Abstract
Increasing productivity is one of the main objectives in animal production. Traditional breeding methods have led to increased gains in some traits but gains are not easily attainable in traits with low heritabilities. Exploiting the genetic variations underlying desired phenotypes is the goal of today’s animal producers. Such positive genetic variants must, however, be known before possible application. Consequently, candidate genes of traits of interest have been searched for possible relationships with such traits or to explain reported quantitative trait loci (QTL) for such traits. DNA variants or polymorphisms have been identified in many such genes and their relationships with production traits determined. However, only a few genes have been evaluated, given the wealth of information on reported QTL for production traits, and in most cases genes are only partially investigated. This review presents available information on DNA variants for production traits and discusses steps that are required for effective utilization of this information for successful marker-assisted selection programs.
Similar content being viewed by others
References
Alexander LJ, MacNeil MD, Geary TW, Snelling WM, Rule DC et al (2007) Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population. Anim Genet 38:506–513
Allison CP, Johnson RC, Doumit ME (2005) The effects of halothane sensitivity on carcass composition and meat quality in HAL-1843-normal pigs. J Anim Sci 83:671–678
Amigo L, Recio I, Ramos M (2000) Genetic polymorphism of ovine milk protein: its influence on technological properties of milk. Int Dairy J 10:135–149
Badaoui B, Serradilla JM, Tomàs A, Urrutia B, Ares JL et al (2007a) Goat acetyl-coenzyme A carboxylase α: molecular characterization, polymorphism, and association with milk traits. J Dairy Sci 90:1039–1043
Badaoui B, Serradilla JM, Tomàs A, Urrutia B, Ares JL et al (2007b) Identification of two polymorphisms in the goat lipoprotein gene and their association with milk traits. J Dairy Sci 90:3012–3017
Banos G, Woolliams JA, Woodward BW, Forbes AB, Coffey MP (2008) Impact of single nucleotide polymorphisms in leptin, leptin receptor, growth hormone receptor, and diacylglycerol acyltransferase (DGAT1) gene loci on milk production, feed and body energy traits of UK dairy cows. J Dairy Sci 91:3190–32000
Barendse W (1997) Assessing lipid metabolism. Patent publication W09923248, Patent US 6383751. Available at http://ep.espacenet.com
Barendse W, Harrison BE, Hawken RJ, Ferguson DM, Thompson JM et al (2007a) Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle. Genetics 176:2601–2610
Barendse W, Reverter A, Bunch RJ, Harrison BE, Barris W et al (2007b) A validated whole-genome association study of efficient food conversion in cattle. Genetics 176:1893–1905
Bennewitz J, Reinsch N, Paul S, Looft C, Kaupe B et al (2004) The DGAT1 K232A mutation is not solely responsible for the milk production QTL on bovine chromosome 14. J Dairy Sci 87:431–442
Bevilacqua C, Ferranti P, Garro G, Veltri C, Lagonigro R et al (2002) Interallelic recombination is probably responsible for the occurrence of a new alpha (s1)-casein variant found in the goat species. Eur J Biochem 269, 1293–1303
Blott S, Kim JJ, Moisio S, Schmidt-Küntzel A, Cornet A et al (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 163:253–266
Bodin L, Di Pasquale E, Fabre S, Bontoux M, Monget P et al (2007) A novel mutation in the bone morphogenetic protein 15 gene causing defective protein secretion is associated with both increased ovulation rate and sterility in Lacaune sheep. Endocrinology 148:393–400
Boichard D, Grohs C, Bourgeois F, Cerqueira F, Faugeras R et al (2003) Detection of genes influencing economic traits in three French dairy cattle breeds. Genet Sel Evol 35:77–101
Boucher D, Palin MF, Castonguay F, Gariepy C, Pothier F (2006) Detection of polymorphisms in the ovine leptin (LEP) gene: association of single nucleotide polymorphism with muscle growth and meat quality traits. Can J Anim Sci 86:31–35
Bouniol C, Brignon G, Mahé MF, Printz C (1994) Biochemical and genetic analysis of variant C of caprine αS2-casein. Anim Genet 25:173–177
Brym P, Kamiński S, Wójcik E (2005) Nucleotide sequence polymorphism within exon 4 of the bovine prolactin gene and its associations with milk performance traits. J Appl Genet 45:176–185
Buchanan FC, Fitzsimmons CJ, Van Kessel AG, Thue TD, Winkelman-Sim DC et al (2002) Association of a missense mutation in the bovine leptin gene with carcass fat content and leptin mRNA levels. Genet Sel Evol 34:105–116
