Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition

详细信息    查看全文

• 作者：Lesley-Ann Raven (30) (31) (32)
  Benjamin G Cocks (30) (31) (32)
  Michael E Goddard (30) (32) (33)
  Jennie E Pryce (30) (32)
  Ben J Hayes (30) (31) (32)
  
  30. Biosciences Research Division ; Department of Primary Industries Victoria ; AgriBio ; 5 Ring Road ; Bundoora ; 3086 ; Australia
  31. La Trobe University ; Bundoora ; Victoria ; 3086 ; Australia
  32. Dairy Futures Co-operative Research Centre ; Bundoora ; Victoria ; 3086 ; Australia
  33. Faculty of Land and Food Resources ; University of Melbourne ; Parkville ; Victoria ; 3010 ; Australia
  
• 刊名：Genetics Selection Evolution
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：46
• 期：1
• 全文大小：683 KB
• 参考文献：1. Hayes, BJ, Pryce, J, Chamberlain, AJ, Bowman, PJ, Goddard, ME (2010) Genetic architecture of complex traits and accuracy of genomic prediction: Coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genet 6: pp. e1001139 CrossRef
  2. Cole, JB, VanRaden, PM, O鈥機onnell, JR, Van Tassell, CP, Sonstegard, TS, Schnabel, RD, Taylor, JF, Wiggans, GR (2009) Distribution and location of genetic effects for dairy traits. J Dairy Sci 92: pp. 2931-2946 CrossRef
  3. Cohen-Zinder, M, Seroussi, E, Larkin, DM, Loor, JJ, Wind, AE-v, Lee, J-H, Drackley, JK, Band, MR, Hernandez, AG, Shani, M, Lewin, HA, Weller, JI, Ron, M (2005) Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. Genome Res 15: pp. 936-944 CrossRef
  4. Grisart, B, Coppieters, W, Farnir, F, Karim, L, Ford, C, Berzi, P, Cambisano, N, Mni, M, Reid, S, Simon, P, Spelman, R, Georges, M, Snell, R (2002) Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res 12: pp. 222-231 CrossRef
  5. Blott, S, Kim, JJ, Moisio, S, Schmidt-Kuntzel, A, Cornet, A, Berzi, P, Cambisano, N, Ford, C, Grisart, B, Johnson, D, Karim, L, Simon, P, Snell, R, Spelman, R, Wong, J, Vilkki, J, Georges, M, Farnir, F, Coppieters, W (2003) Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 163: pp. 253-266
  6. Cohen, M, Reichenstein, M, Everts-van der Wind, A, Heon-Lee, J, Shani, M, Lewin, HA, Weller, JI, Ron, M, Seroussi, E (2004) Cloning and characterization of FAM13A1 gene near a milk protein QTL on BTA6: evidence for population-wide linkage disequilibrium in Israeli Holsteins. Genomics 84: pp. 374-383 CrossRef
  7. Viitala, S, Szyda, J, Blott, S, Schulman, N, Lidauer, M, M盲ki-Tanila, A, Georges, M, Vilkki, J (2006) The role of the bovine growth hormone receptor and prolactin receptor genes in milk, fat and protein production in Finnish Ayrshire dairy cattle. Genetics 173: pp. 2151-2164 CrossRef
  8. Lynch, M, Walsh, B (1998) Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland
  9. Chamberlain, AJ, McPartlan, HC, Goddard, ME (2007) The number of loci that affect milk production traits in dairy cattle. Genetics 177: pp. 1117-1123 CrossRef
  10. Gjorevski, N, Nelson, CM (2011) Integrated morphodynamic signalling of the mammary gland. Nat Rev Mol Cell Biol 12: pp. 581-593 CrossRef
  11. Sternlicht, M (2006) Key stages in mammary gland development: the cues that regulate ductal branching morphogenesis. Breast Cancer Res 8: pp. 201 CrossRef
  12. Macias, H, Hinck, L (2012) Mammary gland development. Wiley Interdiscip Rev Dev Biol 1: pp. 533-557 CrossRef
  13. Lemay, DG, Neville, MC, Rudolph, MC, Pollard, KS, German, JB (2007) Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol 1: pp. 56 CrossRef
  14. Oakes, SR, Rogers, RL, Naylor, MJ, Ormandy, CJ (2008) Prolactin regulation of mammary gland development. J Mammary Gland Biol Neoplasia 13: pp. 13-28 CrossRef
  15. Akers, RM (2002) Lactation and the mammary gland. Iowa State Press, Ames
  16. Liu, X, Robinson, GW, Wagner, KU, Garrett, L, Wynshaw-Boris, A, Hennighausen, L (1997) Stat5a is mandatory for adult mammary gland development and lactogenesis. Genes Dev 11: pp. 179-186 CrossRef
  17. Nagy, EVA, Berczi, I (1991) Hypophysectomized rats depend on residual prolactin for survival. Endocrinology 128: pp. 2776-2784 CrossRef
  Industry Statistics for 2002鈥?012.
  18. Moser, G, Khatkar, MS, Hayes, BJ, Raadsma, HW (2010) Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers. Genet Sel Evol 42: pp. 37 CrossRef
  19. Pryce, JE, Bolormaa, S, Chamberlain, AJ, Bowman, PJ, Savin, K, Goddard, ME, Hayes, BJ (2010) A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes. J Dairy Sci 93: pp. 3331-3345 CrossRef
  20. Matukumalli, LK, Lawley, CT, Schnabel, RD, Taylor, JF, Allan, MF, Heaton, MP, O鈥機onnell, J, Moore, SS, Smith, TPL, Sonstegard, TS, Van Tassell, CP (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4: pp. e5350 CrossRef
