A copy number variant near KITLG is associated with the roan pattern in alpacas
Ishani Shah A , Naomi Gray A , David Groth A , Samantha Brooks
B and Kylie Munyard A *
+ Author Affiliations
- Author Affiliations
A Curtin Medical School and Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Perth, WA, Australia.
B Animal Sciences, University of Florida, Gainesville, FL, USA.
Animal Production Science 63(11) 1008-1016 https://doi.org/10.1071/AN22463
Submitted: 15 December 2022 Accepted: 13 March 2023 Published: 4 April 2023
© 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)
Abstract
Context: The alpaca roan pattern is characterised by white and coloured fibre interspersed together, with a distinctive lighter body and darker extremities, and commonly is believed to be inherited in an autosomal dominant manner. It is of interest to the alpaca fibre industry as it causes ‘contamination’ of coloured fibre with white fibres, but cannot be detected in white or light fawn animals. Other livestock species, such as horses, cattle, goats, and pigs, exhibit comparable phenotypes, which are associated with candidate variant(s) in either KIT or KITLG.
Aims: To identify a region or regions of the genome that is/are causative of the roan pattern in alpacas.
Methods: We conducted a genome-wide association study (GWAS) by using 13 roan and 14 non-roan alpacas sampled from the USA, Australia, and New Zealand. Regions of genome-wide significance were examined for variants that correlated with the roan phenotype.
Key results: A novel candidate single-nucleotype polymorphism (SNP; Super-Scaffold_15:39 742 851T > A), located 272 kb upstream of KITLG, was identified in 1 of 12 regions with genome-wide significant association (P ≤ 5 × 10−8). We identified the candidate SNP-containing region (Super-Scaffold_15:39 742 096–39 887 419) to be a 145 kb copy number variant (CNV) that is likely to be a tandem duplication. All 13 roan alpacas had one or two copies of the roan-associated T allele and all except three non-roans had zero copies. Furthermore, we determined the Mendelian inheritance of copy number haplotypes and their allelic composition in a roan and a non-roan family.
Conclusions: Our data support the hypothesised autosomal incomplete dominant mode of inheritance of the roan pattern in alpacas and suggests that the effect of the T allele CNV version is likely to be suppressed when in cis with the A allele CNV version. However, additional verification is required to validate the finding and determine the functional effect.
Implications: Identification of the cause, or a marker for roan pattern will allow alpaca breeders to select for or against the roan pattern, even when the phenotype is hidden, and therefore increase production output and profitability.
Keywords: alpaca, CNV, colour, fibre, genotyping by sequencing, GWAS, KITLG, pattern, roan, SNP.
References
Baxter LL, Watkins-Chow DE, Pavan WJ, Loftus SK (2019) A curated gene list for expanding the horizons of pigmentation biology. Pigment Cell & Melanoma Research 32, 348–358.| A curated gene list for expanding the horizons of pigmentation biology.Crossref | GoogleScholarGoogle Scholar |
Bedell MA, Brannan CI, Evans EP, Copeland NG, Jenkins NA, Donovan PJ (1995) DNA rearrangements located over 100 kb 5’ of the Steel (Sl)-coding region in Steel-panda and Steel-contrasted mice deregulate Sl expression and cause female sterility by disrupting ovarian follicle development. Genes & Development 9, 455–470.
| DNA rearrangements located over 100 kb 5’ of the Steel (Sl)-coding region in Steel-panda and Steel-contrasted mice deregulate Sl expression and cause female sterility by disrupting ovarian follicle development.Crossref | GoogleScholarGoogle Scholar |
Bedell MA, Cleveland LS, O’Sullivan TN, Copeland NG, Jenkins NA (1996) Deletion and interallelic complementation analysis of Steel mutant mice. Genetics 142, 935–944.
| Deletion and interallelic complementation analysis of Steel mutant mice.Crossref | GoogleScholarGoogle Scholar |
Besmer P, Manova K, Duttlinger R, Huang EJ, Packer A, Gyssler C, Bachvarova RF (1993) The kit-ligand (steel factor) and its receptor c-kit/W: pleiotropic roles in gametogenesis and melanogenesis. Development 119, 125–137.
