Hostname: page-component-77c89778f8-cnmwb Total loading time: 0 Render date: 2024-07-19T19:27:51.413Z Has data issue: false hasContentIssue false
  • English
  • Français

Review of QTL mapping results in chickens

Published online by Cambridge University Press:  18 September 2007

P.M. Hocking
P.M. Hocking
Affiliation:
Roslin Institute, Roslin, Midlothian, Scotland, EH25 9PS E-mail: paul.hocking@bbsrc.ac.uk
Get access

Abstract

A review of QTL for production, behaviour and disease resistance traits published to the end of 2004 is presented. QTL were located randomly over the genome and there was little commonality between different studies for similar traits. However, there were several reports of QTL from different experiments in similar regions of chromosomes 1 (at 250 and 450 cM), 4 and 8 and for disease resistance on chromosome 5. Generally there were 6 to 8 QTL affecting the major production traits in experimental breed crosses and collectively they accounted for a substantial proportion of the line difference where this information was provided. The size of typical genome-wide significant effects for production traits was 0.3 to 1.0 phenotypic standard deviations. Genetic effects for growth traits were generally additive whereas about one-third of QTL for other production traits showed significant dominance effects. Variable reporting standards were noted and proposals for minimum published information are presented. Currently there are scientific opportunities for meta-analyses of results from experiments on body weight gain and considerable potential for combining data and results from different studies for other traits in the future.

Keywords

Quantitative Trait Loci (QTL)growthfategg productionegg weightbehaviourfeather peckingdisease resistance
Type
Reviews
Information
World's Poultry Science Journal , Volume 61 , Issue 2 , June 2005 , pp. 215 - 226
Copyright
Copyright © Cambridge University Press 2005

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Buitenhuis, A.J., Rodenburg, T.B., Hierden, Y.M.V., Siwek, M., Cornelissen, S.J.B., Nieuwland, M.G.B., Crooijmans, R.P.M.A., Groenen, M.A.M., Koene, P., Korte, S.M., Bovenhuis, H. and Van Der Poel, J.J. (2003a) Mapping Quantitative Trait Loci affecting feather pecking behavior and stress response in laying hens. Poultry Science 82: 1215–1222.CrossRefGoogle ScholarPubMed
Buitenhuis, A.J., Rodenburg, T.B., Siwek, M., Cornelissen, S.J.B., Nieuwland, M.G.B., Crooijmans, R., Groenen, M.A.M., Koene, P., Bovenhuis, H. and Van Der Poel, J.J. (2003b) Identification of quantitative trait loci for receiving pecks in young and adult laying hens. Poultry Science 82: 1661–1667.CrossRefGoogle Scholar
Buitenhuis, A.J., Rodenburg, T.B., Siwek, M., Cornelissen, S.J.B., Nieuwland, M.G.B., Crooijmans, R., Groenen, M.A.M., Koene, P., Bovenhuis, H. and Van Der Poel, J.J. (2004) Identification of QTLs involved in open-field behavior in young and adult laying hens. Behavior Genetics 34:325–333.CrossRefGoogle Scholar
Bumstead, N. (1998) Genomic mapping of resistance to Marek's disease. Avian Pathology 27: S78–S81.CrossRefGoogle Scholar
Carlborg, Ö., Hocking, P.M., Burt, D.W. and Haley, C.S. (2004) Simultaneous mapping of epistatic QTL in chickens reveals clusters of QTL pairs with similar genetic effects on growth. Genetical Research 83: 197–209.CrossRefGoogle ScholarPubMed
