Four loci explain 83% of size variation in the horse

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Makvandi Nejad, Shokouh ^a   Hoffman, Gabriel E ^b   Allen, Jeremy J ^a   Chu, Erin ^a   Gu, Esther ^a   Chandler, Alyssa M ^a   Loredo, Ariel I ^a,c   Bellone, Rebecca R ^d   Mezey, Jason G ^b   Brooks, Samantha A ^a   Sutter, Nathan B ^a  

^a Department of Obstetrics Gynecology   (United States)

^b Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^c LA SIERRA UNIVERSITY   (United States)

^d UNIVERSITY OF TAMPA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BODY HEIGHT; BODY SIZE; BREEDING; CATTLE; CONTROLLED STUDY; DOG; DOMESTICATION; FEMALE; GENE IDENTIFICATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HMGA2 GENE; HORSE; LCORL GENE; MALE; NCAPG; NONHUMAN; ZFAT GENE;

ANIMALS; BODY SIZE; BREEDING; CATTLE; CELL CYCLE PROTEINS; DOGS; FEMALE; GENETIC LOCI; GENETIC VARIATION; GENOME; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HMGA2 PROTEIN; HORSES; HUMANS; MALE; TRANSCRIPTION FACTORS; ZINC FINGERS;

BOS; CANIS FAMILIARIS; EQUIDAE; MAMMALIA;

EID: 84863815949     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039929     Document Type: Article

References (37)

1. Clutton-Brock J, Natural History Museum (London England) (1999) A natural history of domesticated mammals. Cambridge, U.K.; New York, NY, USA London;: Cambridge University Press; Natural History Museum. viii, 238 p. p.
2. Brooks SA, Makvandi-Nejad S, Chu E, Allen JJ, Streeter C, et al. (2010) Morphological variation in the horse: defining complex traits of body size and shape. Animal Genetics 41: 159-165.
3. Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467: 832-838.
4. Weedon MN, Lettre G, Freathy RM, Lindgren CM, Voight BF, et al. (2007) A common variant of HMGA2 is associated with adult and childhood height in the general population. Nat Genet 39: 1245-1250.
5. Gudbjartsson DF, Walters GB, Thorleifsson G, Stefansson H, Halldorsson BV, et al. (2008) Many sequence variants affecting diversity of adult human height. Nat Genet 40: 609-615.
6. Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, et al. (2008) Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet 40: 575-583.
7. Lettre G, Jackson AU, Gieger C, Schumacher FR, Berndt SI, et al. (2008) Identification of ten loci associated with height highlights new biological pathways in human growth. Nat Genet 40: 584-591.
8. Kim JJ, Lee HI, Park T, Kim K, Lee JE, et al. (2010) Identification of 15 loci influencing height in a Korean population. J Hum Genet 55: 27-31.
9. Liu JZ, Medland SE, Wright MJ, Henders AK, Heath AC, et al. (2010) Genome-wide association study of height and body mass index in Australian twin families. Twin Research and Human Genetics 13: 179-193.
10. Sovio U, Bennett AJ, Millwood IY, Molitor J, O'Reilly PF, et al. (2009) Genetic determinants of height growth assessed longitudinally from infancy to adulthood in the northern Finland birth cohort 1966. PLoS Genet 5: e1000409.
11. Takeuchi F, Nabika T, Isono M, Katsuya T, Sugiyama T, et al. (2009) Evaluation of genetic loci influencing adult height in the Japanese population. J Hum Genet 54: 749-752.
12. N'Diaye A, Chen GK, Palmer CD, Ge B, Tayo B, et al. (2011) Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. PLoS Genet 7: e1002298.
13. Carty CL, Johnson NA, Hutter CM, Reiner AP, Peters U, et al. (2011) Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe). Hum Mol Genet.
14. Okada Y, Kamatani Y, Takahashi A, Matsuda K, Hosono N, et al. (2010) A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. Hum Mol Genet 19: 2303-2312.
15. Perola M, (2011) Genome-wide association approaches for identifying loci for human height genes. Best Pract Res Clin Endocrinol Metab 25: 19-23.
16. Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, et al. (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316: 112-115.
17. Chase K, Carrier DR, Adler FR, Jarvik T, Ostrander EA, et al. (2002) Genetic basis for systems of skeletal quantitative traits: principal component analysis of the canid skeleton. Proc Natl Acad Sci U S A 99: 9930-9935.
18. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, et al. (2010) A simple genetic architecture underlies morphological variation in dogs. PLoS Biol 8: e1000451.
19. Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, et al. (2011) Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet 7: e1002316.
20. Jones P, Chase K, Martin A, Davern P, Ostrander EA, et al. (2008) Single-nucleotide-polymorphism-based association mapping of dog stereotypes. Genetics 179: 1033-1044.
21. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, et al. (2012) A high density SNP array for the domestic horse and extant perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet 8: e1002451.
22. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, et al. (2008) Efficient control of population structure in model organism association mapping. Genetics 178: 1709-1723.
23. Balding DJ, (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7: 781-791.
24. Cadieu E, Neff MW, Quignon P, Walsh K, Chase K, et al. (2009) Coat variation in the domestic dog is governed by variants in three genes. Science 326: 150-153.
25. Parker HG, vonHoldt BM, Quignon P, Margulies EH, Shao S, et al. (2009) An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325: 995-998.
26. Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC, et al. (2007) Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 39: 1321-1328.
27. Flori L, Fritz S, Jaffrezic F, Boussaha M, Gut I, et al. (2009) The genome response to artificial selection: a case study in dairy cattle. PLoS One 4: e6595.
28. Eberlein A, Takasuga A, Setoguchi K, Pfuhl R, Flisikowski K, et al. (2009) Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex, subunit G (NCAPG) gene. Genetics 183: 951-964.
29. Cleynen I, Van de Ven WJ, (2008) The HMGA proteins: a myriad of functions (Review). Int J Oncol 32: 289-305.
30. Zhou X, Benson KF, Ashar HR, Chada K, (1995) Mutation responsible for the mouse pygmy phenotype in the developmentally regulated factor HMGI-C. Nature 376: 771-774.
31. Tsunoda T, Takashima Y, Tanaka Y, Fujimoto T, Doi K, et al. (2010) Immune-related zinc finger gene ZFAT is an essential transcriptional regulator for hematopoietic differentiation in blood islands. Proc Natl Acad Sci U S A 107: 14199-14204.
32. Loughran G, Huigsloot M, Kiely PA, Smith LM, Floyd S, et al. (2005) Gene expression profiles in cells transformed by overexpression of the IGF-I receptor. Oncogene 24: 6185-6193.
33. Hermann-Kleiter N, Ghaffari-Tabrizi N, Blumer MJ, Schwarzer C, Mazur MA, et al. (2009) Lasp1 misexpression influences chondrocyte differentiation in the vertebral column. Int J Dev Biol 53: 983-991.
34. Zheng ZY, Cheng CM, Fu XR, Chen LY, Xu L, et al. (2012) CHMP6 and VPS4A mediate the recycling of Ras to the plasma membrane to promote growth factor signaling. Oncogene.
35. Signer-Hasler H, Flury C, Haase B, Burger D, Simianer H, et al. (2012) A genome-wide association study reveals Loci influencing height and other conformation traits in horses. PLoS One 7: e37282.
36. Barrett JC, Fry B, Maller J, Daly MJ, (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
37. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.