Genetic heterogeneity and selection signature at the KIT gene in pigs showing different coat colours and patterns

Animal Genetics

Volumn 41, Issue 5, 2010, Pages 478-492

  Fontanesi, L ^a   D'Alessandro, E ^b   Scotti, E ^a   Liotta, L ^b   Crovetti, A ^c   Chiofalo, V ^b   Russo, V ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSITY OF MESSINA   (Italy)

^c UNIVERSITY OF FLORENCE   (Italy)

Author keywords

coat colour; KIT; pig breeds; polymorphisms; selection signature

Indexed keywords

MELANOCORTIN 1 RECEPTOR; STEM CELL FACTOR RECEPTOR;

ANIMAL; ARTICLE; CLASSIFICATION; GENETIC HETEROGENEITY; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETICS; HAIR COLOR; SWINE;

ANIMALS; GENETIC HETEROGENEITY; HAIR COLOR; POLYMORPHISM, GENETIC; PROTO-ONCOGENE PROTEINS C-KIT; RECEPTOR, MELANOCORTIN, TYPE 1; SELECTION, GENETIC; SWINE;

PIERIS BRASSICAE; SUIDAE; SUS; SUS SCROFA;

EID: 76449100982     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2010.02054.x     Document Type: Article

References (64)

1. Amaral A.J., Megens H.J., Crooijmans R.P., Heuven H.C. Groenen M.A. (2008) Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179, 569 579.
2. Bandelt H.J., Forster P. Röhl A. (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology Evolution 16, 37 48.
3. Barrett J.C., Fry B., Maller J. Daly M.J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263 265.
4. Besmer P., Manova K., Duttlinger R., Huang E.J., Packer A., Gyssler C. Bachvarova R.F. (1993) The kit-ligand (steel factor) and its receptor c-kit/W: pleiotropic roles in gametogenesis and melanogenesis. Development (Suppl. 125 137.
5. Brooks S.A. Bailey E. (2005) Exon skipping in the KIT gene causes a Sabino spotting pattern in horses. Mammalian Genome 16, 893 902.
6. Chicoli N. (1870) Riproduzione, allevamento e miglioramento degli animali domestici in Sicilia. Stamperia di G. 4. Lorsnaider, Palermo.
7. Chiofalo L. Liotta L. (2003) Suino nero, una perla in terra siciliana. Suinicoltura 44, 79 86.
8. Cooper G.M., Nickerson D.A. Eichler E.E. (2007) Mutational and selective effects on copy-number variants in the human genome. Nature Genetics 39 (7 Suppl. S22 9.
9. D'Alessandro E., Fontanesi L., Liotta L., Davoli R., Chiofalo V. Russo V. (2007) Analysis of the MC1R gene in the Nero Siciliano pig breed and usefulness of this locus for breed traceability. Veterinary Research Communication 31 (Suppl. 1 389 392.
10. De Sepulveda P., Peyrieras N. Panthier J.J. (1994) Instability at the W/c-kit locus in mice: analysis of melanocyte cell lines derived from reversion spots. Oncogene 9, 2655 2661.
11. Dondi G. (1924) La razza suina Cinta. Rivista di Zootecnia 1, 237 245.
12. Egan C.M., Sridhar S., Wigler M. Hall I.M. (2007) Recurrent DNA copy number variation in the laboratory mouse. Nature Genetics 39, 1384 1389.
13. Faelli F. (1928) Razze bovine, equine, suine, ovine, caprine. Hoepli, Milan, Italy.
14. Fang M. Andersson L. (2006) Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication. Proceedings of the Royal Society B Biological Sciences 273, 1803 1810.
15. Fang M., Larson G., Ribeiro H.S., Li N. Andersson L. (2009) Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genetics 5, e1000341.
16. Fay J. Wu C.-I. (2000) Hitchhiking under positive Darwinian selection. Genetics 155, 1405 1413.
17. Fésüs L., Zsolnai A. Komlósi I. (2005) Influence of porcine coat color genotypes on haematological parameters, piglet birth weight and body weight gain until weaning. Journal of Animal Breeding and Genetics 122, 127 130.
18. Fontanesi L., Tazzoli M., Russo V. Beever J. (2009) Genetic heterogeneity at the bovine KIT gene in cattle breeds carrying different putative alleles at the spotting locus. Animal Genetics, doi :.
19. Franci O. Pugliese C. (2007) Italian autochthonous pigs: progress report and research perspectives. Italian Journal of Animal Science 6 (Suppl. 1 663 671.