Buchanan FC, Van Kessel AG, Waldner C, Christensen DA, Laarveld B et al (2003) An association between leptin single nucleotide polymorphism and milk and protein yield. J Dairy Sci 86:3164–3166
Buske B, Brunsch C, Zeller K, Reinecke P, Brockmann G (2005) Analysis of properdin (BF) genotypes associated with litter size in a commercial pig cross population. J Anim Breed Genet 122:259–2623
Buske B, Sternstein I, Brockmann G (2006a) QTL and candidate genes for fecundity in sows. Anim Reprod Sci 95:167–183
Buske B, Sternstein I, Reißmann M, Brockmann G (2006b) Detection of novel single-nucleotide polymorphisms (SNPs) in the CYP21 gene and association analysis of two SNPs for CYP21 and ESR2 with litter size in a commercial sow population. J Anim Breed Genet 123:343–348
Caroli A, Chiatti F, Chessa S, Rignanese D, Bolla P et al (2006) Focusing on the goat casein complex. J Dairy Sci 89:3178–3187
Caroli A, Chiatti F, Chessa S, Rignanese D, Ibeagha-Awemu EM et al (2007) Characterization of the casein gene complex in West African goats and description of a new αS1-casein polymorphism. J Dairy Sci 90:2989–2996
Casas E, White SN, Riley DG, Smith TP, Brenneman RA et al (2005) Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle. J Anim Sci 83:13–19
Charlier C, Coppieters W, Rollin F, Desmecht D, Agerholm JS et al (2008) Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet 40:449–454
Cheong HS, Yoon DH, Kim LH, Park BL, Choi YH et al (2006) Growth hormone-releasing hormone (GHRH) polymorphisms associated with carcass traits of meat in Korean cattle. BMC Genet 7:35
Chiatti F, Chessa S, Bolla P, Cigalino G, Caroli A et al (2007) Effect of κ-casein polymorphism on milk composition in the Orobica goat. J Dairy Sci 90:1962–1966
Choudhary V, Kumar P, Bhattacharya TK, Bhushan B, Sharma A et al (2007) DNA polymorphism of insulin-like growth factor- binding protein-3 and its association with birth weight and body weight in cattle. J Anim Breed Genet 124:29–34
Cho S, Park TS, Yoon DH, Cheong HS, Namgoong S et al (2008) Identification of genetic polymorphisms in FABP3 and FABP4 and putative association with back fat thickness in Korean native cattle. BMB Rep 41:29–34
Chu MX, Liu ZH, Jiao CL, He YQ, Fang L et al (2007) Mutations in BMPR-IB and BMP-15 genes are associated with litter size in small tailed Han sheep (Ovis aries). J Anim Sci 85:598–603
Chung ER, Rhim TJ, Han SK (1996) Associations between PCR-RFLP markers of growth hormone and prolactin genes and production traits in dairy cattle. Korean J Anim Sci 38:321–336
Ciobanu DC, Bastiaansen JWM, Lonergan SM, Thomsen H, Dekkers JCM et al (2004) New alleles in calpastatin gene are associated with meat quality traits in pigs. J Anim Sci 82:2829–2839
Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X et al (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38:813–818
Cobanoglu O, Zaitoun I, Chang YM, Shook GE, Khatib H (2006) Effects of the signal transducer and activator of transcription 1 (STAT1) gene on milk production traits in Holstein dairy cattle. J Dairy Sci 89:4433–4437
Conde SB, Guimaraes SEF, Euclydes RF, Silva LOC, Euclides Fildo K (2000) Marcadores moleculares associados com crescimento em bovinos. Rev Bras Repro Anim 25:485–486
Cosenza G, Illario R, Rando A, Di Gregorio P, Masina P et al (2003) Molecular characterization of the goat CSN1S101 allele. J Dairy Res 70:237–240
Cosenza G, Pauciullo A, Colimoro L, Mancusi A, Rando A et al (2007) An SNP in the goat CSN2 promoter is associated with the absence of β-casein in milk. Anim Genet 38:655–658
Curi RA, Palmieri DA, Suguisawa L, de Oliveira HN, Silveira AC et al (2006) Growth and carcass traits associated with GH1/AluI and POU1F1/HinfI gene polymorphisms in Zebu and crossbred beef cattle. Genet Mol Biol 29:56–61
Davis GH (2005) Major genes affecting ovulation rate in sheep. Genet Sel Evol 37(Suppl. 1):S11–S23
Davis GH, McEwan JC, Fennessy PF, Dodds KG (1995) Discovery of the Inverdale gene (FecX). Proc NZ Soc Anim Prod 55:289–290
De Faria DA, Guimarães SEF, Lopes PS, Pires AV, Paiva SR et al (2006) Association between G316A growth hormone polymorphisms and economic traits in pigs. Genet Mol Biol 29:634–640
Dekkers JCM, Hospital F (2002) The use of molecular genetics in improvement of agricultural populations. Nat Rev Genet 3:22–32
Dekkers JCM, van de Werf JHJ (2007) Strategeies, limitations and opportunities for marker-assisted selection in livestock. In: Guimarães E, Ruane J, Scherf B, Sonnino A, Dargie J (eds) Marker-assisted selection: current status and future perspectives in crops, livestock, forestry and fish. Food and Agricultural Organization, Rome, pp 167-184. Available at http://www.fao.org/docrep/010/a1120e/a1120e00.htm
