1
|
Zorc M, Horvat T, Tanšek A, Ferme T, Dovč P. Selection Signatures Reveal Candidate Genes for the Cornish Rex Breed-Specific Phenotype. Genes (Basel) 2024; 15:368. [PMID: 38540427 PMCID: PMC10969784 DOI: 10.3390/genes15030368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 06/14/2024] Open
Abstract
Many coat color, behavioral and morphological traits are specific and fixed across cat breeds, with several variants influencing these traits being common among different breeds. In the domestic cat, rexoid mutations have been documented in several breeds. In the Cornish Rex, four bp deletion in the LPAR6 gene has been found to cause a frame shift and a premature stop codon. In addition to the rexoid coat, Cornish Rex cats also have a characteristic head, ear shape and body type. Analysis of the selection signatures in the Cornish Rex genome revealed several regions that are under selective pressure. One of these is located in CFA B4, in the region where the ALX1 gene is located. The ALX1 gene in Burmese cats disrupts the cranial morphogenesis and causes brachycephaly in the heterozygous state. In our study, we confirmed the presence of a deletion in LPAR6 in 20 Cornish Rex and in four F1 hybrids between Cornish Rex and domestic cat. However, we did not confirm the presence of the deletion in ALX1 in Cornish Rex cats. Genome-wide selection signature analysis was performed using ROH islands and integrated haplotype score (iHS) statistics based on publicly available SNP array data of 11 Cornish Rex cats. The selection signatures were detected on chromosomes A1, A3, C2, B1, B4 and D1.
Collapse
Affiliation(s)
| | | | | | | | - Peter Dovč
- University of Ljubljana, Biotechnical Faculty, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia; (M.Z.); (T.H.); (A.T.); (T.F.)
| |
Collapse
|
2
|
Abstract
Diseases affecting the hair follicle are common in domestic animals, but despite the importance of an intact skin barrier and a fully functional hair coat, knowledge about the detailed morphological features and the diversity of these complex mini-organs are often limited, although mandatory to evaluate skin biopsies with a history of alopecia. The factors that regulate the innate hair follicle formation and the postnatal hair cycle are still not completely understood in rodents, only rudimentarily known in humans, and are poorly understood in our companion animals. This review aims to summarize the current knowledge about hair follicle and hair shaft anatomy, the arrangement of hair follicles, hair follicle morphogenesis in the embryo, and the lifelong regeneration during the postnatal hair cycle in domestic animals. The role of follicular stem cells and the need for a multitude of interacting signaling events during hair follicle morphogenesis and regeneration is unquestioned. Because of the lack of state of the art methods that can be applied in rodents but are not feasible in companion animals, most of the information in this review is based on rodent studies. However, the few data from domestic animals that are available will be discussed, and it can be assumed that at least the principal molecular mechanisms are similar in rodents and other species.
Collapse
|
3
|
Khaveh N, Schachler K, Berghöfer J, Jung K, Metzger J. Altered hair root gene expression profiles highlight calcium signaling and lipid metabolism pathways to be associated with curly hair initiation and maintenance in Mangalitza pigs. Front Genet 2023; 14:1184015. [PMID: 37351343 PMCID: PMC10282778 DOI: 10.3389/fgene.2023.1184015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Hair types have been under strong targeted selection in domestic animals for their impact on skin protection, thermoregulation and exterior morphology, and subsequent economic importance. In pigs, a very special hair phenotype was observed in Mangalitza, who expresses a thick coat of curly bristles and downy hair. Two breed-specific missense variants in TRPM2 and CYP4F3 were suggested to be associated with the Mangalitza pig's hair shape due to their role in hair follicle morphogenesis reported for human and mice. However, the mechanism behind this expression of a curly hair type is still unclear and needs to be explored. In our study, hair shafts were measured and investigated for the curvature of the hair in Mangalitza and crossbreeds in comparison to straight-coated pigs. For molecular studies, hair roots underwent RNA sequencing for a differential gene expression analysis using DESeq2. The output matrix of normalized counts was then used to construct weighted gene co-expression networks. The resulting hair root gene expression profiles highlighted 454 genes to be significantly differentially expressed for initiation of curly hair phenotype in newborn Mangalitza piglets versus post-initiation in later development. Furthermore, 2,554 genes showed a significant differential gene expression in curly hair in comparison to straight hair. Neither TRPM2 nor CYP4F3 were identified as differentially expressed. Incidence of the genes in weighted co-expression networks associated with TRPM2 and CYP4F3, and prominent interactions of subsequent proteins with lipids and calcium-related pathways suggested calcium signaling and/or lipid metabolism as essential players in the induction of the curly hair as well as an ionic calcium-dependency to be a prominent factor for the maintenance of this phenotype. Subsequently, our study highlights the complex interrelations and dependencies of mutant genes TRPM2 and CYP4F3 and associated gene expression patterns, allowing the initiation of curly hair type during the development of a piglet as well as the maintenance in adult individuals.