| The kit-ligand (steel factor) and its receptor c-kit/W: pleiotropic roles in gametogenesis and melanogenesis.Crossref | GoogleScholarGoogle Scholar |
Bian Y, Wei G, Song X, Yuan L, Chen H, Ni T, Lu D (2019) Global downregulation of pigmentation-associated genes in human premature hair graying. Experimental and Therapeutic Medicine 18, 1155–1163.
| Global downregulation of pigmentation-associated genes in human premature hair graying.Crossref | GoogleScholarGoogle Scholar |
Brancalion L, Haase B, Wade CM (2022) Canine coat pigmentation genetics: a review. Animal Genetics 53, 3–34.
| Canine coat pigmentation genetics: a review.Crossref | GoogleScholarGoogle Scholar |
Broad Institute (2019) ‘Picard tools.’ Broad Institute, GitHub repository. http://broadinstitute.github.io/picard/
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10, 421
| BLAST+: architecture and applications.Crossref | GoogleScholarGoogle Scholar |
Charlier C, Denys B, Belanche JI, Coppieters W, Grobet L, Mni M, Womack J, Hanset R, Georges M (1996) Microsatellite mapping of the bovine roan locus: a major determinant of White Heifer Disease. Mammalian Genome 7, 138–142.
| Microsatellite mapping of the bovine roan locus: a major determinant of White Heifer Disease.Crossref | GoogleScholarGoogle Scholar |
Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890.
| fastp: an ultra-fast all-in-one FASTQ preprocessor.Crossref | GoogleScholarGoogle Scholar |
Cho I-C, Zhong T, Seo B-Y, Jung E-J, Yoo C-K, Kim J-H, Lee J-B, Lim H-T, Kim B-W, Lee J-H, Ko M-S, Jeon J-T (2011) Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig. Genes & Genomics 33, 17–23.
| Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig.Crossref | GoogleScholarGoogle Scholar |
Cieslak M, Reissmann M, Hofreiter M, Ludwig A (2011) Colours of domestication. Biological Reviews 86, 885–899.
| Colours of domestication.Crossref | GoogleScholarGoogle Scholar |
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H (2021) Twelve years of SAMtools and BCFtools. GigaScience giab008
| Twelve years of SAMtools and BCFtools.Crossref | GoogleScholarGoogle Scholar |
Endou M, Aoki H, Kobayashi T, Kunisada T (2014) Prevention of hair graying by factors that promote the growth and differentiation of melanocytes. The Journal of Dermatology 41, 716–723.
| Prevention of hair graying by factors that promote the growth and differentiation of melanocytes.Crossref | GoogleScholarGoogle Scholar |
Feeley NL, Munyard KA (2009) Characterisation of the melanocortin-1 receptor gene in alpaca and identification of possible markers associated with phenotypic variations in colour. Animal Production Science 49, 675–681.
| Characterisation of the melanocortin-1 receptor gene in alpaca and identification of possible markers associated with phenotypic variations in colour.Crossref | GoogleScholarGoogle Scholar |
Feeley NL, Bottomley S, Munyard KA (2011) Three novel mutations in ASIP associated with black fibre in alpacas (Vicugna pacos). The Journal of Agricultural Science 149, 529–538.
| Three novel mutations in ASIP associated with black fibre in alpacas (Vicugna pacos).Crossref | GoogleScholarGoogle Scholar |
Fontanesi L, Russo V (2013) Molecular genetics of coat colour in pigs. Acta Agriculturae Slovenica 16
Grilz-Seger G, Reiter S, Neuditschko M, Wallner B, Rieder S, Leeb T, Jagannathan V, Mesarič M, Cotman M, Pausch H, Lindgren G, Velie B, Horna M, Brem G, Druml T (2020) A genome-wide association analysis in Noriker horses identifies a SNP associated with roan coat color. Journal of Equine Veterinary Science 88, 102950
| A genome-wide association analysis in Noriker horses identifies a SNP associated with roan coat color.Crossref | GoogleScholarGoogle Scholar |
Hachiya A, Sriwiriyanont P, Kobayashi T, Nagasawa A, Yoshida H, Ohuchi A, Kitahara T, Visscher MO, Takema Y, Tsuboi R, Boissy RE (2009) Stem cell factor-KIT signalling plays a pivotal role in regulating pigmentation in mammalian hair. The Journal of Pathology 218, 30–39.
