Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Utsunomiya, Yuri Tani ^a   Pérez O'Brien, Ana Maria ^b   Sonstegard, Tad Stewart ^c   Van Tassell, Curtis Paul ^c   do Carmo, Adriana Santana ^a   Mészáros, Gábor ^b   Sölkner, Johann ^b   Garcia, José Fernando ^a  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALPAIN; CALPASTATIN; GANGLIOSIDE;

ALLELE; ARTICLE; BEEF CATTLE; BIOGENESIS; BIOLOGICAL ACTIVITY; CNIH3 GENE; CONTROLLED STUDY; DAIRY CATTLE; DAIRY PRODUCT; DATA ANALYSIS; DNA FOOTPRINTING; GENE; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC SELECTION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GLUCONEOGENESIS; GLYCOLYSIS; HAPLOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; LUTEINIZING HORMONE RELEASE; MEAT; NONHUMAN; POPULATION GENETICS; RIBOSOME; SIGNAL DETECTION; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATTLE; GENOME-WIDE ASSOCIATION STUDY; MODELS, THEORETICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC;

EID: 84877834696     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064280     Document Type: Article

References (56)

1. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
2. Oleksyk TK, Smith MW, O'Brien SJ, (2010) Genome-wide scans for footprints of natural selection. Phil. Trans. R. Soc. B 365: 185-205.
3. Nielsen R, Yang Z, (1988) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
4. Rubin CJ, Zody MC, Eriksson J, Meadows JRS, Sherwood E, et al. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-593.
5. Oleksyk TK, Zhao K, De La Vega FM, Gilbert DA, O'Brien SJ, et al. (2008) Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations. PLoS ONE 3(3): e1712.
6. Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, et al. (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327: 883-886.
7. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
8. Fu YX, Li WH, (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
9. Fay JC, Wu I, (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
10. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, et al. (2007) Localizing recent adaptive evolution in the human genome. PLoS Genet. 3: e90.
11. Weir BS, Cockerham CC, (1984) Estimating F-Statistics for the analysis of population structure. Evolution 38(6): 1358-1370.
12. Voight BF, Kudaravalli S, Wen X, Pritchard JK, (2009) A map of recent positive selection in the human genome. PLoS Biol. 4: e72.
13. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
14. Tang K, Thornton KR, Stoneking M, (2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biology 5: e171.
15. Ong RT-H, Teo YY, (2010) varLD: a program for quantifying variation in linkage disequilibrium patterns between populations. Bioinformatics 26(9): 1269-1270.
16. Andersen KG, Shylakhter I, Tabrizi S, Grossman SR, Happi CT, et al. (2012) Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever. Phil. Trans. R. Soc. B 367: 868-877.
17. Murray C, Huerta-Sanchez E, Casey F, Bradley DG, (2010) Cattle demographic history modelled from autosomal sequence variation. Phil. Trans. R. Soc. B. 365: 2531-2539.
18. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics 81(3): 559-575.
19. Scheet P, Stephens M, (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 78: 629-644.
20. Gautier M, Vitalis R, (2012) rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics 28(8): 1176-7.
21. Whitlock MC, (2005) Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach. J. Evol. Biol. 18: 1368-1373.
22. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, et al. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology 10(4): R42.
23. Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G et al. (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford). 2011 Published online Jul 23.
24. Quinlan A.R., Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6): 841-842.
25. Huang DW, Sherman BT, Lempicki RA, (2009a) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc 4(1): 44-57.
26. Huang DW, Sherman BT, Lempicki RA, (2009b) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1): 1-13.
27. Merico D, Isserlin R, Stueker O, Emili A, Bader GD, (2010) Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation. PLoS One 5(11): e13984.
28. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, et al. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4(4): e5350.
29. The Bovine HapMap Consortium, Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, et al. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324(5926): 528-532.