Collapse
Affiliation(s)
- Nadia Khaveh
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Kathrin Schachler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jan Berghöfer
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Klaus Jung
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Julia Metzger
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| |
Collapse
|
4
|
Shukla H, Suryamohan K, Khan A, Mohan K, Perumal RC, Mathew OK, Menon R, Dixon MD, Muraleedharan M, Kuriakose B, Michael S, Krishnankutty SP, Zachariah A, Seshagiri S, Ramakrishnan U. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. Gigascience 2022; 12:6963323. [PMID: 36576130 PMCID: PMC9795480 DOI: 10.1093/gigascience/giac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/17/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
Collapse
Affiliation(s)
| | | | | | - Krishna Mohan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Rajadurai C Perumal
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Oommen K Mathew
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Ramesh Menon
- MedGenome Labs Ltd., Narayana Health City, Bangalore, Karnataka 560099, India
| | - Mandumpala Davis Dixon
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Megha Muraleedharan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Boney Kuriakose
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Saju Michael
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Sajesh P Krishnankutty
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Arun Zachariah
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India,Wayanad Wildlife Sanctuary, Sultan Bathery, Kerala 673592, India
| | - Somasekar Seshagiri
- Correspondence address. Somasekar Seshagiri, Department of Research and Development SciGenom Research Foundation 3rd Floor, Narayana Nethralaya Building, Narayana Health City, #258/A, Bommasandra, Hosur Road, Bangalore 560099, India. E-mail:
| | - Uma Ramakrishnan
- Correspondence address. Uma Ramakrishnan, National Centre for Biological Sciences, TIFR Bellary Road, Bangalore 560065, India. E-mail:
| |
Collapse
|
5
|
Gong G, Fan Y, Li W, Yan X, Yan X, Zhang L, Wang N, Chen O, Zhang Y, Wang R, Liu Z, Jiang W, Li J, Wang Z, Lv Q, Su R. Identification of the Key Genes Associated with Different Hair Types in the Inner Mongolia Cashmere Goat. Animals (Basel) 2022; 12:ani12111456. [PMID: 35681921 PMCID: PMC9179306 DOI: 10.3390/ani12111456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/10/2022] Open
Abstract
The Inner Mongolia cashmere goat is an excellent local breed in China. According to the characteristics of wool quilts, the Inner Mongolia cashmere goat can be divided into three types: a long-hair type (hair length of >22 cm), a short-hair type (hair length of ≤13 cm), and an intermediate type (hair length of >13 cm and ≤22 cm). It is found that hair length has a certain reference value for the indirect selection of other important economic traits of cashmere. In order to explore the molecular mechanisms and related regulatory genes of the different hair types, a weighted gene coexpression network analysis (WGCNA) was carried out on the gene expression data and phenotypic data of 12-month-old Inner Mongolia cashmere goats with a long-hair type (LHG) and a short-hair type (SHG) to explore the coexpression modules related to different coat types and nine candidate genes, and detect the relative expression of key candidate genes. The results showed that the WGCNA divided these genes into 19 coexpression modules and found that there was a strong correlation between one module and different hair types. The expression trends of this module’s genes were different in the two hair types, with high expression in the LHG and low expression in the SHG. GO functions are mainly concentrated in cellular components, including intermediate filaments (GO:0005882), intermediate filament cytoskeletons (GO:0045111), and cytoskeletal parts (GO:0044430). The KEGG pathway is mainly enriched in arginine as well as proline metabolism (chx00330) and the MAPK signaling pathway (chx04010). The candidate genes of the different hair types, including the KRT39, KRT74, LOC100861184, LOC102177231, LOC102178767, LOC102179881, LOC106503203, LOC108638293, and LOC108638298 genes, were screened. Through qRT-PCR, it was found that there were significant differences in these candidate genes between the two hair types, and most of them had a significant positive correlation with hair length. It was preliminarily inferred that these candidate genes could regulate the different hair types of cashmere goats and provide molecular markers for hair growth.
Collapse
Affiliation(s)
- Gao Gong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Yixing Fan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China;
| | - Wenze Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Xiaomin Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Ludan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Na Wang
- Inner Mongolia Yiwei White Cashmere Goat Co., Ltd., Hohhot 010018, China; (N.W.); (O.C.)
| | - Oljibilig Chen
- Inner Mongolia Yiwei White Cashmere Goat Co., Ltd., Hohhot 010018, China; (N.W.); (O.C.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Wei Jiang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China
- Correspondence: (Q.L.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China
- Correspondence: (Q.L.); (R.S.)
| |
Collapse
|
6
|
First genome-wide association study investigating blood pressure and renal traits in domestic cats. Sci Rep 2022; 12:1899. [PMID: 35115544 PMCID: PMC8813908 DOI: 10.1038/s41598-022-05494-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 12/28/2021] [Indexed: 11/08/2022] Open
Abstract
Hypertension (HTN) and chronic kidney disease (CKD) are common in ageing cats. In humans, blood pressure (BP) and renal function are complex heritable traits. We performed the first feline genome-wide association study (GWAS) of quantitative traits systolic BP and creatinine and binary outcomes HTN and CKD, testing 1022 domestic cats with a discovery, replication and meta-analysis design. No variants reached experimental significance level in the discovery stage for any phenotype. Follow up of the top 9 variants for creatinine and 5 for systolic BP, one SNP reached experimental-wide significance for association with creatinine in the combined meta-analysis (chrD1.10258177; P = 1.34 × 10–6). Exploratory genetic risk score (GRS) analyses were performed. Within the discovery sample, GRS of top SNPs from the BP and creatinine GWAS show strong association with HTN and CKD but did not validate in independent replication samples. A GRS including SNPs corresponding to human CKD genes was not significant in an independent subset of cats. Gene-set enrichment and pathway-based analysis (GSEA) was performed for both quantitative phenotypes, with 30 enriched pathways with creatinine. Our results support the utility of GWASs and GSEA for genetic discovery of complex traits in cats, with the caveat of our findings requiring validation.