Carlborg, Ö., Kerje, S., Schutz, K., Jacobsson, L., Jensen, P. and Andersson, L. (2003) A global search reveals epistatic interaction between QTL for early growth in the chicken. Genome Organisation 13: 413–421.Google ScholarPubMed
Churchill, G.A. and Doerge, R.W. (1994) Empirical Threshold Values For Quantitative Trait Mapping. Genetics 138: 963–971.CrossRefGoogle ScholarPubMed
Darvasi, A. and Soller, M. (1992) Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus. Theoretical and Applied Genetics 85: 353–359.CrossRefGoogle Scholar
De Koning, D.J., Haley, C.S., Windsor, D., Hocking, P.M., Burt, D.W., Morris, A., Vincent, J. and Griffin, H. (2004) Segregation of QTL for production traits in commercial meat-type chickens. Genetical Research: 211–220.CrossRefGoogle ScholarPubMed
De Koning, D.J., Windsor, D., Hocking, P.M., Burt, D.W., Law, A., Haley, C.S., Morris, A., Vincent, J. and Griffin, H. (2003) QTL detection in commercial broiler lines using candidate regions. Journal of Animal Science 203: 1158–1165.CrossRefGoogle Scholar
Etzel, C.J. and Guerra, R. (2002) Meta-analysis of genetic-linkage analysis of quantitative-trait loci. American Journal of Human Genetics 71: 56–65.CrossRefGoogle ScholarPubMed
Fernando, R.L., Nettleton, D., Southey, B.R., Dekkers, J.C.M., Rothschild, M.F. and Soller, M. (2004) Controlling the proportion of false positives in multiple dependent tests. Genetics 166: 611–619.CrossRefGoogle ScholarPubMed
Hillier, L.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A.M., Delany, M.E., Dodgson, J.B., Chinwalla, A.T., Cliften, P.F., Clifton, S.W., Delehaunty, K.D., Fronick, C., Fulton, R.S., Graves, T.A., Kremitzki, C., Layman, D., Magrini, V., McPherson, J.D., Miner, T.L., Minx, P., Nash, W.E., Nhan, M.N., Nelson, J.O., Oddy, L.G., Pohl, C.S., Randall-Maher, J., Smith, S.M., Wallis, J.W., Yang, S.P., Romanov, M.N., Rondelli, C.M., Paton, B., Smith, J., Morrice, D., Daniels, L., Tempest, H.G., Robertson, L., Masabanda, J.S., Griffin, D.K., Vignal, A., Fillon, V., Jacobbson, L., Kerje, S., Andersson, L., Crooijmans, R.P.M., Aerts, J., Van Der Poel, J.J., Ellegren, H., Caldwell, R.B., Hubbard, S.J., Grafham, D.V., Kierzek, A.M., McLaren, S.R., Overton, I.M., Arakawa, H., Beattie, K.J., Bezzubov, Y., Boardman, P.E., Bonfield, J.K., Croning, M.D.R., Davies, R.M., Francis, M.D., Humphray, S.J., Scott, C.E., Taylor, R.G., Tickle, C., Brown, W.R.A., Rogers, J., Buerstedde, J.M., Wilson, S.A., Stubbs, L., Ovcharenko, I., Gordon, L., Lucas, S., Miller, M.M., Inoko, H., Shiina, T., Kaufman, J., Salomonsen, J., Skjoedt, K., Wong, G.K.S., Wang, J., Liu, B., Wang, J., Yu, J., Yang, H.M., Nefedov, M., Koriabine, M., Dejong, P.J., Goodstadt, L., Webber, C., Dickens, N.J., Letunic, I., Suyama, M., Torrents, D., Von Mering, C., Zdobnov, E.M., Makova, K., Nekrutenko, A., Elnitski, L., Eswara, P., King, D.C., Yang, S., Tyekucheva, S., Radakrishnan, A., Harris, R.S., Chiaromonte, F., Taylor, J., He, J.B., Rijnkels, M., Griffiths-Jones, S., Ureta-Vidal, A., Hoffman, M.M., Severin, J., Searle, S.M.J., Law, A.S., Speed, D., Waddington, D., Cheng, Z., Tuzun, E., Eichler, E., Bao, Z.R., Flicek, P., Shteynberg, D.D., Brent, M.R., Bye, J. M., Huckle, E.J., Chatterji, S., Dewey, C., Pachter, L., Kouranov, A., Mourelatos, Z., Hatzigeorgiou, A.G., Paterson, A.H., Ivarie, R., Brandstrom, M., Axelsson, E., Backstrom, N., Berlin, S., Webster, M.T., Pourquie, O., Reymond, A., Ucla, C., Antonarakis, S.E., Long, M.Y., Emerson, J.J., Betran, E., Dupanloup, I., Kaessmann, H., Hinrichs, A.S., Bejerano, G., Furey, T.S., Harte, R.A., Raney, B., Siepel, A., Kent, W.J., Haussler, D., Eyras, E., Castelo, R., Abril, J.F., Castellano, S., Camara, F., Parra, G., Guigo, R., Bourque, G., Tesler, G., Pevzner, P.A., Smit, A., Fulton, L.A., Mardis, E.R. and Wilson, R.K. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695–716.Google Scholar
