Light whole genome sequence for SNP discovery across domestic cat breeds.
BACKGROUND
The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus--FeLV, feline coronavirus--FECV, feline immunodeficiency virus--FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery.


METHODS
To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly available 2X cat whole genome sequence. All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs. To reduce potential false positive SNPs due to the low coverage assembly, a low upper-limit was placed on sequence coverage and a high lower-limit on the quality of the discrepant bases at a potential variant site. In all domestic cats of different breeds: female Abyssinian, female American shorthair, male Cornish Rex, female European Burmese, female Persian, female Siamese, a male Ragdoll and a female African wildcat were sequenced lightly. We report a total of 964 k common SNPs suitable for a domestic cat SNP genotyping array and an additional 900 k SNPs detected between African wildcat and domestic cats breeds. An empirical sampling of 94 discovered SNPs were tested in the sequenced cats resulting in a SNP validation rate of 99%.


CONCLUSIONS
These data provide a large collection of mapped feline SNPs across the cat genome that will allow for the development of SNP genotyping platforms for mapping feline diseases.
Mullikin
James C
JC
Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. mullikin@mail.nih.gov
Hansen
Nancy F
NF
Shen
Lei
L
Ebling
Heather
H
Donahue
William F
WF
Tao
Wei
W
Saranga
David J
DJ
Brand
Adrianne
A
Rubenfield
Marc J
MJ
Young
Alice C
AC
Cruz
Pedro
P
Driscoll
Carlos
C
David
Victor
V
Al-Murrani
Samer W K
SW
Locniskar
Mary F
MF
Abrahamsen
Mitchell S
MS
O'Brien
Stephen J
SJ
Smith
Douglas R
DR
Brockman
Jeffrey A
JA
D000818:Animals; D002415:Cats / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D017931:DNA Primers / Q000235:genetics; D030541:Databases, Genetic; D005260:Female; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods*; D008297:Male; D016254:Mutagenesis, Insertional; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
D017931:DNA Primers