Collapse
|
7
|
Alhaddad H, Abdi M, Lyons LA. Patterns of allele frequency differences among domestic cat breeds assessed by a 63K SNP array. PLoS One 2021; 16:e0247092. [PMID: 33630878 PMCID: PMC7906347 DOI: 10.1371/journal.pone.0247092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/01/2021] [Indexed: 01/11/2023] Open
Abstract
Cats are ubiquitous companion animals that have been keenly associated with humans for thousands of years and only recently have been intentionally bred for aesthetically appealing coat looks and body forms. The intense selection on single gene phenotypes and the various breeding histories of cat breeds have left different marks on the genomes. Using a previously published 63K Feline SNP array dataset of twenty-six cat breeds, this study utilized a genetic differentiation-based method (di) to empirically identify candidate regions under selection. Defined as three or more overlapping (500Kb) windows of high levels of population differentiation, we identified a total of 205 candidate regions under selection across cat breeds with an average of 6 candidate regions per breed and an average size of 1.5 Mb per candidate region. Using the combined size of candidate regions of each breed, we conservatively estimate that a minimum of ~ 0.1-0.7% of the autosomal genome is potentially under selection in cats. As positive controls and tests of our methodology, we explored the candidate regions of known breed-defining genes (e.g., FGF5 for longhaired breeds) and we were able to detect the genes within candidate regions, each in its corresponding breed. For breed specific exploration of candidate regions under selection, eleven representative candidate regions were found to encompass potential candidate genes for several phenotypes such as brachycephaly of Persian (DLX6, DLX5, DLX2), curled ears of American Curl (MCRIP2, PBX1), and body-form of Siamese and Oriental (ADGRD1), which encourages further molecular investigations. The current assessment of the candidate regions under selection is empiric and detailed analyses are needed to rigorously disentangle effects of demography and population structure from artificial selection.
Collapse
Affiliation(s)
- Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Safat, Kuwait
| | - Mona Abdi
- Department of Biological Sciences, Kuwait University, Safat, Kuwait
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, Missouri, United States of America
| |
Collapse
|
8
|
Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza. Sci Rep 2020; 10:22142. [PMID: 33335158 PMCID: PMC7747725 DOI: 10.1038/s41598-020-79037-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/02/2020] [Indexed: 12/30/2022] Open
Abstract
Selection for desirable traits and breed-specific phenotypes has left distinctive footprints in the genome of pigs. As representative of a breed with strong selective traces aiming for robustness, health and performance, the Mangalitza pig, a native curly-haired pig breed from Hungary, was investigated in this study. Whole genome sequencing and SNP chip genotyping was performed to detect runs of homozygosity (ROH) in Mangalitza and Mangalitza-crossbreeds. We identified breed specific ROH regions harboring genes associated with the development of the curly hair type and further characteristics of this breed. Further analysis of two matings of Mangalitza with straight-coated pig breeds confirmed an autosomal dominant inheritance of curly hair. Subsequent scanning of the genome for variant effects on this trait revealed two variants potentially affecting hair follicle development and differentiation. Validation in a large sample set as well as in imputed SNP data confirmed these variants to be Mangalitza-specific. Herein, we demonstrated how strong artificial selection has shaped the genome in Mangalitza pigs and left traces in the form of selection signatures. This knowledge on genomic variation promoting unique phenotypes like curly hair provides an important resource for futures studies unraveling genetic effects for special characteristics in livestock.
Collapse
|
9
|
Buckley RM, Gandolfi B, Creighton EK, Pyne CA, Bouhan DM, LeRoy ML, Senter DA, Gobble JR, Abitbol M, Lyons LA. Werewolf, There Wolf: Variants in Hairless Associated with Hypotrichia and Roaning in the Lykoi Cat Breed. Genes (Basel) 2020; 11:E682. [PMID: 32580512 PMCID: PMC7348984 DOI: 10.3390/genes11060682] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/22/2022] Open
Abstract
A variety of cat breeds have been developed via novelty selection on aesthetic, dermatological traits, such as coat colors and fur types. A recently developed breed, the lykoi (a.k.a. werewolf cat), was bred from cats with a sparse hair coat with roaning, implying full color and all white hairs. The lykoi phenotype is a form of hypotrichia, presenting as a significant reduction in the average numbers of follicles per hair follicle group as compared to domestic shorthair cats, a mild to severe perifollicular to mural lymphocytic infiltration in 77% of observed hair follicle groups, and the follicles are often miniaturized, dilated, and dysplastic. Whole genome sequencing was conducted on a single lykoi cat that was a cross between two independently ascertained lineages. Comparison to the 99 Lives dataset of 194 non-lykoi cats suggested two variants in the cat homolog for Hairless (HR) (HR lysine demethylase and nuclear receptor corepressor) as candidate causal gene variants. The lykoi cat was a compound heterozygote for two loss of function variants in HR, an exon 3 c.1255_1256dupGT (chrB1:36040783), which should produce a stop codon at amino acid 420 (p.Gln420Serfs*100) and, an exon 18 c.3389insGACA (chrB1:36051555), which should produce a stop codon at amino acid position 1130 (p.Ser1130Argfs*29). Ascertainment of 14 additional cats from founder lineages from Canada, France and different areas of the USA identified four additional loss of function HR variants likely causing the highly similar phenotypic hair coat across the diverse cats. The novel variants in HR for cat hypotrichia can now be established between minor differences in the phenotypic presentations.