Ikeobi, C.O.N., Woolliams, J.A., Morrice, D.R., Law, A.S., Windsor, D., Burt, D.W. and Hocking, P.M. (2002) Quantitative Trait Loci affecting fatness in the chicken. Animal Genetics 33: 421–425.CrossRefGoogle ScholarPubMed
Ikeobi, C.O.N., Woolliams, J.A., Morrice, D.R., Law, A., Windsor, D., Burt, D.W. and Hocking, P.M. (2004) Quantitative trait loci for meat yield and muscle distribution in a broiler layer cross. Livestock Production Science 87:143–151.CrossRefGoogle Scholar
Jennen, D.G.J., Vereijken, A.L.J., Bovenhuis, H., Crooijmans, R., Veenendaal, A., Van Der Poel, J.J. and Groenen, M.A.M. (2004) Detection and localization of quantitative trait loci affecting fatness in broilers. Poultry Science 83: 295–301.CrossRefGoogle ScholarPubMed
Kaiser, M.G. and Lamont, S.F. (2002) Microsatellites linked to Salmonella enterica serovar enteritidis burden in spleen and cecal content of young F-1 broiler-cross chicks. Poultry Science 81: 657–663.CrossRefGoogle Scholar
Keeling, L., Anderson, L., Schutz, K.E., Kerje, S., Fredriksson, R., Carlborg, O., Cornwallis, C.K., Pizzari, T. and Jensen, P. (2004) Chicken genomics: Feather-pecking and victim pigmentation. Nature 431: 645–646.CrossRefGoogle ScholarPubMed
Kerje, S., Carlborg, O., Schutz, K., Jacobsson, L., Hartmann, C., Jensen, P. and Andersson, L. (2003) The two-fold difference in adult size between Red Junglefowl and White Leghorn chickens is largely explained by a limited number of QTL. Animal Genetics 34: 264–274.CrossRefGoogle Scholar
Lander, E. and Kruglyak, L. (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genetics 11: 241–247.CrossRefGoogle ScholarPubMed
Lohmueller, K.E., Pearce, C.L., Pike, M., Lander, E.S. and Hirschhorn, J.N. (2003) Metaanalysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nature Genetics 33:177–182.CrossRefGoogle ScholarPubMed
Mariani, P., Barrow, P.A., Cheng, H.H., Groenen, M.A.M., Negrini, R. and Bumstead, N. (2001) Localization to chicken Chromosome 5 of a novel locus determining salmonellosis resistance. Immunogenetics 53: 786–791.CrossRefGoogle ScholarPubMed
Muranty, H. and Goffinet, B. (1997) Selective genotyping for location and estimation of the effect of a quantitative trait locus. Biometrics 53:629–643.CrossRefGoogle Scholar
Sasaki, O., Odawara, S., Takahashi, H., Nirasawa, K., Oyamada, Y., Yamamoto, R., Ishii, K., Nagamine, Y., Takeda, H., Kobayashi, E. and Furukawa, T. (2004) Genetic mapping of quantitative trait loci affecting body weight, egg character and egg production in F2 intercross chickens. Animal Genetics 35:188–194.CrossRefGoogle ScholarPubMed
Sax, K. (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8: 552–560.CrossRefGoogle ScholarPubMed
Schmid, M., Nandra, I., Guttenbach, M., Steinlein, C., Hoehn, H., Schartl, M., Haaf, T., Weigend, S., Fries, R., Buerstedde, J.M., Wimmers, K., Burt, D.W., Smith, J., A'Hara, S., Law, A., Griffin, D.K., Bumstead, N., Kaufman, J., Thomson, P.A., Burke, T., Groenen, M.A.M., Crooijmans, R.P.M.A., Vignal, A., Fillon, V., Morisson, M., Pitel, F., Tixier-Boichard, M., Ladjali-Mohammedi, K., Hillel, J., Maki-Tanila, A., Cheng, H.H., Delany, M.E., Burnside, J. and Mizuno, S. (2000) First report on chicken genes and chromosomes 2000. Cytogenetics and Cell Genetics 90: 169–218.CrossRefGoogle ScholarPubMed