| Stem cell factor-KIT signalling plays a pivotal role in regulating pigmentation in mammalian hair.Crossref | GoogleScholarGoogle Scholar |
Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA (2015) Large multiallelic copy number variations in humans. Nature Genetics 47, 296–303.
| Large multiallelic copy number variations in humans.Crossref | GoogleScholarGoogle Scholar |
Hemesath TJ, Price ER, Takemoto C, Badalian T, Fisher DE (1998) MAP kinase links the transcription factor Microphthalmia to c-Kit signalling in melanocytes. Nature 391, 298–301.
| MAP kinase links the transcription factor Microphthalmia to c-Kit signalling in melanocytes.Crossref | GoogleScholarGoogle Scholar |
Hintz HF, Van Vleck LD (1979) Lethal dominant roan in horses. Journal of Heredity 70, 145–146.
| Lethal dominant roan in horses.Crossref | GoogleScholarGoogle Scholar |
Jones M, Sergeant C, Richardson M, Groth D, Brooks S, Munyard K (2019) A non-synonymous SNP in exon 3 of the KIT gene is responsible for the classic grey phenotype in alpacas (Vicugna pacos). Animal Genetics 50, 493–500.
| A non-synonymous SNP in exon 3 of the KIT gene is responsible for the classic grey phenotype in alpacas (Vicugna pacos).Crossref | GoogleScholarGoogle Scholar |
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357–359.
| Fast gapped-read alignment with Bowtie 2.Crossref | GoogleScholarGoogle Scholar |
Lim HT, Zhong T, Cho IC, Seo BY, Kim JH, Lee SS, Ko MS, Park HB, Kim BW, Lee JH, Jeon JT (2011) Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrossed population of Landrace and Korean Native pigs. Animal Genetics 42, 451–455.
| Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrossed population of Landrace and Korean Native pigs.Crossref | GoogleScholarGoogle Scholar |
Marklund S, Moller M, Sandberg K, Andersson L (1999) Close association between sequence polymorphism in the KIT gene and the roan coat color in horses. Mammalian Genome 10, 283–288.
| Close association between sequence polymorphism in the KIT gene and the roan coat color in horses.Crossref | GoogleScholarGoogle Scholar |
Mathews M, Mathews T, Kostiakos ECK (2019) Gorgeous Greys. Camelid Connections Magazine – Specialty Publications. Candelo New South Wales, Australia. https://camelidconnections.com.au
McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PIW, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genetics 40, 1166–1174.
| Integrated detection and population-genetic analysis of SNPs and copy number variation.Crossref | GoogleScholarGoogle Scholar |
Miller CT, Beleza S, Pollen AA, Schluter D, Kittles RA, Shriver MD, Kingsley DM (2007) cis-regulatory changes in kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell 131, 1179–1189.
| cis-regulatory changes in kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans.Crossref | GoogleScholarGoogle Scholar |
Munyard K (2013) ‘Inheritance of white colour in alpacas: identifying the genes involved.’ (Rural Industries Research and Development Corporation: Wagga Wagga, NSW, Australia)
Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M (2015) Haplotype phasing and inheritance of copy number variants in nuclear families. PLoS ONE 10, e0122713
| Haplotype phasing and inheritance of copy number variants in nuclear families.Crossref | GoogleScholarGoogle Scholar |
Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, Van der Auwera GA, Kling DE, Gauthier LD, Levy-Moonshine A, Roazen D, Shakir K, Thibault J, Chandran S, Whelan C, Lek M, Gabriel S, Daly MJ, Neale B, MacArthur DG, Banks E (2018) Scaling accurate genetic variant discovery to tens of thousands of samples. BioRxiv: The Preprint Server for Biology 201178
| Scaling accurate genetic variant discovery to tens of thousands of samples.Crossref | GoogleScholarGoogle Scholar |
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81, 559–575.
| PLINK: a tool set for whole-genome association and population-based linkage analyses.Crossref | GoogleScholarGoogle Scholar |
Qiu W, Chuong C-M, Lei M (2019) Regulation of melanocyte stem cells in the pigmentation of skin and its appendages: biological patterning and therapeutic potentials. Experimental Dermatology 28, 395–405.