Den Dunnen JT, Antonarakis SE (2000) Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 15:7–12
Di Stasio L, Brugiapaglia A, Destefanis G, Albera A, Sartore S (2003) GH1 as a candidate gene for variability of meat production traits in Piedmontese cattle. J Anim Breed Genet 120:358–361
Dybus A (2002) Associations of growth hormone (GH) and prolactin (PRL) genes polymorphisms with milk production traits in Polish Black-and- White cattle. Animal Science Papers and Reports, vol 20. Institute of Genetics and Animal Breeding, Jastrzebiec, Poland, pp 203-212
Falaki M, Prandi A, Corradini C, Sneyers M, Gengler N et al (1997) Relationships of growth hormone gene and milk protein polymorphisms to milk production traits in Simmental cattle. J Dairy Res 64:47–56
Farrell HM Jr, Jimenez-Flores R, Bleck GT, Brown EM, Butler JE (2004) Nomenclature of the proteins of cow’s milk- sixth revision. J Dairy Sci 87:1641–1674
Ferranti P, Malorni A, Nitti G, Laezza P, Pizzano R et al (1995) Primary structure of ovine αS1-caseins: localization of phosphorylation sites and characterization of genetic variants A, C and D. J Dairy Res 62:281–296
Fitzsimmons CJ, Schmutz SM, Bergen RD, McKinnon JJ (1998) A potential association between the BM1500 microsatellite and fat deposition in beef cattle. Mamm Genome 9:432–434
Folch JM, Dovc P, Medrano JF (1999) Differential expression of bovine b-lactoglobulin A and B promoter variants in transiently transfected HC11 cells. J Dairy Res 66:537–544
Formaggioni P, Summer A, Malacarne M, Mariani P (1999) Milk protein polymorphism: detection and diffusion of the genetic variants in Bos genus. Ann Fac Med Vet Univ Parma XIX:127–165
Franco MM, Antunes RC, de Oliveira KM, Pereira CD, Biase FH et al (2005a) Association of PIT1 gene polymorphism with growth hormone mRNA levels in pig pituitary glands. Genet Mol Biol 28:16–21
Franco MM, Antunes RC, Silva HD, Goulart LR (2005b) Association of PIT1, GH and GHRH polymorphisms with performance and carcass traits in Landrace pigs. J Appl Genet 46:195–200
Fujii J, Ostu K, Zorzato F, Leon SD, Khama VK et al (1991) Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. Science 253:448–451
Galloway SM, McNatty KP, Cambridge LM, Laitinen MPE, Juengel JL et al (2000) Mutations in an oocyte-derived growth factor gene (BMP15) cause increased ovulation rate and infertility in a dosage-sensitive manner. Nat Genet 25:279–283
Ge W, Davis ME, Hines HC, Irvin KM, Simmen RCM (2001) Association of genetic marker with blood serum insulin-like growth factor-I concentration and growth traits in Angus cattle. J Anim Sci 79:1757–1762
Gerbens F, Rettenberger G, Lenstra JA, Veerkamp JH, te Pas MFW (1997) Characterization, chromosomal localization and genetic variation of the porcine heart fatty acid-binding protein gene. Mamm Genome 8:328–332
Gerbens F, de Konig DJ, Harders FL, Meuwissen TH, Janss LL et al (2000) The effect of adipocyte and heart fatty acid-binding protein gene on intramuscular fat and back fat content in Meishan crossbred pigs. J Anim Sci 78:552–559
Gerbens F, Verburg FJ, Van Moerkerk HT, Engel B, Buist W et al (2001) Associations of heart and adipocyte fatty acid-binding protein gene expression with intramuscular fat content in pigs. J Anim Sci 79:347–354
Girard T, Urwyler A, Censier K, Mueller CR, Zorzato F et al (2001) Genotype-phenotype comparison of the Swiss malignant hyperthermia population. Hum Mutat 449:1–8
Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298:2345–2349
Grisart B, Coppieters W, Farnir F, Karim L, Ford C et al (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 12:222–231
Grisart B, Farnir F, Karim L, Cambisano N, Kim JJ et al (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 101:2398–2403
Grobet L, Martin LJ, Poncelet D, Pirottin D, Brouwers B et al (1997) A deletion in the bovine myostatin gene causes double-muscled phenotype in cattle. Nat Genet 17:71–74
Grobet L, Poncelet D, Royo LJ, Brouwers B, Pirottin D et al (1998) Molecular definition of an allelic series of mutations disrupting the myostatin function and causing double-muscling in cattle. Mamm Genome 9:210–213
Grosclaude F, Martin P (1997) Genetic polymorphisms in the goat. Proc IDF Milk Protein Polymorphism Seminar II, Palmerston North, New Zealand. International Dairy Federation, Brussels, pp 241–253