Schutz, K., Kerje, S., Carlborg, O., Jacobsson, L., Andersson, L. and Jensen, P. (2002) QTL analysis of a Red Junglefowl x White Leghorn intercross reveals trade-off in resource allocation between behavior and production traits. Behavior Genetics 32: 423–433.CrossRefGoogle ScholarPubMed
Sewalem, A., Morrice, D.M., Law, A.S., Windsor, D., Haley, C.S., Ikeobi, C.O.N., Burt, D.W. and Hocking, P.M. (2002) Mapping of Quantitative Trait Loci (QTL) for body weight at 3, 6 and 9 weeks of age in a broiler layer cross. Poultry Science 81: 1775–1781.CrossRefGoogle Scholar
Siwek, M., Buitenhuis, A.J., Cornelissen, S.J.B., Nieuwland, M.G.B., Bovenhuis, H., Crooijmans, R.P.M.A., Groenen, M.A.M., Vries-Reilingh, G.D., Parmentier, H.K. and Van Der Poel, J.J. (2003a) Detection of different Quantitative Trait Loci for antibody responses to Keyhole Lympet Hemocyanin and Mycobacterim butyricum in two unrelated populations of laying hens. Poultry Science 82: 1845–1852.CrossRefGoogle Scholar
Siwek, M., Cornelissen, S.J.B., Nieuwland, M.G.B., Buitenhuis, A.J., Bovenhuis, H., Crooijmans, R., Groenen, M.A.M., Vries-Reilingh, G., Parmentier, H.K. and Van Der Poel, J.J. (2003b) Detection of QTL for immune response to sheep red blood cells in laying hens. Animal Genetics 34: 422–428.CrossRefGoogle ScholarPubMed
Siwek, M., Cornelissen, S.J.B., Buitenhuis, A.J., Nieuwland, M.G.B., Bovenhuis, H., Crooijmans, R., Groenen, M.A.M., Parmentier, H.K. and Van Der Poel, J.J. (2004) Quantitative trait loci for body weight in layers differ from quantitative trait loci specific for antibody responses to sheep red blood cells. Poultry Science 83:853–859.CrossRefGoogle ScholarPubMed
Tatsuda, K. and Fujinaka, K. (2001a) Genetic mapping of the QTL affecting abdominal fat deposition in chickens. Journal of Poultry Science 38: 266–274.CrossRefGoogle Scholar
Tatsuda, K. and Fujinaka, K. (2001b) Genetic mapping of the QTL affecting body weight in chickens using a F-2 family. British Poultry Science 42: 333–337.CrossRefGoogle Scholar
Tuiskula-Haavisto, M., Honkatukia, M., Vilkki, J., De Koning, D.J., Schulman, N.F. and Maki-Tanila, A. (2002) Mapping of quantitative trait loci affecting quality and production traits in egg layers. Poultry Science 81: 919–927.CrossRefGoogle ScholarPubMed
Tuiskula-Haavisto, M., De Koning, D.J., Honkatukia, M., Schulman, N.F., Makitanila, A. and Vilkki, J. (2004) Quantitative trait loci with parent-of-origin effects in chicken. Genetical Research 84: 57–66.CrossRefGoogle ScholarPubMed
Vallejo, R.L., Bacon, L.D., Liu, H.C., Witter, R.L., Groenen, M.A.M., Hillel, J. and Cheng, H.H. (1998) Genetic mapping of quantitative trait loci affecting susceptibility to Marek's disease virus induced tumors in F-2 intercross chickens. Genetics 148: 349–360.CrossRefGoogle Scholar
Van Kaam, J.B.C.H.M., Groenen, M.A.M., Bovenhuis, H., Veenendaal, A., Vereijken, A.L.J. and Van Arendonk, J.A.M. (1999) Whole genome scan in chickens for quantitative trait loci affecting growth and feed efficiency. Poultry Science 78: 15–23.CrossRefGoogle ScholarPubMed
Van Kaam, J.B.C.M.H., Van Arendonk, J.A.M., Groenen, M.A.M., Bovenhuis, H., Vereijken, A.L.J., Crooijmans, R., Van Der Poel, J.J. and Veenendaal, A. (1998) Whole genome scan for quantitative trait loci affecting body weight in chickens using a three generation design. Livestock Production Science 54: 133–150.CrossRefGoogle Scholar
