title: Identification of putative SNPs in progressive retinal atrophy affected Canis lupus familiaris using exome sequencing.
abstract: Progressive retinal atrophy (PRA) is one of the major causes of retinal photoreceptor cell degeneration in canines. The inheritance pattern of PRA is autosomal recessive and genetically heterogeneous. Here, using targeted sequencing technology, we have performed exome sequencing of 10 PRA-affected (Spitz=7, Cocker Spaniel=1, Lhasa Aphso=1 and Spitz-Labrador cross breed=1) and 6 normal (Spitz=5, Cocker Spaniel=1) dogs. The high-throughput sequencing using 454-Roche Titanium sequencer generated about 2.16 Giga bases of raw data. Initially, we have successfully identified 25,619 single nucleotide polymorphisms (SNPs) that passed the stringent SNP calling parameters. Further, we performed association study on the cohort, and the highly significant (0.001) associations were short-listed and investigated in-depth. Out of the 171 significant SNPs, 113 were previously unreported. Interestingly, six among them were non-synonymous coding (NSC) SNPs, which includes CPPED1 A>G (p.M307V), PITRM1 T>G (p.S715A), APP G>A (p.T266M), RNF213 A>G (p.V1482A), C>A (p.V1456L), and SLC46A3 G>A (p.R168Q). On the other hand, 35 out of 113 unreported SNPs were falling in regulatory regions such as 3'-UTR, 5'-UTR, etc. In-depth bioinformatics analysis revealed that majority of NSC SNPs have damaging effect and alter protein stability. This study highlighted the genetic markers associated with PRA, which will help to develop genetic assay-based screening in effective breeding.
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.|Department of Zoology, Genetic Diagnostic Centre, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
authors.forename: Bhaskar
authors.initials: B
authors.lastname: Reddy
authors.affiliation: Department of Veterinary Surgery & Radiology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Divyesh N
authors.initials: DN
authors.lastname: Kelawala
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Tejas
authors.initials: T
authors.lastname: Shah
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Anand B
authors.initials: AB
authors.lastname: Patel
authors.affiliation: Department of Veterinary Surgery & Radiology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Deepak B
authors.initials: DB
authors.lastname: Patil
authors.affiliation: Department of Veterinary Surgery & Radiology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Pinesh V
authors.initials: PV
authors.lastname: Parikh
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Namrata
authors.initials: N
authors.lastname: Patel
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Nidhi
authors.initials: N
authors.lastname: Parmar
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Amit B
authors.initials: AB
authors.lastname: Mohapatra
authors.affiliation: Datar Genetics Ltd, F-8, D Road, Ambad, Nasik, Maharashtra, 422010, India.
authors.forename: Krishna M
authors.initials: KM
authors.lastname: Singh
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Ramesh
authors.initials: R
authors.lastname: Menon
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Dipal
authors.initials: D
authors.lastname: Pandya
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Subhash J
authors.initials: SJ
authors.lastname: Jakhesara
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
authors.forename: Prakash G
authors.initials: PG
authors.lastname: Koringa
authors.affiliation: Department of Zoology, Genetic Diagnostic Centre, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
authors.forename: Mandava V
authors.initials: MV
authors.lastname: Rao
authors.affiliation: Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India. cgjoshi@aau.in.
authors.forename: Chaitanya G
authors.initials: CG
authors.lastname: Joshi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016022:Case-Control Studies; D017124:Conserved Sequence; D004283:Dog Diseases / Q000235:genetics*; D004285:Dogs; D059472:Exome; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D008297:Male; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D020125:Mutation, Missense; D020641:Polymorphism, Single Nucleotide; D012162:Retinal Degeneration / Q000235:genetics / Q000662:veterinary*; D017422:Sequence Analysis, DNA