  21. Erbe, M, Hayes, BJ, Matukumalli, LK, Goswami, S, Bowman, PJ, Reich, CM, Mason, BA, Goddard, ME (2012) Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. J Dairy Sci 95: pp. 4114-4129 CrossRef
  22. Garrick, DJ, Taylor, JF, Fernando, RL (2009) Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet Sel Evol 41: pp. 55 CrossRef
  23. Gilmour, AR, Gogel, BJ, Cullis, BR, Thompson, R (2006) ASReml User Guide Release 2.0. Hemel Hempstead, VSN International Ltd
  24. Sutherland, KD, Lindeman, GJ, Visvader, JE (2007) The Molecular culprits underlying precocious mammary gland involution. J Mammary Gland Biol Neoplasia 12: pp. 15-23 CrossRef
  25. Rincon, G, Islas-Trejo, A, Castillo, AR, Bauman, DE, German, BJ, Medrano, JF (2012) Polymorphisms in genes in the SREBP1 signalling pathway and SCD are associated with milk fatty acid composition in Holstein cattle. J Dairy Res 79: pp. 66-75 CrossRef
  26. Hubbard, TJP, Aken, BL, Beal, K, Ballester, B, Caccamo, M, Chen, Y, Clarke, L, Coates, G, Cunningham, F, Cutts, T, Down, T, Dyer, SC, Fitzgerald, S, Fernandez-Banet, J, Graf, S, Haider, S, Hammond, M, Herrero, J, Holland, R, Howe, K, Howe, K, Johnson, N, Kahari, A, Keefe, D, Kokocinski, F, Kulesha, E, Lawson, D, Longden, I, Melsopp, C, Megy, K (2007) Ensembl 2007. Nucleic Acids Res 35: pp. D610-D617 CrossRef
  27. European Bioinformatics Institute http://www.ebi.ac.uk/
  28. Gibbs, RA, Taylor, JF, Van Tassell, CP, Barendse, W, Eversole, KA, Gill, CA, Green, RD, Hamernik, DL, Kappes, SM, Lien, S, Matukumalli, LK, McEwan, JC, Nazareth, LV, Schnabel, RD, Weinstock, GM, Wheeler, DA, Ajmone-Marsan, P, Boettcher, PJ, Caetano, AR, Garcia, JF, Hanotte, O, Mariani, P, Skow, LC, Sonstegard, TS, Williams, JL, Diallo, B, Hailemariam, L, Martinez, ML, Morris, CA, Silva, LO (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: pp. 528-532 CrossRef
  29. Villa-Angulo, R, Matukumalli, LK, Gill, CA, Choi, J, Van Tassell, CP, Grefenstette, JJ (2009) High-resolution haplotype block structure in the cattle genome. BMC Genet 10: pp. 19 CrossRef
  30. Ogata, H, Goto, S, Sato, K, Fujibuchi, W, Bono, H, Kanehisa, M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27: pp. 29-34 CrossRef
  31. Kanehisa, M, Goto, S, Sato, Y, Furumichi, M, Tanabe, M (2011) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40: pp. D109-D114 CrossRef
  32. Yang, J, Benyamin, B, McEvoy, BP, Gordon, S, Henders, AK, Nyholt, DR, Madden, PA, Heath, AC, Martin, NG, Montgomery, GW, Goddard, ME, Visscher, PM (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: pp. 565-569 CrossRef
  33. Chamberlain, AJ, Hayes, BJ, Savin, K, Bolormaa, S, McPartlan, HC, Bowman, PJ, Van Der Jagt, C, MacEachern, S, Goddard, ME (2012) Validation of single nucleotide polymorphisms associated with milk production traits in dairy cattle. J Dairy Sci 95: pp. 864-875 CrossRef
  34. Wickenden, JA, Watson, CJ (2010) Key signalling nodes in mammary gland development and cancer. Signalling downstream of PI3 kinase in mammary epithelium: a play in 3 Akts. Breast Cancer Res 12: pp. 202 CrossRef
  35. Cadigan, KM, Nusse, R (1997) Wnt signaling: a common theme in animal development. Genes Dev 11: pp. 3286-3305 CrossRef
  36. Grisart, B, Farnir, F, Karim, L, Cambisano, N, Kim, JJ, Kvasz, A, Mni, M, Simon, P, Fr猫re, JM, Coppieters, W, George, M (2004) Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proc Natl Acad Sci U S A 101: pp. 2398-2403 CrossRef
  37. Khatib, H, Monson, RL, Schutzkus, V, Kohl, DM, Rosa, GJM, Rutledge, JJ (2008) Mutations in the STAT5A gene are associated with embryonic survival and milk composition in cattle. J Dairy Sci 91: pp. 784-793 CrossRef
  38. Khatib, H, Monson, RL, Huang, W, Khatib, R, Schutzkus, V, Khateeb, H, Parrish, JJ (2010) Short communication: validation of in vitro fertility genes in a Holstein bull population. J Dairy Sci 93: pp. 2244-2249 CrossRef
  39. Lemay, DG, Lynn, DJ, Martin, WF, Neville, MC, Casey, TM, Rincon, G, Kriventseva, EV, Barris, WC, Hinrichs, AS, Molenaar, AJ (2009) The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol 10: pp. R43 CrossRef
  40. Strucken, EM, Bortfeldt, RH, de Koning, DJ, Brockmann, GA (2011) Genome-wide associations for investigating time-dependent genetic effects for milk production traits in dairy cattle. Anim Genet 43: pp. 375-382 CrossRef
  41. Raven, L, Cocks, BG, Hayes, BJ (2013) Multi-breed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle. BMC Genomics 15: pp. 62-76 CrossRef
  