Hanrahan JP, Gregan SM, Mulsant P, Mullen M, Davis GH et al (2004) Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both increased ovulation rate and sterility in Cambridge and Belclare sheep (Ovis aries). Biol Reprod 70:900–909
Hayes BJ, Goddard ME (2008) Technical note: prediction of breeding values using marker derived relationship matrices. J Anim Sci 86:2089–2092
Hayes B, Hagesæther N, Ådnøy T, Pellerud G, Berg PR et al (2006) Effects on production traits of haplotypes among casein genes in Norwegian goats and evidence for a site of preferential recombination. Genetics 174:455–464
Hernández-Sánchez J, Visscher P, Plastow G, Haley C (2003) Candidate gene analysis for quantitative traits using the transmission disequilibrium test: the example of the melanocortin-4 receptor in pigs. Genetics 164:637–644
Houde AA, Murphy BD, Mathieu O, Bordignon V, Palin MF (2008) Characterization of swine adiponectin and adiponectin receptor polymorphisms and their association with reproductive traits. Anim Genet 39:249–257
Houston RD, Rance KA, Sutcliffe E, Archibald AL, Haley CS (2008) The cholecystokinin type A receptor g.179A>G polymorphism affects feeding rate. Anim Genet 39:187–188
Ibeagha-Awemu EM, Kgwatalala P, Ibeagha AE, Zhao X (2008) A critical analysis of disease associated DNA polymorphisms in the genes of cattle, goat, sheep and pig. Mamm Genome 19:226–245
Jankowiak H (2005) Effect of colipase gene (CLPS) polymorphisms on carcass and meat quality in pigs. Folia Biol 53:91–94
Jansà-Pérez M, Leroux C, Sànchez Bonastre A, Martin P (1994) Occurrence of a LINE element sequence in the 3′UTR of the goat αS1-casein E allele associated with a reduced protein synthesis. Gene 147:179–187
Jokubka R, Maak S, Kerziene S, Swalve HH (2006) Association of melanocortin 4 receptor (MC4R) polymorphism with performance traits in Lithuanian White pigs. J Anim Breed Genet 123:17–22
Kamiński S, Brym P, Ruść A, Wójcik E, Ahman A et al (2006) Associations between milk performance traits in Holstein cows and 16 candidate SNPs identified by arrayed primer extension (APEX) microarray. Anim Biotechnol 17:1–11
Kapelański W, Grajewska A, Kurył J, Bocian M, Wyszyńska-Koko J et al (2005) Polymorphism in the coding and non-coding regions of the MyoD gene family and meat quality in pigs. Folia Biol (Kraków) 53(Suppl):44–49
Karpf AR (2007) Epigenomic reactivation screening to identify genes silenced by DNA hypermethylation in human cancer. Curr Opin Mol Ther 9:231–241
Kgwatalala PM, Ibeagha-Awemu EM, Mustafa AF, Zhao X (2008) Influence of stearoyl-CoA desaturase (SCD) genotype and stage of lactation on desaturase indices and fatty acid composition of Canadian Jersey cows. J Dairy Sci (accepted)
Khatib H, Leonard SD, Schutzkus V, Luo Chang YM (2006) Association of the OLR1 gene with milk composition in Holstein dairy cattle. J Dairy Sci 89:1753–1760
Khatib H, Rosa GJ, Weigel K, Schiavini F, Santus E et al (2007a) Additional support for an association between OLR1 and milk fat traits in cattle. Anim Genet 38:308–310
Khatib H, Zaitoun I, Wiebelhaus-Finger J, Chang YM, Rosa GJ (2007b) The association of bovine PPARGC1A and OPN genes with milk composition in two independent Holstein cattle populations. J Dairy Sci 90:2966–2970
Khatib H, Monson RL, Schutzkus V, Kohl DM, Rosa GJ et al (2008) Mutations in the STAT5A gene are associated with embryonic survival and milk composition in cattle. J Dairy Sci 91:784–793
Kijas JW, McCulloch R, Hocking Edwards JE, Hutton Oddy V, Hong Lee S et al (2007) Evidence for multiple alleles affecting muscling and fatness at the ovine GDF8 locus. BMC Genet 8:80
Kim KS, Larsen NJ, Short T, Plastow G, Rothschild MF (2000) A missense variant of porcine melanocortin-4 receptor (MC4R) gene is associated with fatness, growth and feed intake traits. Mamm Genome 11:131–135
Kim KS, Reecy JM, Hsu WH, Anderson LL, Rothschild MF (2004) Functional and phylogenetic analyses of a melanocortin-4 receptor mutation in domestic pig. Livest Prod Sci 26:75–86
Koohmaraie M (1996) Biochemical factors regulating the toughening and tenderization process of meat. Meat Sci 43:S193–S201
Kühn C, Thaller G, Winter A, Bininda-Emonds ORP, Kaupe B et al (2004) Evidence of multiple alleles at the DGAT1 locus better explains a QTL with major effect on milk fat content in cattle. Genetics 167:1873–1881
Kuryl J, Pierzchala M, Kapelanski W, Bocian M, Grajewska S (2001) Polymorphism of GH, LEP, COL, LIPE genes in chosen breeds of pigs in Poland and their influence on quality of carcass. XIVth Conference of the Polish Genetic Society (PTG), Poznań, 11–13 June 2001, Book of Abstracts, p 63
