Genome-wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines

Genetics Selection Evolution

Volumn 45, Issue 1, 2013, Pages

  Demeure, Olivier ^a,b   Duclos, Michel J ^c   Bacciu, Nicola ^a,b   Le Mignon, Guillaume ^a,b   Filangi, Olivier ^a,b   Pitel, Frédérique ^d   Boland, Anne ^e   Lagarrigue, Sandrine ^a,b   Cogburn, Larry A ^f   Simon, Jean ^c   Le Roy, Pascale ^a,b   Le Bihan Duval, Elisabeth ^c  

^a PEGASE   (France)

^b AGROCAMPUS OUEST   (France)

^c STATION DE RECHERCHES AVICOLES   (France)

^d CEMAGREF   (France)

^e DIF   (France)

^f UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BODY CONDITION; BODY TEMPERATURE; CHROMOSOME; FAT; GENETIC MARKER; GENOME; GENOTYPE; GLUCOSE; MUSCLE; PHYSIOLOGY; POULTRY;

ACETYL COENZYME A CARBOXYLASE; GHRELIN RECEPTOR;

ANIMAL; ARTICLE; BODY COMPOSITION; BODY WEIGHT; CHICKEN; CROSS BREEDING; GENETIC LINKAGE; GENETIC VARIABILITY; GENETICS; GENOME; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

ACETYL-COA CARBOXYLASE; ANIMALS; BODY COMPOSITION; BODY WEIGHT; CHICKENS; CROSSES, GENETIC; GENETIC LINKAGE; GENETIC VARIATION; GENOME; GENOTYPE; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RECEPTORS, GHRELIN;

EID: 84885395334     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-45-36     Document Type: Article

References (48)