Walling, G.A., Archibald, A.L., Cattermole, J.A., Downing, A.C., Finlayson, H.A., Nicholson, D., Visscher, P.M., Walker, C.A. and Haley, C.S. (1998) Mapping of quantitative trait loci on porcine chromosome 4. Animal Genetics 29: 415–424.CrossRefGoogle ScholarPubMed
Wardecka, B., Olszewski, R., Jaszczak, K., Zieba, G., Pierzchala, M. and Wicinska, K. (2002) Relationships between microsatellite marker alleles on chromosomes 1–5 originating from Rhode Island Red and Green-legged Partrigenous breeds and egg production and quality traits in F2 mapping population. Journal of Applied Genetics 43: 319–329.Google ScholarPubMed
Wong, G.K.S., Liu, B., Wang, J., Zhang, Y., Yang, X., Zhang, Z.J., Meng, Q.S., Zhou, J., Li, D.W., Zhang, J.J., Ni, P.X., Li, S.G., Ran, L.H., Li, H., Zhang, J.G., Li, R.Q., Li, S.T., Zheng, H.K., Lin, W., Li, G.Y., Wang, X.L., Zhao, W.vvvM., Li, J., Ye, C., Dai, M.T., Ruan, J., Zhou, Y., Li, Y.Z., He, X.M., Zhang, Y.Z., Wang, J., Huang, X.G., Tong, W., Chen, J., Ye, J., Chen, C., Wei, N., Li, G. Q., Dong, L., Lan, F.D., Sun, Y.Q., Zhang, Z.P., Yang, Z., Yu, Y.P., Huang, Y.Q., He, D.D., Xi, Y., Wei, D., Qi, Q.H., Li, W.J., Shi, J.P., Wang, M.H., Xie, F., Wang, J.J., Zhang, X.W., Wang, P., Zhao, Y.Q., Li, N., Yang, N., Dong, W., Hu, S.N., Zeng, C.Q., Zheng, W.M., Hao, B.L., Hillier, L.W., Yang, S.P., Warren, W.C., Wilson, R.K., Brandstrom, M., Ellegren, H., Crooijmans, R., Van Der Poel, J.J., Bovenhuis, H., Groenen, M.A.M., Ovcharenko, I., Gordon, L., Stubbs, L., Lucas, S., Glavina, T., Aerts, A., Kaiser, P., Rothwell, L., Young, J.R., Rogers, S., Walker, B.A., Van Hateren, A., Kaufman, J., Bumstead, N., Lamont, S.J., Zhou, H.J., Hocking, P.M., Morrice, D., De Koning, D.J., Law, A., Bartley, N., Burt, D.W., Hunt, H., Cheng, H.H., Gunnarsson, U., Wahlberg, P., Andersson, L., Kindlund, E., Tammi, M.T., Andersson, B., Webber, C., Ponting, C.P., Overton, I.M., Boardman, P.E., Tang, H.Z., Hubbard, S.J., Wilson, S.A., Yu, J., Wang, J. and Yang, H.M. (2004) A genetic variation map for chicken with 2.8 million single- nucleotide polymorphisms. Nature 432:717–722.Google ScholarPubMed
Yonash, N., Bacon, L.D., Witter, R.L. and Cheng, H.H. (1999) High resolution mapping and identification of new quantitative trait loci (QTL) affecting susceptibility to Marek's disease. Animal Genetics 30: 126–135.CrossRefGoogle ScholarPubMed
Yonash, N., Cheng, H.H., Hillel, J., Heller, D.E. and Cahaner, A. (2001) DNA microsatellites linked to quantitative trait loci affecting antibody response and survival rate in meat-type chickens. Poultry Science 80: 22–28.CrossRefGoogle ScholarPubMed
Yunis, R., Heller, E.D., Hillel, J. and Cahaner, A. (2002) Microsatellite markers associated with quantitative trait loci controlling antibody response to Escherichia coli and Salmonella enteritidis in young broilers. Animal Genetics 33: 407–414.CrossRefGoogle ScholarPubMed
Zhou, H., Li, H. and Lamont, S.J. (2003) Genetic markers associated with antibody response kinetics in adult chickens. Poultry Science 82: 699–708.CrossRefGoogle ScholarPubMed
Zhu, J.J., Lillehoj, H.S., Allen, P.C., Van Tassell, C.P., Sonstegard, T.S., Cheng, H.H., Pollock, D., Sadjadi, M., Min, W. and Emara, M.G. (2003) Mapping quantitative trait loci associated with resistance to coccidiosis and growth. Poultry Science 82: 9–16.CrossRefGoogle ScholarPubMed