Collapse
Affiliation(s)
- Reuben M. Buckley
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Erica K. Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Connor A. Pyne
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Delia M. Bouhan
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Michelle L. LeRoy
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
- Veterinary Allergy and Dermatology Clinic, LLC., Overland Park, KS 66210, USA
| | - David A. Senter
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
- Veterinary Allergy and Dermatology Clinic, LLC., Overland Park, KS 66210, USA
| | | | - Marie Abitbol
- NeuroMyoGène Institute, CNRS UMR 5310, INSERM U1217, Faculty of Medicine, Rockefeller, Claude Bernard Lyon I University, 69008 Lyon, France;
- VetAgro Sup, University of Lyon, Marcy-l’Etoile, 69280 Lyon, France
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | | |
Collapse
|
10
|
Manakhov AD, Andreeva TV, Rogaev EI. The curly coat phenotype of the Ural Rex feline breed is associated with a mutation in the lipase H gene. Anim Genet 2020; 51:584-589. [PMID: 32463158 DOI: 10.1111/age.12958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2020] [Indexed: 01/03/2023]
Abstract
Mutations in lipase H (LIPH) and lysophosphatidic acid receptor 6 (LPAR6), which are essential for the lysophosphatidic acid (LPA) signalling pathway, are associated with hypotrichosis and wooly hair in humans. Mutations in LPAR6 and keratin 71 (KRT71), result in unusual fur growth and hair structure in several cat breeds (Cornish Rex, Devon Rex and Selkirk Rex). Here, we performed target sequencing of the LIPH, LPAR6 and KRT71 genes in six cat breeds with specific hair-growth phenotypes. A LIPH genetic variant (LIPH:c.478_483del; LIPH:p.Ser160_Gly161del) was found in Ural Rex cats with curly coats from Russia, but was absent in all other cat breeds tested. In silico three-dimensional analysis of the LIPH mutant protein revealed a contraction of the α3-helix structure in the enzyme phospholipid binding site that may affect its activity.
Collapse
Affiliation(s)
- A D Manakhov
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str., 3, Moscow, 119333, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Lomonosovsky prospekt, 27-1, Moscow, 119192, Russia
| | - T V Andreeva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str., 3, Moscow, 119333, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Lomonosovsky prospekt, 27-1, Moscow, 119192, Russia
| | - E I Rogaev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str., 3, Moscow, 119333, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Lomonosovsky prospekt, 27-1, Moscow, 119192, Russia.,Department of Psychiatry, University of Massachusetts Medical School, Maple Avenue, 222, Shrewsbury, MA, 01545, USA
| |
Collapse
|
11
|
A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle. Livest Sci 2019. [DOI: 10.1016/j.livsci.2019.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Bauer A, Hadji Rasouliha S, Brunner MT, Jagannathan V, Bucher I, Bannoehr J, Varjonen K, Bond R, Bergvall K, Welle MM, Roosje P, Leeb T. A second KRT71 allele in curly coated dogs. Anim Genet 2018; 50:97-100. [PMID: 30444027 DOI: 10.1111/age.12743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2018] [Indexed: 01/20/2023]
Abstract
Major characteristics of coat variation in dogs can be explained by variants in only a few genes. Until now, only one missense variant in the KRT71 gene, p.Arg151Trp, has been reported to cause curly hair in dogs. However, this variant does not explain the curly coat in all breeds as the mutant 151 Trp allele, for example, is absent in Curly Coated Retrievers. We sequenced the genome of a Curly Coated Retriever at 22× coverage and searched for variants in the KRT71 gene. Only one protein-changing variant was present in a homozygous state in the Curly Coated Retriever and absent or present in a heterozygous state in 221 control dogs from different dog breeds. This variant, NM_001197029.1:c.1266_1273delinsACA, was an indel variant in exon 7 that caused a frameshift and an altered and probably extended C-terminus of the KRT71 protein NP_001183958.1:p.(Ser422ArgfsTer?). Using Sanger sequencing, we found that the variant was fixed in a cohort of 125 Curly Coated Retrievers and segregating in five of 14 additionally tested breeds with a curly or wavy coat. KRT71 variants cause curly hair in humans, mice, rats, cats and dogs. Specific KRT71 variants were further shown to cause alopecia. Based on this knowledge from other species and the predicted molecular consequence of the newly identified canine KRT71 variant, it is a compelling candidate causing a second curly hair allele in dogs. It might cause a slightly different coat phenotype than the previously published p.Arg151Trp variant and could potentially be associated with follicular dysplasia in dogs.
Collapse
Affiliation(s)
- A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - S Hadji Rasouliha
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - M T Brunner
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - I Bucher
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - J Bannoehr
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermatology Department, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK
| | - K Varjonen
- Department Clinical Sciences and Services, Royal Veterinary College, Hatfield, AL9 7TA, UK.,Anicura Albano Animal Hospital, Danderyd, 18236, Sweden
| | - R Bond
- Department Clinical Sciences and Services, Royal Veterinary College, Hatfield, AL9 7TA, UK
| | - K Bergvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, Uppsala, 750 07, Sweden
| | - M M Welle
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - P Roosje
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| |
Collapse
|
13
|
Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, Decker JE, Dodman NH, Ginns EI, Grahn JC, Grahn RA, Haase B, Haggstrom J, Hamilton MJ, Helps CR, Kurushima JD, Lohi H, Longeri M, Malik R, Meurs KM, Montague MJ, Mullikin JC, Murphy WJ, Nilson SM, Pedersen NC, Peterson CB, Rusbridge C, Saif R, Shelton GD, Warren WC, Wasim M, Lyons LA. Applications and efficiencies of the first cat 63K DNA array. Sci Rep 2018; 8:7024. [PMID: 29728693 PMCID: PMC5935720 DOI: 10.1038/s41598-018-25438-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/16/2018] [Indexed: 12/02/2022] Open
Abstract
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.