Kuss AW, Gogol J, Geldermann H (2003) Associations of a polymorphic AP-2 binding site in the 5′-flanking region of the bovine β-lactoglobulin gene with milk proteins. J Dairy Sci 86:2213–2218
Kuss AW, Gogol J, Bartenschlager H, Geldermann H (2005) Polymorphic AP-1 binding site in bovine CSN1S1 shows quantitative differences in protein binding associated with milk protein expression. J Dairy Sci 88:2246–2252
Le Hir H, Nott A, Moore MJ (2003) How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci 28:215–220
Leroux C, Mazure N, Martin P (1992) Mutations away from splice site recognition sequences might cis-modulate alternative splicing of goat αS1-casein transcripts. Structural organization of the relevant gene. J Biol Chem 267:6147–6157
Leonard S, Khatib H, Schutzkus V, Chang YM, Maltecca C (2005) Effects of the osteopontin gene variants on milk production traits in Dairy cattle. J Dairy Sci 88:4083–4086
Lewin HA, Schmitt K, Hubert R, Van Eijk MJ, Arnheim N (1992) Close linkage between bovine prolactin and Bola-DRB3 genes: genetic mapping in cattle by single sperm typing. Genomics 13:44–48
Li N, Zhao YF, Xiao L, Zhang FJ, Chen YZ, et al (1998) Candidate gene approach for identification of genetic loci controlling controlling litter size in swine. Proceedings of the 6th World Congress on Genetics Applied to Livestock Production, Armidale, NSW, Australia, 11–16 January 1998, vol 26, pp 183–186
Li S, Creshaw EB, Rawson EJ, Simmons DM, Swanson LW et al (1990) Dwarf locus mutants lacking three pituitary cell types result from mutations in the POU-domain gene Pit-1. Nature 347:528–533
Lin Z, Lou Y, Peacock J, Squires EJ (2005) A novel polymorphism in the 5′ untranslated region of the porcine cytochrome b5 (CYB5) gene is associated with decreased fat androstenone level. Mamm Genome 16:367–373
Lum LS, Dovc P, Medrano JF (1997) Polymorphisms of bovine b-lactoglobulin promoter and differences in the binding affinity of activator protein-2 transcription factor. J Dairy Sci 80:1389–1397
Macciotta NPP, Mele M, Pagnacco G, Cassandro M, Conte G et al (2007) Stearoly-CoA desaturase gene polymorphism and milk production traits in Italian Holsteins. J Dairy Sci 90(Suppl 1):596
Macciotta NPP, Mele M, Conte G, Serra A, Cassandro M et al (2008) Association between a polymorphism at the stearoyl CoA desaturase locus and milk production traits in Italian Holsteins. J Dairy Sci 91:3184–3189
Madeja Z, Adamowicz T, Chmurzynska A, Jankowski T, Melonek J et al (2004) Effect of leptin gene polymorphisms on breeding value of milk production traits. J Dairy Sci 87:3925–3927
Malveiro E, Marques PX, Santos IC, Belo C, Cravador A (2001) Association between SSCPs at Algarvia goat GH gene and milk traits. Arch Zootec 50:49–57
Manfredi E, Serradilla JM, Leroux C, Martin P, Sánchez A (2000) Genetics for milk production. In: Proceedings of the 7th International Conference on Goats, Poitiers, France, 15-18 May 2000. INRA, Paris, vol 2, pp 191-196
Martin P, Ollivier-Bousquet M, Grosclaude F (1999) Genetic polymorphism of caseins: a tool to investigate casein micelle organization. Int Dairy J 9:163–171
Martin P, Szymanowska M, Zwierzchowski L, Leroux C (2002) The impact of genetic polymorphisms on the protein composition of ruminant milks. Reprod Nutr Dev 42:433–459
Martinez-Royo A, Jurado JJ, Smulders JP, Martí JI, Alabart JL et al (2008) A deletion in the bone morphogenetic protein 15 gene causes sterility and increased prolificacy in Rasa Aragonesa sheep. Anim Genet 39:294–297
Matsumoto M, Fuduka W, Circolo A, Goellner J, Strauss-Schoenberger J et al (1997) Abrogation of the alternative compliment pathway by targeted deletion of murine factor B. Immunology 94:8720–8725
McPherron AC, Lee S (1997) Double muscling in cattle due to mutations in the myostatin gene. Proc Natl Acad Sci USA 95:12457–12461
Michal JJ, Zhang ZW, Gaskins CT, Jiang Z (2006) The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu × limousine F2 crosses. Anim Genet 37:400–402
Mohr U, Koczan D, Linder D, Hobom G, Erhardt G (1994) A single point mutation results in A allele-specific exon skipping in the bovine αS1-casein mRNA. Gene 143:187–192
Moore RK, Shimasaki S (2005) Molecular biology and physiological role of the oocyte factor, BMP-15. Mol Cell Endocrinol 234:67–73
Morris CA, Cullen NG, Glass BC, Hyndman DL, Manley TR et al (2007) Fatty acid synthase effects on bovine adipose fat and milk fat. Mamm Genome 18:64–74
Mulsant P, Lecerf F, Fabre S, Schibler L, Monget P et al (2001) Mutation in bone morphogenetic protein receptor-IB is associated with increased ovulation rate in Booroola Merino ewes. Proc Natl Acad Sci USA 98:5104–5109