• 刊物主题：Animal Genetics and Genomics; Evolutionary Biology; Agriculture;
• 出版者：BioMed Central
• ISSN：1297-9686

文摘

Background The maintenance of lactation in mammals is the result of a balance between competing signals from mammary development, prolactin signalling and involution pathways. Dairy cattle are an interesting case study to investigate the effect of polymorphisms that affect the function of genes in these pathways. In dairy cattle, lactation yields and milk composition (for example protein percentage and fat percentage) are routinely recorded, and these vary greatly between individuals. In this study, we test 8058 single nucleotide polymorphisms in or close to genes in these pathways for association with milk production traits and determine the proportion of variance explained by each pathway, using data on 16 812 dairy cattle, including Holstein-Friesian and Jersey bulls and cows. Results Single nucleotide polymorphisms close to genes in the mammary development, prolactin signalling and involution pathways were significantly associated with milk production traits. The involution pathway explained the largest proportion of genetic variation for production traits. The mammary development pathway also explained additional genetic variation for milk volume, fat percentage and protein percentage. Conclusions Genetic variants in the involution pathway explained considerably more genetic variation in milk production traits than expected by chance. Many of the associations for single nucleotide polymorphisms in genes in this pathway have not been detected in conventional genome-wide association studies. The pathway approach used here allowed us to identify some novel candidates for further studies that will be aimed at refining the location of associated genomic regions and identifying polymorphisms contributing to variation in lactation volume and milk composition.