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A new domestic cat draft genome assembly

Li G, Hillier LW, et al. A high-resolution SNP array-based linkage map anchors a new domestic cat draft genome assembly and provides detailed patterns of recombination.  G3 (Bethesda). 2016 Jun 1;6(6):1607-16. (Winn funded study in part)

Considerable work has been put into developing increasingly detailed gene maps and sequence assemblies of the domestic cat genome. This work has provided tools for mapping and determining the heritable bases of morphological traits and genetic diseases. Some examples are mutations in functional genes that control coat morphology along with mutations that are causative for monogenic diseases such as hypertrophic cardiomyopathy (Maine Coon cats), progressive retinal atrophy in different breeds and a large number of others.

One limiting factor has been the quality of the domestic cat genome assembly and an inadequate genetic variant (mutation) database.  Geneticists have recently developed a moderate-density Illumina SNP array. This has led a transition in recent years from the mapping of feline traits from family-based linkage approaches to GWAS (genome-wide association studies) for finding simple or polygenic traits.

This paper describing a high-resolution genetic linkage map of the domestic cat genome is based on genotyping 453 domestic cats from several multi-generational pedigrees involving three separate pedigrees. This new Illumina SNP-based linkage map provides a > 20-fold increased in improvement in marker density compared to the previous linkage map and substantial improvements in contiguity.

While this work is considered a major step forward in generating a more complete reference, the future work of incorporating data from long single molecule sequencing  (Pacific BioSciences) – reference grants MT14-009 and W15-008 by Dr. William Murphy of Texas A&M – and other emerging scaffolding technologies will likely lead to further improvements in the quality and completeness of the domestic cat genome. (VT)

See also:
Menotti-Raymond M, David VA, et al. An autosomal genetic linkage map of the domestic cat, Felis silvestris catus. Genomics. 2009 Apr;93(4):305-13.