Collapse
Affiliation(s)
- Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Safat, Kuwait.
| | - Mona Abdi
- Department of Biological Sciences, Kuwait University, Safat, Kuwait
| | - Leslie H Bach
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,University of San Francisco, San Francisco, CA, USA
| | - Erica K Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Nicholas H Dodman
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Edward I Ginns
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennifer C Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Bianca Haase
- Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Jens Haggstrom
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michael J Hamilton
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Department of Biochemistry, University of California - Riverside, Riverside, CA, USA
| | | | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Foothill College, Los Altos Hills, CA, USA
| | - Hannes Lohi
- Department of Veterinary Biosciences, Research Programs Unit, Molecular Neurology, University of Helsinki, and The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Richard Malik
- Centre for Veterinary Education, University of Sydney, New South Wales, Australia
| | - Kathryn M Meurs
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Michael J Montague
- Department of Neuroscience, Parelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Carlyn B Peterson
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Clare Rusbridge
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Rashid Saif
- Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
| | - G Diane Shelton
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Muhammad Wasim
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA.
| |
Collapse
|
14
|
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses. Sci Rep 2018; 8:6374. [PMID: 29686323 PMCID: PMC5913262 DOI: 10.1038/s41598-018-24865-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 04/06/2018] [Indexed: 12/30/2022] Open
Abstract
Curly coat represents an extraordinary type of coat in horses, particularly seen in American Bashkir Curly Horses and Missouri Foxtrotters. In some horses with curly coat, a hypotrichosis of variable extent was observed, making the phenotype appear more complex. In our study, we aimed at investigating the genetic background of curly coat with and without hypotrichosis using high density bead chip genotype and next generation sequencing data. Genome-wide association analysis detected significant signals (p = 1.412 × 10−05–1.102 × 10−08) on horse chromosome 11 at 22–35 Mb. In this significantly associated region, six missense variants were filtered out from whole-genome sequencing data of three curly coated horses of which two variants within KRT25 and SP6 could explain all hair phenotypes. Horses heterozygous or homozygous only for KRT25 variant showed curly coat and hypotrichosis, whereas horses with SP6 variant only, exhibited curly coat without hypotrichosis. Horses with mutant alleles in both variants developed curly hair and hypotrichosis. Thus, mutant KRT25 allele is masking SP6 allele effect, indicative for epistasis of KRT25 variant over SP6 variant. In summary, genetic variants in two different genes, KRT25 and SP6, are responsible for curly hair. All horses with KRT25 variant are additionally hypotrichotic due to the KRT25 epistatic effect on SP6.
Collapse
|
15
|
Abstract
The evolution of keratins was closely linked to the evolution of epithelia and epithelial appendages such as hair. The characterization of keratins in model species and recent comparative genomics studies have led to a comprehensive scenario for the evolution of keratins including the following key events. The primordial keratin gene originated as a member of the ancient gene family encoding intermediate filament proteins. Gene duplication and changes in the exon-intron structure led to the origin of type I and type II keratins which evolved further by nucleotide sequence modifications that affected both the amino acid sequences of the encoded proteins and the gene expression patterns. The diversification of keratins facilitated the emergence of new and epithelium type-specific properties of the cytoskeleton. In a common ancestor of reptiles, birds, and mammals, a rise in the number of cysteine residues facilitated extensive disulfide bond-mediated cross-linking of keratins in claws. Subsequently, these cysteine-rich keratins were co-opted for an additional function in epidermal follicular structures that evolved into hair, one of the key events in the evolution of mammals. Further diversification of keratins occurred during the evolution of the complex multi-layered organisation of hair follicles. Thus, together with the evolution of other structural proteins, epithelial patterning mechanisms, and development programmes, the evolution of keratins underlied the evolution of the mammalian integument.
Collapse
Affiliation(s)
- Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.
| | - Florian Ehrlich
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
16
|
Morgenthaler C, Diribarne M, Capitan A, Legendre R, Saintilan R, Gilles M, Esquerré D, Juras R, Khanshour A, Schibler L, Cothran G. A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse. Genet Sel Evol 2017; 49:85. [PMID: 29141579 PMCID: PMC5686958 DOI: 10.1186/s12711-017-0359-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 11/03/2017] [Indexed: 12/30/2022] Open
Abstract
Background Curly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypotheses have been formulated to explain the diversity in phenotype, including the combination of autosomal dominant and recessive alleles. Our purpose was to map the autosomal dominant curly hair locus and identify the causal variant using genome-wide association study (GWAS) and whole-genome sequencing approaches. Results A GWAS was performed using a Bayesian sparse linear mixed model, based on 51 curly and 19 straight-haired French and North American horses from 13 paternal families genotyped on the Illumina EquineSNP50 BeadChip. A single strong signal was observed on equine chromosome 11, in a region that encompasses the type I keratin gene cluster. This region was refined by haplotype analysis to a segment including 36 genes, among which are 10 keratin genes (KRT-10, -12, -20, -23, -24, -25, -26, -27, -28, -222). To comprehensively identify candidate causal variants within all these genes, whole-genome sequences were obtained for one heterozygous curly stallion and its straight-haired son. Among the four non-synonymous candidate variants identified and validated in the curly region, only variant g.21891160G>A in the KRT25 gene (KRT25:p.R89H) was in perfect agreement with haplotype status in the whole pedigree. Genetic association was then confirmed by genotyping a larger population consisting of 353 horses. However, five discordant curly horses were observed, which carried neither the variant nor the main haplotype associated with curliness. Sequencing of KRT25 for two discordant horses did not identify any other deleterious variant, which suggests locus rather than allelic heterogeneity for the curly phenotype. Conclusions We identified the KRT25:p.R89H variant as responsible for the dominant curly trait, but a second dominant locus may also be involved in the shape of hairs within North American Curly horses. Electronic supplementary material The online version of this article (10.1186/s12711-017-0359-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Caroline Morgenthaler
- UMR1313, Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Mathieu Diribarne
- UMR1313, Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Département R&D, ALLICE, 149 rue de Bercy, 75595, Paris Cedex 12, France
| | - Aurélien Capitan
- UMR1313, Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Département R&D, ALLICE, 149 rue de Bercy, 75595, Paris Cedex 12, France
| | - Rachel Legendre
- UMR1313, Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Romain Saintilan
- UMR1313, Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Département R&D, ALLICE, 149 rue de Bercy, 75595, Paris Cedex 12, France
| | - Maïlys Gilles
- UMR1313, Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Diane Esquerré
- UMR444, Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan, 31326, France
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Anas Khanshour
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.,Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Laurent Schibler
- UMR1313, Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Département R&D, ALLICE, 149 rue de Bercy, 75595, Paris Cedex 12, France.