Muñoz G, Alves E, Fernández A, Óvilo C, Barragán C (2007a) QTL detection on porcine chromosome 12 for fatty-acid composition and association an alyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes. Anim Genet 38:639–646
Muñoz G, Ovilo C, Estelle J, Silio L, Fernandez A et al (2007b) Association with litter size of new polymorphisms on ESR1 and ESR2 genes in a Chinese-European pig line. Genet Sel Evol 39:195–206
Naqvi AN (2007) Application of molecular genetics technologies in livestock production: potentials for developing countries. Advan Biol Res 1:72–84
Nelson WG, Yegnasubramanian S, Agoston AT, Bastian PJ, Lee BH et al (2007) Abnormal DNA methylation, epigenetics, and prostate cancer. Front Biosci 12:4254–4266
Neveu C, Mollé D, Morena J, Martin P, Léonid L (2002) Heterogeneity of caprine beta-casein elucidated by RP-HPLC/MS: genetic variants and phosphorylation. J Protein Chem 21:557–567
Ng-Kwai-Hang KF (2006) Genetic variants of milk proteins and their effects on the yield and quality of cheese. Perspect Agric Vet Sci Nutr Nat Resources 56:1–11
Nkrumah JD, Li C, Yu J, Hansen C, Keisler DH et al (2005) Polymorphisms in the bovine leptin promoter associated with serum leptin concentration, growth, feed intake, feeding behaviour, and measures of carcass merit. J Anim Sci 83:20–28
O’Brien PJ, MacLennan DH (1992) Application in the swine industry of a DNA-based test for porcine stress syndrome. Proc Am Assoc Swine Pract 433-435
Otsuka F, Yao Z, Lee T, Yamamoto S, Erickson GF et al (2000) Bone morphogenetic protein-15. Identification of target cells and biological functions. J Biol Chem 275:39523–39528
Otsuka F, Yamamoto S, Erickson GF, Shimasaki S (2001) Bone morphogenetic protein-15 inhibits follicle-stimulating hormone (FSH) action by suppressing FSH receptor expression. J Biol Chem 276:11387–11392
Pagani F, Baralle FE (2004) Genomic variants in exons and introns: identifying the splicing spoilers. Nat Rev Genet 5:389–396
Page BT, Casas E, Heaton MP, Cullen NG, Hyndman DL et al (2002) Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. J Anim Sci 80:3077–3085
Page BT, Casas E, Quaas RL, Thallman RM, Wheeler TL et al (2004) Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires. J Anim Sci 82:3474–3481
Peacock J, Lou Y, Lundström K, Squires EJ (2008) The effect of a c.-8G>T polymorphism on the expression of cytochrome b5A and boar taint in pigs. Anim Genet 39:15–21
Pereira AP, de Alencar MM, de Oliveira HN, Almeida DR (2005) Association of GH and IG-1 polymorphisms with growth traits in a synthetic beef cattle breed. Genet Mol Biol 28:230–236
Persuy MA, Printz C, Medrano JF, Mercier JC (1999) A single nucleotide deletion resulting in a premature stop codon in associated with marked reduction of transcripts from a goat β-casein null allele. Anim Genet 30:444–451
Pirisi A, Piredda G, Papoff CM, Di Salvo R, Pintus S et al (1999) Effects of sheep αs1-casein CC, CD and DD genotypes on milk composition and cheesemaking properties. J Dairy Res 66:409–419
Pollak EJ (2005) Application and impact of new genetic technologies on beef cattle breeding: a ‘real world’ perspective. Aust J Exp Agric 45:739–748
Prinzenberg EM, Weimann C, Brandt H, Bennewitz J, Kalm E et al (2003) Polymorphism of the bovine CSN1S1 promoter: linkage mapping, intragenic haplotypes, and effects on milk production traits. J Dairy Sci 86:2696–2705
Ramunno L, Mariani P, Pappalardo M, Rando A, Capuano M, et al. (1995) Un gene ad effetto maggiore sul contenuto di casein β nel latte di capra. In: Proceedings of the XIth Congress of the Italian National Science Association of Animal Production (ASPA), Grado, Italy, 19–22 June, pp 185–186
Ramunno L, Cosenza G, Pappalardo M, Longobardi E, Gallo D et al (2001a) Characterization of two new alleles at the goat CSN1S2 locus. Anim Genet 32:264–268
Ramunno L, Longobardi E, Pappalardo M, Rando A, Di Gregorio P et al (2001b) An allele associated with a non-dectable amount of αs2-casein in goat milk. Anim Genet 32:19–26
Ramunno L, Cosenza G, Rando A, Pauciullo A, Illario R et al (2005) Comparative analysis of gene sequence of goat CSN1S1 F and N alleles and characterization of CSN1S1 transcript variants in mammary gland. Gene 345:289–299
Rando A, Ramunno L, Masina P (2000) Mutations in casein genes. Zoot Nutr Anim 26:105–114
Rempel WE, Lu M, Kandelgy SE, Kennedy CF, Irvin LR et al (1993) Relative accuracy of the halothane challenge test and a molecular genetic test in detecting the gene for porcine stress syndrome. J Anim Sci 71:1395–1399