| Regulation of melanocyte stem cells in the pigmentation of skin and its appendages: biological patterning and therapeutic potentials.Crossref | GoogleScholarGoogle Scholar |
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nature Biotechnology 29, 24–26.
| Integrative genomics viewer.Crossref | GoogleScholarGoogle Scholar |
Seitz JJ, Schmutz SM, Thue TD, Buchanan FC (1999) A missense mutation in the bovine MGF gene is associated with the roan phenotype in Belgian Blue and Shorthorn cattle. Mammalian Genome 10, 710–712.
| A missense mutation in the bovine MGF gene is associated with the roan phenotype in Belgian Blue and Shorthorn cattle.Crossref | GoogleScholarGoogle Scholar |
Suvakov M, Panda A, Diesh C, Holmes I, Abyzov A (2021) CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. GigaScience giab074
| CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.Crossref | GoogleScholarGoogle Scholar |
Talenti A, Bertolini F, Williams J, Moaeen-ud-Din M, Frattini S, Coizet B, Pagnacco G, Reecy J, Rothschild MF, Crepaldi P, Italian Goat Consortium (2018) Genomic analysis suggests KITLG is responsible for a roan pattern in two Pakistani goat breeds. Journal of Heredity 109, 315–319.
| Genomic analysis suggests KITLG is responsible for a roan pattern in two Pakistani goat breeds.Crossref | GoogleScholarGoogle Scholar |
Team Geospiza (2004) ‘FinchTV 1.4.0.’ (Geospiza, Inc.: Seattle, WA, USA)
Thangavel K, Rathinamoorthy R, Ganesan P (2015) Sustainable luxury natural fibers – production, properties, and prospects. In ‘Handbook of sustainable luxury textiles and fashion. Vol. 1’. (Eds MA Gardetti, SM Subramanian) pp. 59–98. (Springer: Singapore)
Toro MA (2010) Future trends in animal breeding due to new genetic technologies. Advances in Animal Biosciences 1, 546–557.
| Future trends in animal breeding due to new genetic technologies.Crossref | GoogleScholarGoogle Scholar |
Van der Auwera GA, O’Connor BD (2020) ‘Genomics in the cloud: using Docker, GATK, and WDL in terra.’ 1st edn. (O’Reilly Media: Sebastopol, CA, USA)
Voß K, Tetens J, Thaller G, Becker D (2020) Coat color roan shows association with KIT variants and no evidence of lethality in Icelandic horses. Genes 11, 680
| Coat color roan shows association with KIT variants and no evidence of lethality in Icelandic horses.Crossref | GoogleScholarGoogle Scholar |
Wang S, Dvorkin D, Da Y (2012) SNPEVG: a graphical tool for GWAS graphing with mouse clicks. BMC Bioinformatics 13, 319
| SNPEVG: a graphical tool for GWAS graphing with mouse clicks.Crossref | GoogleScholarGoogle Scholar |
Wehrle-Haller B (2003) The role of kit-ligand in melanocyte development and epidermal homeostasis. Pigment Cell Research 16, 287–296.
| The role of kit-ligand in melanocyte development and epidermal homeostasis.Crossref | GoogleScholarGoogle Scholar |
Weich K, Affolter V, York D, Rebhun R, Grahn R, Kallenberg A, Bannasch D (2020) Pigment intensity in dogs is associated with a copy number variant upstream of KITLG. Genes 11, 75
| Pigment intensity in dogs is associated with a copy number variant upstream of KITLG.Crossref | GoogleScholarGoogle Scholar |
Zsebo KM, Williams DA, Geissler EN, Broudy VC, Martin FH, Atkins HL, Hsu R-Y, Birkett NC, Okino KH, Murdock DC, et al. (1990) Stem cell factor is encoded at the SI locus of the mouse and is the ligand for the c-kit tyrosine kinase receptor. Cell 63, 213–224.
| Stem cell factor is encoded at the SI locus of the mouse and is the ligand for the c-kit tyrosine kinase receptor.Crossref | GoogleScholarGoogle Scholar |