1. Industrial perspective on problems and issues associated with poultry breeding. Arthur JA, Albers GAA, Poultry Genetics, Breeding and Biotechnology Cambridge: CABI Publishing, Muir WM, 2003 1 12
2. Selection experiment for body composition in mice and rats: a review. Eisen EJ, Livest Prod Sci 1989 23 17 32 10.1016/0301-6226(89)90003-1
3. Leclercq B, Whitehead CC, Leanness in Domestic Birds: Genetic, Metabolic and Hormonal Aspects London: Butterworths 1988
4. Nitrogen metabolism in genetically fat and lean chickens. Geraert PA, MacLeod MG, Larbier M, Leclercq B, Poult Sci 1990 69 1911 1921 10.3382/ps.0691911 2087450
5. Selecting broilers for low or high abdominal fat: initial observations. Leclercq B, Blum JC, Boyer JP, Br Poult Sci 1980 21 107 113 10.1080/ 00071668008416644
6. Review of quantitative trait loci identified in the chicken. Abasht B, Dekkers JC, Lamont SJ, Poult Sci 2006 85 2079 2096 17135661 (Pubitemid 46063978)
7. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, et al. Nature 2004 432 717 722 10.1038/nature03156 15592405 (Pubitemid 39656286)
8. Chicken lines divergent for low or high abdominal fat deposition: a relevant model to study the regulation of energy metabolism. Baéza E, Le Bihan-Duval E, Animal 2013 7 965 973 10.1017/S1751731113000153 23433003
9. Glucagon-Insulin balance in genetically lean or fat chickens. Leclercq B, Simon J, Karmann H, Diabete Metab 1988 14 641 645 3069508 (Pubitemid 19019235)
10. Fatness QTL on chicken chromosome 5 and interaction with sex. Abasht B, Pitel F, Lagarrigue S, Le Bihan-Duval E, Le Roy P, Demeure O, Vignoles F, Simon J, Cogburn L, Aggrey S, Vignal A, Douaire M, Genet Sel Evol 2006 38 297 311 10.1186/1297-9686-38-3-297 16635451 (Pubitemid 43788170)
11. Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness. Lagarrigue S, Pitel F, Carre W, Abasht B, Le Roy P, Neau A, Amigues Y, Sourdioux M, Simon J, Cogburn L, Aggrey S, Leclercq B, Vignal A, Douaire M, Genet Sel Evol 2006 38 85 97 10.1186/1297-9686-38-1-85 16451793 (Pubitemid 43075125)
12. Alternative models for QTL detection in livestock. I. General introduction. Elsen JM, Mangin B, Goffinet B, Boichard D, Le Roy P, Genet Sel Evol 1999 31 213 224 10.1186/1297-9686-31-3-213 (Pubitemid 29319033)
13. QTLMap, a software for QTL detection in outbred populations. Filangi O, Moreno C, Gilbert H, Legarra A, Le Roy P, Elsen J, Proceedings of the 9th World Congress on Genetics Applied to Livestock Production: 1-6 August 2010 Leipzig 2010 D787 http://www.kongressband.de/wcgalp2010/assets/pdf/0787.pdf
14. Effects of infusions of various doses of bovine growth hormone-releasing factor on blood hormones and metabolites in lactating Holstein cows. Enright WJ, Chapin LT, Moseley WM, Zinn SA, Kamdar MB, Krabill LF, Tucker HA, J Endocrinol 1989 122 671 679 10.1677/joe.0.1220671 2509616 (Pubitemid 19220623)
15. MarkerSet: a marker selection tool based on markers location and informativity in experimental designs. Demeure O, Lecerf F, BMC Res Notes 2008 1 9 10.1186/1756-0500-1-9 18710478
16. Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques. de Givry S, Palhiere I, Vitezica Z, Schiex T, Constraints 2008 13 130 154 10.1007/s10601-007-9029-5
17. R Development Core Team R Foundation for Statistical Computing, R: A language and environment for statistical computing Vienna: R Foundation for Statistical Computing 2005 http://www.R-project.org
18. Groeneveld E, Kovac M, Mielenz N, VCE User's Guide and Reference Manual Version 6.0 2010 http://vce.tzv.fal.de/software/documentation/manual
19. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Groenen MA, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans RP, Besnier F, Lathrop M, Muir WM, Wong GK, Gut I, Andersson L, Genome Res 2009 19 510 519 19088305
20. A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps. Elsen JM, Filangi O, Gilbert H, Le Roy P, Moreno C, Genet Sel Evol 2009 41 50 10.1186/1297-9686-41-50 19919698
21. GPU accelerated QTL detection. Chapuis G, Filangi O, Elsen JM, Lavenier D, Le Roy P, J Comput Biol 2013 in press
22. Methods for the detection of multiple linked QTL applied to a mixture of full and half sib families. Gilbert H, Le Roy P, Genet Sel Evol 2007 39 139 158 10.1186/1297-9686-39-2-139 17306198 (Pubitemid 46650915)
23. Ott J, Analysis of Human Genetic Linkage London: John Hopkins University Press 3 1991
24. A new distribution-free quantile estimator. Harrel FE, Davis CE, Biometrika 1982 69 635 640 10.1093/biomet/69.3.635
25. Linkage disequilibrium reveals different demographic history in egg laying chickens. Qanbari S, Hansen M, Weigend S, Preisinger R, Simianer H, BMC Genet 2010 11 103 21078133
26. QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth. Park HB, Jacobsson L, Wahlberg P, Siegel PB, Andersson L, Physiol Genomics 2006 25 216 223 10.1152/physiolgenomics.00113.2005 16390876
27. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. IV. Metabolic traits. Zhou H, Evock-Clover CM, McMurtry JP, Ashwell CM, Lamont SJ, Poult Sci 2007 86 267 276 17234839 (Pubitemid 47581109)
28. Single marker and haplotype analysis of the chicken apolipoprotein B gene T123G and D9500D9- polymorphism reveals association with body growth and obesity. Zhang S, Li H, Shi H, Poult Sci 2006 85 178 184 16523611 (Pubitemid 44514957)
29. Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate. Ankra-Badu GA, Shriner D, Le Bihan-Duval E, Mignon-Grasteau S, Pitel F, Beaumont C, Duclos MJ, Simon J, Porter TE, Vignal A, Cogburn LA, Allison DB, Yi N, Aggrey SE, BMC Genomics 2010 11 107 10.1186/1471-2164-11-107 20149241
30. Quantitative trait loci for performance traits in a broiler x layer cross. Ambo M, Moura AS, Ledur MC, Pinto LF, Baron EE, Ruy DC, Nones K, Campos RL, Boschiero C, Burt DW, Coutinho LL, Anim Genet 2009 40 200 208 10.1111/j.1365-2052.2008.01824.x 19170675
31. QTLs detected in a multigenerational resource chicken population. Atzmon G, Blum S, Feldman M, Cahaner A, Lavi U, Hillel J, J Hered 2008 99 528 538 10.1093/jhered/esn030 18492652
32. A single nucleotide polymorphism of chicken acetyl-CoA carboxylase A gene associated with fatness traits. Tian J, Wang S, Wang Q, Leng L, Hu X, Li H, Anim Biotechnol 2010 21 42 50 20024786
33. Genome-wide association analysis reveals cryptic alleles as an important factor in heterosis for fatness in chicken F2 population. Abasht B, Lamont SJ, Anim Genet 2007 38 491 498 10.1111/j.1365-2052.2007.01642.x 17894563 (Pubitemid 47480953)
34. QTL for several metabolic traits map to loci controlling growth and body composition in an F2 intercross between high- and low-growth chicken lines. Nadaf J, Pitel F, Gilbert H, Duclos MJ, Vignoles F, Beaumont C, Vignal A, Porter TE, Cogburn LA, Aggrey SE, Simon J, Le Bihan-Duval E, Physiol Genomics 2009 38 241 249 10.1152/physiolgenomics.90384.2008 19531576
35. A comprehensive analysis of QTL for abdominal fat and breast muscle weights on chicken chromosome 5 using a multivariate approach. Le Mignon G, Pitel F, Gilbert H, Le Bihan-Duval E, Vignoles F, Demeure O, Lagarrigue S, Simon J, Cogburn LA, Aggrey SE, Douaire M, Le Roy P, Anim Genet 2009 40 157 164 10.1111/j.1365-2052.2008.01817.x 19243366
36. Multipoint oligogenic linkage analysis of quantitative traits. Blangero J, Almasy L, Genet Epidemiol 1997 14 959 964 10.1002/(SICI)1098-2272(1997)14: 6<959::AID-GEPI66>3.0.CO;2-K 9433607 (Pubitemid 28027516)
37. AnnotQTL: a new tool to gather functional and comparative information on a genomic region. Lecerf F, Bretaudeau A, Sallou O, Desert C, Blum Y, Lagarrigue S, Demeure O, Nucleic Acids Res 2011 39 328 W333 10.1093/nar/gkr361 21596783
38. Circulating insulin-like growth factors (IGF-I and -II) and IGF binding proteins in divergently selected fat or lean chickens: effect of prolonged fasting. Beccavin C, Chevalier B, Simon J, Duclos MJ, Growth Horm IGF Res 1999 9 187 194 10.1054/ghir.1999.0109 10502455 (Pubitemid 29468751)
39. Identification of genetic determinants of IGF-1 levels and longevity among mouse inbred strains. Leduc MS, Hageman RS, Meng Q, Verdugo RA, Tsaih SW, Churchill GA, Paigen B, Yuan R, Aging Cell 2010 9 823 836 10.1111/j.1474-9726. 2010.00612.x 20735370
40. Genetic increase in serum insulin-like growth factor-I (IGF-I) in C3H/HeJ compared with C57BL/6J mice is associated with increased transcription from the IGF-I exon 2 promoter. Adamo ML, Ma X, Ackert-Bicknell CL, Donahue LR, Beamer WG, Rosen CJ, Endocrinology 2006 147 2944 2955 10.1210/en.2005-0742 16527837 (Pubitemid 43764630)
41. Associations of GHSR gene polymorphisms with chicken growth and carcass traits. Fang M, Nie Q, Luo C, Zhang D, Zhang X, Mol Biol Rep 2010 37 423 428 10.1007/s11033-009-9556-9 19437137
42. Transgenic mice over-expressing dicarbonyl/L-xylulose reductase gene crossed with KK-Ay diabetic model mice: an animal model for the metabolism of renal carbonyl compounds. Sudo T, Ishii A, Asami J, Uematsu Y, Saitoh M, Nakamura A, Tada N, Ohnuki T, Komurasaki T, Nakagawa J, Exp Anim 2005 54 385 394 10.1538/expanim.54.385 16365515 (Pubitemid 43071725)
43. Gene regulation mediating fiber-type transformation in skeletal muscle cells is partly glucose- and ChREBP-dependent. Hanke N, Scheibe RJ, Manukjan G, Ewers D, Umeda PK, Chang KC, Kubis HP, Gros G, Meissner JD, Biochim Biophys Acta 1813 2011 377 389
44. Gas1 cooperates with Cdo and promotes myogenic differentiation via activation of p38MAPK. Leem YE, Han JW, Lee HJ, Ha HL, Kwon YL, Ho SM, Kim BG, Tran P, Bae GU, Kang JS, Cell Signal 2011 23 2021 2029 10.1016/j.cellsig.2011. 07.016 21820049
45. Simultaneous mapping of epistatic QTL in chickens reveals clusters of QTL pairs with similar genetic effects on growth. Carlborg O, Hocking PM, Burt DW, Haley CS, Genet Res 2004 83 197 209 10.1017/S0016672304006779 15462413 (Pubitemid 39137181)
46. A global search reveals epistatic interaction between QTL for early growth in the chicken. Carlborg O, Kerje S, Schütz K, Jacobsson L, Jensen P, Andersson L, Genome Res 2003 13 413 421 10.1101/gr.528003 12618372 (Pubitemid 36395399)
47. Dissection of the genetic architecture of body weight in chicken reveals the impact of epistasis on domestication traits. Le Rouzic A, Alvarez-Castro JM, Carlborg O, Genetics 2008 179 1591 1599 10.1534/genetics.108.089300 18622035
48. Genetic analysis of an F(2) intercross between two chicken lines divergently selected for body-weight. Wahlberg P, Carlborg O, Foglio M, Tordoir X, Syvänen AC, Lathrop M, Gut IG, Siegel PB, Andersson L, BMC Genomics 2009 10 248 10.1186/1471-2164-10-248 19473501