20. Franci O., Gandini G. Bozzi R. (2007) Why and how to select a local porcine breed? The case of the Cinta Senese breed. Options Mé diterranéennes Series A 76, 13 21.
21. Gandini G., Fortina F., Franci O., Madonia G. Matassino D. (2001) Pig genetic resources in Italy. In : Pig Genetic Resources in Europe (Ed. by L. Ollivier, F. Labroue, P. Glodek, G. Gandini J.V. Delgado pp. 33 40. EAAP publication No.104, Wageningen.
22. Giuffra E., Evans G., Törnsten A., Wales R., Day A., Looft H., Plastow G. Andersson L. (1999) The Belt mutation in pigs is an allele at the Dominant white (I/KIT) locus. Mammalian Genome 10, 1132 1136.
23. Giuffra E., Kijas J.M., Amarger V., Carlborg O., Jeon J.T. Andersson L. (2000) The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154, 1785 1791.
24. Giuffra E., Törnsten A., Marklund S., Bongcam-Rudloff E., Chardon P., Kijas J.M., Anderson S.I., Archibald A.L. Andersson L. (2002) A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mammalian Genome 13, 569 577.
25. Haase B., Brooks S.A., Schlumbaum A. et al. (2007) Allelic heterogeneity at the equine KIT locus in dominant white (W) horses. PLoS Genetics 3, e195.
26. Hetzer H.O. (1948) Inheritance of coat color in swine. VII. Results of Landrace by Hampshire crosses. Journal of Heredity 39, 123 128.
27. Hirooka H., de Koning D.J., van Arendonk J.A.M., Harlizius B., de Groot P.N. Bovenhuis H. (2002) Genome scan reveals new coat color loci in exotic pig cross. Journal of Heredity 93, 1 8.
28. Innan H. Kim Y. (2004) Pattern of polymorphism after strong artificial selection in a domestication event. Proceedings of the National Academy of Sciences of the United States of America 101, 10667 10672.
29. Jackson I.J. (1994) Molecular and developmental genetics of mouse coat color. Annual Review of Genetics 28, 189 217.
30. Jackson I.J. (1997) Homologous pigmentation mutations in human, mouse and other model organisms. Human Molecular Genetics 6, 1613 1624.
31. Jensen J.D., Kim Y., DuMont V.B., Aquadro C.F. Bustamante C.D. (2005) Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170, 1401 1410.
32. Johansson Moller M., Chaudhary R., Hellmén E., Höyheim B., Chowdhary B. Andersson L. (1996) Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor. Mammalian Genome 7, 822 830.
33. Johansson M., Ellegren H., Marklund L., Gustavsson U., Ringmar-Cederberg E., Andersson K., Edfors-Lilja I. Andersson L. (1992) The gene for dominant white color in the pig is closely linked to ALB and PDGRFRA on chromosome 8. Genomics 14, 965 969.
34. Johansson A., Pielberg G., Andersson L. Edfors-Lilja I. (2005) Polymorphism at the porcine Dominant white/KIT locus influence coat colour and peripheral blood cell measures. Animal Genetics 36, 288 296.
35. Kijas J.M., Wales R., Törnsten A., Chardon P., Moller M. Andersson L. (1998) Melanocortin receptor 1 (MC1R) mutations and coat color in pigs. Genetics 150, 1177 1185.
36. Kijas J.M., Moller M., Plastow G. Andersson L. (2001) A frameshift mutation in MC1R and a high frequency of somatic reversions cause black spotting in pigs. Genetics 158, 779 785.
37. Lai F., Ren J., Ai H., Ding N., Ma J., Zeng D., Chen C., Guo Y. Huang L. (2007) Chinese white Rongchang pig does not have the dominant white allele of KIT but has the dominant black allele of MC1R. Journal of Heredity 98, 84 87.
38. Larson G., Dobney K., Albarella U. et al. (2005) Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618 1621.
39. Lauvergne J.J. Canope I. (1979) Etude de quelques variants colorés du porc Créole de la Guadeloupe. Annales Génétiqué Sélection Animale 11, 381 390.
40. Legault C. (1998) Genetics of colour variation. In : The Genetics of the Pig (Ed. by M.F. Rothschild A. Ruvinsky pp. 51 69. CAB International, Wallingford.
41. Marklund S., Kijas J., Rodriguez-Martinez H., Rönnstrand L., Funa K., Moller M., Lange D., Edfors-Lilja I. Andersson L. (1998) Molecular basis for the dominant white phenotype in the domestic pig. Genome Research 8, 826 833.