Renaville R, Gengler N, Parmentier I, Moryiaux F, Massart S et al (1997) Pit-1 gene HinfI RFLP and growth traits in double-muscled Belgian Blue cattle. J Anim Sci 75(Suppl 1):146 [abstract]
Ron M, Weller JI (2007) From QTL to QTN identification in livestock – winning by points rather than knock-out: a review. Anim Genet 38:429–439
Rothschild MF, Jacobson C, Vaske D, Tuggle C, Wang L et al (1996) The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proc Natl Acad Sci USA 93:201–205
Rothschild MF, Vincent AL, Tuggle CK, Evans G, Short TH et al (1998) A mutation in the prolactin receptor gene is associated with increased litter size in pigs. Anim Genet 29:60–74
Roy R, Gautier M, Hayes H, Laurent P, Eggen A et al (2001) Assignment of the fatty acid synthase (FASN) gene to bovine chromosome 19 by in situ hybridization and confirmation by hybrid somatic cell mapping. Cytogenet Cell Genet 93:141–142
Roy R, Ordavas L, Zaragoza P, Romero A, Moreno C et al (2006) Association of polymorphisms in the bovine FASN gene with milk-fat content. Anim Genet 37:215–218
Sánchez A, Ilahi H, Manfredi E, Serradilla JM (2005) Potential benefit from using the αS1-casein genotype information in a selection scheme for dairy goats. J Anim Breed Genet 122:21–29
Sanders K, Bennewitz J, Reinsch N, Thaller G, Prinzenberg EM et al (2006) Characterization of the DGAT1 mutations and CSN1S1 promoter in German Angeln dairy cattle population. J Dairy Sci 89:3164–3174
Schenkel FS, Miller SP, Ye X, Moore SS, Nkrumah JD et al (2005) Association of single nucleotide polymorphisms in the leptin gene with carcass and meat quality traits of beef cattle. J Anim Sci 83:2009–2020
Schennink A, Stoop WM, Visker MH, Heck JM, Bovenhuis H et al (2007) DGAT1 underlies large genetic variation in milk-fat composition of dairy cows. Anim Genet 38:467–473
Schlee P, Graml R, Schallemberger E, Schams D, Rottmann O et al (1994) Growth hormone and insulin-like growth factor-1 concentrations in bulls of various growth hormone genotypes. Theor Appl Genet 88:497–500
Seeley RJ, Yagaloff KA, Fisher SL, Burn P, Thiele TE et al (1997) Melanocortin receptors in leptin effects. Nature 390:349
Sellick GS, McGrice H, Bouman A, Kruk B, Bottema CD (2006) Polymorphisms within the cattle myostatin gene. Proc 30th Int Congr Anim Genet 30:A494
Sellick GS, Pitchford WS, Morris CA, Cullen NG, Crawford AM et al (2007) Effect of myostatin F94L on carcass yield in cattle. Anim Genet 38:440–446
Sherman EL, Nkrumah JD, Murdoch BM, Moore SS (2008a) Identification of polymorphisms influencing feed intake and efficiency in beef cattle. Anim Genet 39:225–231
Sherman EL, Nkrumah JD, Murdoch BM, Li C, Wang Z et al (2008b) Polymorphisms and haplotypes in the bovine neuropeptide Y, growth hormone receptor, ghrelin, insulin-like growth factor 2, and uncoupling proteins 2 and 3 genes and their associations with measures of growth, performance, feed efficiency, and carcass merit in beef cattle. J Anim Sci 86:1–16
Smith SJ, Cases S, Jensen DR, Chen HC, Sande E (2000) Obesity resistance and multiple mechanisms of triglyceride synthesis in mice lacking DGAT. Nat Genet 25:87–90
Song C, Gao B, Teng Y, Wang X, Li O et al (2005) Msp1 polymorphisms in the 3rd intron of the swine POU1F1 gene and their associations with growth performance. J Appl Genet 46:285–289
Spelman RJ, Ford CA, McElhinney P, Gregory GC, Snell RG (2002) Characterization of the DGAT1 gene in the New Zealand dairy population. J Dairy Sci 85:3514–3517
Stella A, Panzitta F, Gandini G, Boettcher PJ (2007) Use of linked loci as individuals or haplotypes for marker-assisted breed assignment. Anim Genet 39:8–14
Sun WB, Chen H, Lei CZ, Zan LS, Lei XQ et al (2002) Polymorphism of insulin-like growth factor binding protein-3 gene and its relationship with beef performance of Qinchuan cattle. Anim Biotechnol Bull 8:95–99
Szymanowska M, Malewski T, Zwierzchowski L (2004) Transcription factor binding to variable nucleotide sequences in 5′ flanking regions of bovine casein genes. Int Dairy J 14:103–115
Tambasco DD, Paz CCP, Tambasco-Studart M, Pereira AP, Alencar MM et al (2003) Candidate genes for growth traits in beef cattle crosses Bos taurus × Bos indicus. J Anim Breed Genet 120:51–54
Taniguchi M, Utsugi T, Oyama K, Manmen H, Kobayashi M et al (2004) Genotype of stearoyl-CoA desaturase is associated with fatty acid composition in Japanese black cattle. Mamm Genome 14:142–148
Te Pas MFW, Harders FL, Soumillion A, Born L, Buist W et al (1999) Genetic variation at porcine MYF-5 gene locus. Lack of association with meat production traits. Mamm Genome 10:123–127