| | - Gus Cothran
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| |
Collapse
|
17
|
Ostrander EA, Wayne RK, Freedman AH, Davis BW. Demographic history, selection and functional diversity of the canine genome. Nat Rev Genet 2017; 18:705-720. [DOI: 10.1038/nrg.2017.67] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
18
|
A Nonsense Variant in the ST14 Gene in Akhal-Teke Horses with Naked Foal Syndrome. G3-GENES GENOMES GENETICS 2017; 7:1315-1321. [PMID: 28235824 PMCID: PMC5386879 DOI: 10.1534/g3.117.039511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses have almost no hair and show a mild ichthyosis. So far, all known NFS affected horses died between a few weeks and 3 yr of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome. Whole genome sequencing of two affected horses, two obligate carriers, and 75 control horses from other breeds revealed a single nonsynonymous genetic variant on the chromosome 7 segment that was perfectly associated with NFS. The affected horses were homozygous for ST14:c.388G>T, a nonsense variant that truncates >80% of the open reading frame of the ST14 gene (p.Glu130*). The variant leads to partial nonsense-mediated decay of the mutant transcript. Genetic variants in the ST14 gene are responsible for autosomal recessive congenital ichthyosis 11 in humans. Thus, the identified equine ST14:c.388G>T variant is an excellent candidate causative variant for NFS, and the affected horses represent a large animal model for a known human genodermatosis. Our findings will enable genetic testing to avoid the nonintentional breeding of NFS-affected foals.
Collapse
|
19
|
Finch J, Abrams S, Finch A. Analogs of human genetic skin disease in domesticated animals. Int J Womens Dermatol 2017; 3:170-175. [PMID: 28831430 PMCID: PMC5555282 DOI: 10.1016/j.ijwd.2017.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/18/2017] [Accepted: 01/18/2017] [Indexed: 01/24/2023] Open
Abstract
Genetic skin diseases encompass a vast, complex, and ever expanding field. Recognition of the features of these diseases is important to ascertain a correct diagnosis, initiate treatment, consider genetic counseling, and refer patients to specialists when the disease may impact other areas. Because genodermatoses may present with a vast array of features, it can be bewildering to memorize them. This manuscript will explain and depict some genetic skin diseases that occur in both humans and domestic animals and offer a connection and memorization aid for physicians. In addition, we will explore how animal diseases serve as a model to uncover the mechanisms of human disease. The genetic skin diseases we will review are pigmentary mosaicism, piebaldism, albinism, Griscelli syndrome, ectodermal dysplasias, Waardenburg syndrome, and mucinosis in both humans and domesticated animals.
Collapse
Affiliation(s)
- Justin Finch
- Department of Dermatology, University of Connecticut School of Medicine, Farmington, CT
| | - Stephanie Abrams
- The Ohio State University Veterinary Medical Center, Columbus, OH
| | - Amy Finch
- Department of Dermatology, University of Connecticut School of Medicine, Farmington, CT
| |
Collapse
|
20
|
Leeb T, Müller EJ, Roosje P, Welle M. Genetic testing in veterinary dermatology. Vet Dermatol 2016; 28:4-e1. [PMID: 27425028 DOI: 10.1111/vde.12309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular genetics has made significant advances in the analysis of hereditary dermatoses during the last several years. OBJECTIVES To provide an update on currently available genetic tests for skin diseases of dogs, cats and horses, and to aid the veterinary clinician in the appropriate selection and applications of genetic tests. METHODS The scientific literature on the topic was critically reviewed. The list of known causative variants for genodermatoses and hair morphology traits was compiled by searching the Online Mendelian Inheritance in Animals (OMIA) database. RESULTS Genetic testing has become an important diagnostic method in veterinary medicine. Genetic tests can help to establish the correct diagnosis in some diseases with relatively nonspecific signs. Genetic tests are also essential for sustainable breeding programmes and to help minimize the frequency of animals with hereditary diseases. Advances in genetic methodology and bioinformatics already allow genome-wide screening for potential disease causing mutations for research purposes. It is anticipated that this will become a routine process in clinical practice in the future. CONCLUSION AND CLINICAL IMPORTANCE As specific DNA tests and broad genome-wide analyses come into more common use, it is critical that clinicians understand the proper application and interpretation of these test results.
Collapse
Affiliation(s)
- Tosso Leeb
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Eliane J Müller
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland.,Department of Dermatology, Inselspital, University of Bern, Freiburgstrasse, Bern, 3010, Switzerland
| | - Petra Roosje
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, University of Bern, Länggassstrasse 128, Bern, 3001, Switzerland
| | - Monika Welle
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland
| |
Collapse
|
21
|
Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, Murphy WJ. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (BETHESDA, MD.) 2016; 6:1607-16. [PMID: 27172201 PMCID: PMC4889657 DOI: 10.1534/g3.116.028746] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/23/2016] [Indexed: 01/03/2023]
Abstract
High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location.
