Dunham R, Liu Z - DNA Res. (2014)

Bottom Line: In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array.After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome.The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits.

View Article: PubMed Central - PubMed

Affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA.

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Related in: MedlinePlus

Illustration of integration of the linkage map (left) with the physical map (right). The linkage group 12 (LG12) was used for the illustration. Vertical bars represent physical map contigs containing at least two SNPs mapped onto the linkage map, and the dot spots indicate physical map contigs with only one SNP.
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DSU038F6: Illustration of integration of the linkage map (left) with the physical map (right). The linkage group 12 (LG12) was used for the illustration. Vertical bars represent physical map contigs containing at least two SNPs mapped onto the linkage map, and the dot spots indicate physical map contigs with only one SNP.

Mentions: The integration of linkage map and physical map enabled the cross-validation of the quality of the physical map and the genetic map (Table 6). A total of 1,467 physical map contigs containing 2,961 BES-associated SNPs were placed onto linkage maps. With 615 physical map contigs, two or more SNP markers were mapped that allowed the determination of orientation of the physical map contigs along the chromosome. With such contigs, the quality of physical map contigs was assessed based on the mapped markers. An illustration with linkage group 12 is provided in Fig. 6. The vast majority of physical contigs were validated, but a small fraction of physical map contigs was found incorrectly assembled, or the ordering of the SNP markers onto the map was in error.Table 6.


Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish.

Li Y, Liu S, Qin Z, Waldbieser G, Wang R, Sun L, Bao L, Danzmann RG, Dunham R, Liu Z - DNA Res. (2014)

Illustration of integration of the linkage map (left) with the physical map (right). The linkage group 12 (LG12) was used for the illustration. Vertical bars represent physical map contigs containing at least two SNPs mapped onto the linkage map, and the dot spots indicate physical map contigs with only one SNP.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379976&req=5

DSU038F6: Illustration of integration of the linkage map (left) with the physical map (right). The linkage group 12 (LG12) was used for the illustration. Vertical bars represent physical map contigs containing at least two SNPs mapped onto the linkage map, and the dot spots indicate physical map contigs with only one SNP.
Mentions: The integration of linkage map and physical map enabled the cross-validation of the quality of the physical map and the genetic map (Table 6). A total of 1,467 physical map contigs containing 2,961 BES-associated SNPs were placed onto linkage maps. With 615 physical map contigs, two or more SNP markers were mapped that allowed the determination of orientation of the physical map contigs along the chromosome. With such contigs, the quality of physical map contigs was assessed based on the mapped markers. An illustration with linkage group 12 is provided in Fig. 6. The vast majority of physical contigs were validated, but a small fraction of physical map contigs was found incorrectly assembled, or the ordering of the SNP markers onto the map was in error.Table 6.

Bottom Line: In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array.After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome.The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits.

View Article: PubMed Central - PubMed

Affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA.

Show MeSH
Related in: MedlinePlus