Terman A (2005) Effect of the polymorphism of prolactin receptor (PRLR) and leptin (LEP) genes on litter size in Polish pigs. J Anim Breed Genet 22:400–404
Thaller G, Kramer W, Winter A, Kaupe A, Erhardt G et al (2003) Effects of DGAT1 variants on milk production traits in German cattle breeds. J Anim Sci 81:1911–1918
Thomas MG, Enns RM, Shirley KL, Garcia MD, Garrett AJ et al (2007) Associations of DNA polymorphisms in growth hormone and its transcriptional regulators with growth and carcass traits in two populations of Brangus bulls. Genet Mol Res 6:222–237
Tomás A, Casellas J, Ramírez O, Muñoz G, Noguera JL et al (2006) High amino acid variation in the intracellular domain of the pig prolactin receptor (PRLR) and its relation to ovulation rate and piglet survival traits. J Anim Sci 84:1991–1998
Urban T, Kuciel J, Mikolasova R (2002) Polymorphism of genes encoding for ryanodine receptor, growth hormone, leptin and MYC proto-oncogene protein and meat production in Duroc pigs. Czech J Anim Sci 47:411–417
Van den Maagdenberg K, Stinckens A, Claeys E, Seynaeve M, Clinquart A et al (2007) The Asp298Asn missense mutation in the porcine melanocortin-4 receptor (MC4R) gene can be used to affect growth and carcass traits without an effect on meat quality. Animal 1:1089–1098
Van Eenennaam AL (2006) DNA-based biotechnologies. In: Beef Sire Selection Manual. The National Beef Cattle Evaluation Consortium, pp 66-73. Available at http://www.ansci.cornell.edu/nbcec/sire_selection/manual.pdf
Van Laere AS, Nguyen M, Brauschweig M, Nezer C, Collette C et al (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in pig. Nature 425:832–836
Veltri C, Lagonigro R, Pietrolla ÁE, D’Andrea M, Pilla F et al (2000) Molecular characterisation of the goat αs2-casein E allele and its detection in goat breeds of Italy. In: Proceedings of the Seventh International Conference on Goats, Tours, France, 15–18 May 2000, p 727
Viitala S, Szyda J, Blott S, Schulman N, Lidauer M et al (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 173:2151–2164
Vincent AL, Wang L, Tuggle CK, Robic A, Rothschild MF (1997) Prolcatin receptor maps to pig chromosome 16. Mamm Genome 8:793–794
Vincent AL, Evans G, Short TH, Southwood OI, Plastow GS, et al (1998) The prolactin receptor gene is associated with increased litter size in pigs. In: Proceedings of the 6th World Congress on Genetics Applied to Livestock Production, Armidale, NSW, Australia, 11–16 January 1998, vol 27, pp 15–18
Weikard R, Kühn C, Goldammer T, Freyer G, Schwerin M (2005) The bovine PPARGC1A gene: molecular characterization and association of an SNP with variation of milk fat synthesis. Physiol Genomics 21:1–13
White SN, Casas E, Wheeler TL, Shackelford SD, Koohmaraie M et al (2005) A new single nucleotide polymorphism in CAPN1 extends the current tenderness marker test to include Bos indicus, Bos taurus, and crossbred descent. J Anim Sci 83:2001–2008
Wilson T, Wu XY, Juengel JL, Ross IK, Lumsden JM et al (2001) Highly prolific Booroola sheep have a mutation in the intracellular kinase domain of bone morphogenetic protein IB receptor (ALK-6) that is expressed in both oocytes and granulosa cells. Biol Reprod 64:1225–1235
Wimmers K, Murani E, Te Pas MF, Chang KC, Davoli R et al (2007) Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition. Anim Genet 38:474–484
Winter A, Krämer W, Werner FA, Kollers S, Kata S et al (2002) Association of a lysine-232/alanine polymorphism in bovine gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content. Proc Natl Acad Sci USA 99:9300–9305
Xue K, Chen H, Wang S, Cai X, Liu B et al (2006) Effect of genetic variants of the POU1F1 gene on growth traits of Nanyang cattle. Acta Genet Sin 33:901–907
Zhang S, Knight TJ, Reecy JM, Beitz DC (2008) DNA polymorphisms in bovine fatty acid synthase are associated with beef fatty acid composition. Anim Genet 39:62–70
Zhao Q, Davis ME, Hines HC (2004) Associations of polymorphisms in the Pit-1 gene with growth and carcass traits in Angus beef cattle. J Anim Sci 82:2229–2233
Acknowledgments
Financial support was provided by McGill University’s James McGill Professorship Program and by a grant from the Dairy Cattle Genetics Research and Development (DairyGen) Council of Canadian Dairy Network to X. Zhao.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Ibeagha-Awemu, E.M., Kgwatalala, P. & Zhao, X. A critical analysis of production-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig. Mamm Genome 19, 591–617 (2008). https://doi.org/10.1007/s00335-008-9141-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00335-008-9141-x