Collapse
Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - LaDeana W Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Robert A Grahn
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Aleksey V Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
| | - Victor A David
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702
| | | | | | - Steven Hannah
- Nestlé Purina PetCare Company, St. Louis, Missouri 63134
| | - Sher Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, West Virginia 25443 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Alex Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Stephen J O'Brien
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Pat Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Leslie A Lyons
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
22
|
A Novel Variant in CMAH Is Associated with Blood Type AB in Ragdoll Cats. PLoS One 2016; 11:e0154973. [PMID: 27171395 PMCID: PMC4865243 DOI: 10.1371/journal.pone.0154973] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/21/2016] [Indexed: 11/19/2022] Open
Abstract
The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase is associated with the production of sialic acids on cat red blood cells. The cat has one major blood group with three serotypes; the most common blood type A being dominant to type B. A third rare blood type is known as AB and has an unclear mode of inheritance. Cat blood type antigens are defined, with N-glycolylneuraminic acid being associated with type A and N-acetylneuraminic acid with type B. Blood type AB is serologically characterized by agglutination using typing reagents directed against both A and B epitopes. While a genetic characterization of blood type B has been achieved, the rare type AB serotype remains genetically uncharacterized. A genome-wide association study in Ragdoll cats (22 cases and 15 controls) detected a significant association between blood type AB and SNPs on cat chromosome B2, with the most highly associated SNP being at position 4,487,432 near the candidate gene cytidine monophospho-N-acetylneuraminic acid hydroxylase. A novel variant, c.364C>T, was identified that is highly associated with blood type AB in Ragdoll cats and, to a lesser degree, with type AB in random bred cats. The newly identified variant is probably linked with blood type AB in Ragdoll cats, and is associated with the expression of both antigens (N-glycolylneuraminic acid and N-acetylneuraminic acid) on the red blood cell membrane. Other variants, not identified by this work, are likely to be associated with blood type AB in other breeds of cat.
Collapse
|
23
|
Lyons LA, Creighton EK, Alhaddad H, Beale HC, Grahn RA, Rah H, Maggs DJ, Helps CR, Gandolfi B. Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7. BMC Genomics 2016; 17:265. [PMID: 27030474 PMCID: PMC4815086 DOI: 10.1186/s12864-016-2595-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The reduced cost and improved efficiency of whole genome sequencing (WGS) is drastically improving the development of cats as biomedical models. Persian cats are models for Leber's congenital amaurosis (LCA), the most severe and earliest onset form of visual impairment in humans. Cats with innocuous breed-defining traits, such as a bobbed tail, can also be models for somite segmentation and vertebral column development. METHODS The first WGS in cats was conducted on a trio segregating for LCA and the bobbed tail abnormality. Variants were identified using FreeBayes and effects predicted using SnpEff. Variants within a known haplotype block for cat LCA and specific candidate genes for both phenotypes were prioritized by the predicted variant effect on the proteins and concordant segregation within the trio. The efficiency of WGS of a single trio of domestic cats was evaluated. RESULTS A stop gain was identified at position c.577C > T in cat AIPL1, a predicted p.Arg193*. A c.5A > G variant causing a p.V2A was identified in HES7. The variants segregated concordantly in a Persian - Japanese bobtail pedigree. Over 1700 cats from 40 different breeds and populations were genotyped for the AIPL1 variant, defining an allelic frequency in only Persian -related breeds of 1.15%. A sub-set of cats was genotyped for the HES7 variant, supporting the variant as private to the Japanese bobtail breed. Approximately 18 million SNPs were identified for application in cat research. The cat AIPL1 variant would have been considered a high priority variant for evaluation, regardless of a priori knowledge from previous genetic studies. CONCLUSIONS This study represents the first effort of the 99 Lives Cat Genome Sequencing Initiative to identify disease--causing variants in the domestic cat using WGS. The current cat reference assembly is efficient for gene and variant identification. However, as the feline variant database improves, development of cats as biomedical models for human disease will be more efficient, providing an alternative, large animal model for drug and gene therapy trials. Undiagnosed human patients with early-onset blindness should be screened for this AIPL1 variant. The HES7 variant should further calibrate the somite segmentation clock.
Collapse
Affiliation(s)
- Leslie A. Lyons
- />Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 1600 E. Rollins Street, Columbia, MO 65211 USA
| | - Erica K. Creighton
- />Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 1600 E. Rollins Street, Columbia, MO 65211 USA
| | - Hasan Alhaddad
- />College of Science, Kuwait University, Safat, 13060 Kuwait
| | | | - Robert A. Grahn
- />Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - HyungChul Rah
- />Graduate School of Health Science Business Convergence, College of Medicine, Chungbuk National University, Chongju, Chungbuk Province 28644 South Korea
| | - David J. Maggs
- />Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Christopher R. Helps
- />Langford Veterinary Services, University of Bristol, Langford, Bristol, BS40 5DU UK
| | - Barbara Gandolfi
- />Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 1600 E. Rollins Street, Columbia, MO 65211 USA
| |
Collapse
|
24
|
Evidence of selection signatures that shape the Persian cat breed. Mamm Genome 2016; 27:144-55. [DOI: 10.1007/s00335-016-9623-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/12/2016] [Indexed: 12/22/2022]
|
25
|
Brooks A, Creighton EK, Gandolfi B, Khan R, Grahn RA, Lyons LA. SNP Miniplexes for Individual Identification of Random-Bred Domestic Cats. J Forensic Sci 2016; 61:594-606. [PMID: 27122395 PMCID: PMC5019183 DOI: 10.1111/1556-4029.13026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 03/13/2015] [Accepted: 06/06/2015] [Indexed: 11/30/2022]
Abstract
Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random‐bred domestic cats, focusing on individual and phenotypic identification. Seventy‐eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot®). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10−19 across all Western cat populations and the likelihood ratio was 1.52 × 1018. These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications.