30. Ajmone-Marsan P, Garcia JF, Lenstra JA, The Globaldiv Consortium, (2010) On the Origin of Cattle: How Aurochs Became Cattle and Colonized the World. Evolutionary Anthropology 19: 148-157.
31. The Bovine Genome Sequencing, Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324(5926): 522-528.
32. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39(Database issue): D561-8.
33. Shi Y, Suh YH, Milstein AD, Isozaki K, Schmid SM, (2010) Functional comparison of the effects of TARPs and cornichons on AMPA receptor trafficking and gating. Proc. Natl. Acad. Sci. U.S.A. 107: 16315-16319.
34. Brann DW, Mahesh VB, (1997) Excitatory amino acids: evidence for a role in the control of reproduction and anterior pituitary hormone secretion. Endocr Rev 18: 678-700.
35. Sugimoto M, Sasaki S, Watanabe T, Nishimura S, Ideta A, et al. (2010) Ionotropic glutamate receptor AMPA 1 is associated with ovulation rate. PLoS One 5(11): e13817.
36. Gadient RA, Patterson PH, (1999) Leukemia inhibitory factor, interleukin 6, and other cytokines using the GP130 transducing receptor: roles in inflammation and injury. Stem Cells 17(3): 127-137.
37. Zoico E, Roubenoff R, (2002) The role of cytokines in regulating protein metabolism and muscle function, Nutrition Reviews. 60(2): 39-51.
38. Zhao C, Tian F, Yu Y, Luo J, Mitra A, et al. (2012) Functional Genomic Analysis of Variation on Beef Tenderness Induced by Acute Stress in Angus Cattle. Comparative and Functional Genomics 2012: 756284.
39. Koohmaraie M, Geesink GH, (2006) Contribution of postmortem muscle biochemistry to the delivery of consistent meat quality with particular focus on the calpain system. Meat Science 74: 34-43.
40. Kuhla B, Nürnberg G, Albrecht D, Görs S, Hammon HM, et al. (2011) Involvement of skeletal muscle protein, glycogen, and fat metabolism in the adaptation on early lactation of dairy cows. J Proteome Res. 10(9): 4252-62.
41. Arnandis T, Ferrer-Vicens I, García-Trevijano ER, Miralles VJ, García C, et al. (2012) Calpains mediate epithelial-cell death during mammary gland involution: mitochondria and lysosomal destabilization. Cell Death Differ. 19(9): 1536-48.
42. Wilde CJ, Addey CVP, Li P, Fernig DG, (1997) Programmed cell death in bovine mammary tissue during lactation and involution. Experimental Physiology 82: 943-953.
43. Kiss T, (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109: 145-148.
44. Decatur WA, Fournier MJ, (2002) rRNA modifications and ribosome function. Trends Biochem Sci. 27: 344-351.
45. Bionaz M, Loor JJ, (2011) Gene Networks Driving Bovine Mammary Protein Synthesis During the Lactation Cycle. Bioinform Biol Insights 5: 83-98.
46. Momoeda M, Fukuta S, Iwamori Y, Taketani Y, Iwamori M, (2007) Prolactin-dependent Expression of GD1α Ganglioside, as a Component of Milk Fat Globule, in the Murine Mammary Glands. The Journal of Biochemistry 142(4): 525-531.
47. Bode L, Beermann C, Mank M, Kohn G, Boehm G, (2004) Human and Bovine Milk Gangliosides Differ in Their Fatty Acid Composition. The Journal of Nutrition. 134(11): 3016-3020.
48. Villa-Angulo R, Matukumalli LK, Gill CA, Choi J, Van Tassell CP, et al. (2009) High-resolution haplotype block structure in the cattle genome. BMC Genetics 10: 19.
49. Klungland HD, Vage I, Gomez-Raya L, Adalsteinsson S, Lien S, (1995) The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination. Mamm Genome 6: 636-639.
50. Stella A, Ajmone-Marsan P, Lazzari B, Boettcher P, (2010) Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production. Genetics 185(4): 1451-1461.
51. Grosz MD, Macneil MD, (1999) Brief communication. The 'spotted' locus maps to bovine chromosome 6 in Hereford-cross population. J. Hered. 90: 233-236.
52. Qanbari S, Gianola D, Hayes B, Schenkel F, Miller S, et al. (2011) Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 12: 318.
53. Schwarzenbacher H, Dolezal M, Flisikowski K, Seefried F, Wurmser C, et al. (2012) Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle. BMC Genomics 13: 48.
54. Hayes BJ, Lien S, Nilsen H, Olsen HG, Berg P, et al. (2008) The origin of selection signatures on bovine chromosome 6. Animal Genetics 39: 105-111.
55. Hayes BJ, Chamberlain AJ, Maceachern S, Savin K, McPartlan H, et al. (2009) A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal Genetics 40(2): 176-184.
56. Flori L, Fritz S, Jaffrézic F, Boussaha M, Gut I, et al. (2009) The genome response to artificial selection: a case study in dairy cattle. PLOS ONE 4(8): e6595.