42. 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.
43. Martin D.P., Williamson C. Posada D. (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260 262.
44. McLean J.A. (1914) The shapphire hog. Journal of Heredity 5, 301 304.
45. Montanaro G. (1939) Per il miglioramento della suinicoltura siciliana. Critica Zootecnica 8, 303 319.
46. Ohta H., Tohda A. Nishimune Y. (2003) Proliferation and differentiation of spermatogonial stem cells in the w/wv mutant mouse testis. Biology of Reproduction 69, 1815 1821.
47. Ojeda A., Rozas J., Folch J.M. Pérez-Enciso M. (2006) Unexpected high polymorphism at the FABP4 gene unveils a complex history for pig populations. Genetics 174, 2119 2127.
48. Ojeda A., Huang L.S., Ren J., Angiolillo A., Cho I.C., Soto H., Lemús-Flores C., Makuza S.M., Folch J.M. Pérez-Enciso M. (2008) Selection in the making: a worldwide survey of haplotypic diversity around a causative mutation in porcine IGF2. Genetics 178, 1639 1652.
49. Okumura N., Matsumoto T. Awata T. (2008) Single nucleotide polymorphisms of the KIT and KITL genes in pigs. Animal Science Journal 79, 303 313.
50. Pielberg G., Olsson C., Syvänen A.C. Andersson L. (2002) Unexpectedly high allelic diversity at the KIT locus causing dominant white color in the domestic pig. Genetics 160, 305 311.
51. Porter V. (1993) Pigs: A Handbook to the Breeds of the World. Comstock Publishing Associates, Cornell University Press, Ithaca, NY.
52. Raimondi R. (1955) Studio sperimentale su alcuni indirizzi tradizionali della suinicoltura italiana. Istituto Zootecnico e Caseario per il Piemonte, Torino.
53. Ray P., Krishnamoorthy N. Ray A. (2008) Emerging functions of c-kit and its ligand stem cell factor in dendritic cells: regulators of T cell differentiation. Cell Cycle 7, 2826 2832.
54. Rozas J., Sanchez-DelBarrio J.C., Messeguer X. Rozas R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496 2497.
55. Russo V., Fontanesi L., Davoli R., Chiofalo L., Liotta L. Zumbo A. (2004) Analysis of single nucleotide polymorphisms in major and candidate genes for production traits in Nero Siciliano pig breed. Italian Journal of Animal Science 3, 19 29.
56. Shi K.R., Wang A.G., Yuan X.F., Deng X.M. Li N. (2006) Analysis of the MC1R, KIT and ASIP loci in Chinese and European pigs. Animal Genetics 37, 300 302.
57. Stephens M., Smith N.J. Donnelly P. (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 68, 978 989.
58. Tamura K., Dudley J., Nei M. Kumar S. (2007) mega4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology Evolution 24, 1596 1599.
59. Thomas P.D. Kejariwal A. (2004) Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects. Proceedings of the National Academy of Sciences of the United States of America 101, 15398 15403.
60. Thomas P.D., Campbell M.J., Kejariwal A., Mi H., Karlak B., Daverman R., Diemer K., Muruganujan A. Narechania A. (2003) panther: a library of protein families and subfamilies indexed by function. Genome Research 13, 2129 2141.
61. Thomas P.D., Kejariwal A., Guo N., Mi H., Campbell M.J., Muruganujan A. Lazareva-Ulitsky B. (2006) Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Research 34, W645 50.
62. Waskow C. Rodewald H.R. (2002) Lymphocyte development in neonatal and adult c-Kit-deficient (c-KitW/W) mice. Advances in Experimental Medicine and Biology 512, 1 10.
63. Xu G.L., Ren J., Ding N.S., Ai H.S., Guo Y.M., Chen C.Y. Huang L.S. (2006) Genetic analysis of the KIT and MC1R genes in Chinese indigenous pigs with belt-like coat color phenotypes. Animal Genetics 37, 518 519.
64. Yoshida H., Kunisada T., Grimm T., Nishimura E.K., Nishioka E. Nishikawa S.I. (2001) Review: melanocyte migration and survival controlled by SCF/c-kit expression. Journal of Investigative Dermatology Symposium Proceedings 6, 1 5.