Collapse
Affiliation(s)
- Ashley Brooks
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Erica K Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
| | - Razib Khan
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
| |
Collapse
|
26
|
Ofri R, Reilly CM, Maggs DJ, Fitzgerald PG, Shilo-Benjamini Y, Good KL, Grahn RA, Splawski DD, Lyons LA. Characterization of an Early-Onset, Autosomal Recessive, Progressive Retinal Degeneration in Bengal Cats. Invest Ophthalmol Vis Sci 2015; 56:5299-308. [PMID: 26258614 DOI: 10.1167/iovs.15-16585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE A form of retinal degeneration suspected to be hereditary was discovered in a family of Bengal cats. A breeding colony was established to characterize disease progression clinically, electrophysiologically, and morphologically, and to investigate the mode of inheritance. METHODS Affected and related cats were donated by owners for breeding trials and pedigree analysis. Kittens from test and complementation breedings underwent ophthalmic and neuro-ophthalmic examinations and ERG, and globes were evaluated using light microscopy. RESULTS Pedigree analysis, along with test and complementation breedings, indicated autosomal recessive inheritance and suggested that this disease is nonallelic to a retinal degeneration found in Persian cats. Mutation analysis confirmed the disease is not caused by CEP290 or CRX variants found predominantly in Abyssinian and Siamese cats. Ophthalmoscopic signs of retinal degeneration were noted at 9 weeks of age and became more noticeable over the next 4 months. Visual deficits were behaviorally evident by 1 year of age. Electroretinogram demonstrated reduced rod and cone function at 7 and 9 weeks of age, respectively. Rod responses were mostly extinguished at 14 weeks of age; cone responses were minimal by 26 weeks. Histologic degeneration was first observed at 8 weeks, evidenced by reduced photoreceptor numbers, then rapid deterioration of the photoreceptor layer and, subsequently, severe outer retinal degeneration. CONCLUSIONS A recessively inherited primary photoreceptor degeneration was characterized in the Bengal cat. The disease is characterized by early onset, with histologic, ophthalmoscopic, and electrophysiological signs evident by 2 months of age, and rapid progression to blindness.
Collapse
Affiliation(s)
- Ron Ofri
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Israel
| | - Christopher M Reilly
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, California, United States
| | - David J Maggs
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, United States
| | - Paul G Fitzgerald
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California-Davis, Davis, California, United States
| | - Yael Shilo-Benjamini
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Israel 3Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, United States
| | - Kathryn L Good
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, United States
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States
| | - Danielle D Splawski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States 6Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri-Columb
| |
Collapse
|
27
|
Abstract
Practical relevance: The health of the cat mirrors a complex interaction between its environment (nurture) and its genetics (nature). To date, over 70 genetic mutations (variants) have been defined in the cat; many involve diseases, structural anomalies, coat color and texture, including numerous that are clinically relevant. This trend will continue as more of the feline genome is deciphered. Genetic testing, and eventually whole-genome sequencing, should become routine diagnostic tools in feline healthcare within the foreseeable future. Global importance: Cat breeds have dispersed around the world. Thus, feline medicine clinicians should be aware of breeds common to their region and common mutations found within those regional populations. Random-bred populations of domestic cats can also have defined genetic characteristics and mutations, which are equally worthy of understanding by feline medicine clinicians. Outline: This article reviews the chronology and evolution of genetic and genomic tools pertinent to feline medicine. Possible strategies for mapping genetic traits and defects, and how these impact on feline health, are also discussed. The focus is on three historical periods: (1) research conducted before the availability of the cat genome; (2) research performed immediately after the availability of sequences of the cat genome; and (3) current research that goes beyond one cat genome and utilizes the genome sequences of many cats. Evidence base: The data presented are extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning heritable traits and/or diseases. The authors draw upon their personal experience and expertise in feline genetics.
Collapse
|
28
|
Abstract
PRACTICAL RELEVANCE The health of the cat is a complex interaction between its environment (nurture) and its genetics (nature). Over 70 genetic mutations (variants) have been defined in the cat, many involving diseases, structural abnormalities and clinically relevant health concerns. As more of the cat's genome is deciphered, less commonly will the term 'idiopathic' be used regarding the diagnosis of diseases and unique health conditions. State-of-the-art health care will include DNA profiling of the individual cat, and perhaps its tumor, to establish the best treatment approaches. Genetic testing and eventually whole genome sequencing should become routine diagnostics for feline health care. GLOBAL IMPORTANCE Cat breeds have disseminated around the world. Thus, practitioners should be aware of the breeds common to their region and the mutations found in those regional populations. Specific random-bred populations can also have defined genetic characteristics and mutations. AUDIENCE This review of 'the good, the bad and the ugly' DNA variants provides the current state of knowledge for genetic testing and genetic health management for cats. It is aimed at feline and general practitioners wanting to update and review the basics of genetics, what tests are available for cats and sources for genetic testing. The tables are intended to be used as references in the clinic. Practitioners with a high proportion of cat breeder clientele will especially benefit from the review. EVIDENCE BASE The data presented is extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning the heritable trait and/or disease. The author also draws upon personal experience and expertise in feline genetics.
Collapse
Affiliation(s)
- Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO 65201, USA
| |
Collapse
|
29
|
Genovese DW, Johnson TL, Lamb KE, Gram WD. Histological and dermatoscopic description of sphynx cat skin. Vet Dermatol 2014; 25:523-9, e89-90. [DOI: 10.1111/vde.12162] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2014] [Indexed: 02/04/2023]
Affiliation(s)
- David W. Genovese
- Animal Allergy and Dermatology; 1124 Lynnhaven Parkway Virginia Beach VA 23452 USA
| | - Tammy L. Johnson
- IDEXX Laboratories, Inc.; One IDEXX Drive; Westbrook ME 04092 USA
| | - Ken E. Lamb
- Lamb Consulting; 404 Thompson Avenue West West Saint Paul MN 55118 USA
| | - Wallace D. Gram
- University of Florida College of Veterinary Medicine; 2015 SW 16th Avenue Gainesville FL 32608 USA
| |
Collapse
|