Objectives and applications of phenotyping network set-up for livestock

Animal Science Journal

Volumn 83, Issue 7, 2012, Pages 517-528

  Hocquette, Jean François ^a   Capel, Carine ^b   David, Valérie ^c   Guémené, Daniel ^d   Bidanel, Joël ^e   Ponsart, Claire ^f   Gastinel, Pierre Louis ^g   Bail, Pierre Yves Le ^h   Monget, Philippe ^i,j   Mormède, Pierre ^d,k   Barbezant, Maurice ^l   Guillou, Florian ^i,j   Peyraud, Jean Louis ^m,n  

^a UMR1213 HERBIVORES   (France)

^b Institut de l'Elevage   (France)

^c Institut de l'Elevage   (France)

^d CEMAGREF   (France)

^e IFIP   (France)

^f UNCEIA Union Nationale des Cooperatives d'Elevage et d'Insemination Animale   (France)

^g France Génétique Elevage   (France)

^h Campus de Beaulieu   (France)

ⁱ UMR85 PHYSIOLOGIE DE LA REPRODUCTION ET DES COMPORTEMENTS   (France)

^j UNIVERSITÉ DE TOURS   (France)

^k ENVT   (France)

^l UNCEIA   (France)

^m PEGASE   (France)

ⁿ AGROCAMPUS OUEST   (France)

more..

Author keywords

Genomics; Livestock; Phenotypes

Indexed keywords

ANIMAL; BREEDING; FEMALE; GENETICS; GENOMICS; HIGH THROUGHPUT SCREENING; LIVESTOCK; MALE; PHENOTYPE; REVIEW;

ANIMALS; BREEDING; FEMALE; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; LIVESTOCK; MALE; PHENOTYPE;

ANIMALIA;

EID: 84863775746     PISSN: 13443941     EISSN: 17400929     Source Type: Journal    
DOI: 10.1111/j.1740-0929.2012.01015.x     Document Type: Review

References (50)

1. Allais S, Journaux L, Levéziel H, Payet-Duprat N, Raynaud P, Hocquette JF, Lepetit J, Rousset S, Denoyelle C, Bernard-Capel C, Renand G. 2011. Effects of polymorphisms in the calpastatin and μ-calpain genes on meat tenderness in three French beef breeds. Journal of Animal Science 89, 1-11.
2. Allais S, Leveziel H, Payet N, Hocquette JF, Lepetit J, Rousset S, Denoyelle C, Capel C, Journaux L, Bonnot A, Renand G. 2010. The two mutations Q204X and nt821 of the myostatin gene affect carcass and meat quality in heterozygous young bulls of three French beef breeds. Journal of Animal Science 88, 446-454.
3. Andueza D, Picard F, Jestin M, Andrieu J, Baumont R. 2011. NIRS prediction of the feed value of temperate forages: efficacy of four calibration strategies. Animal 5, 1002-1013.
4. Barbat A, Le Mézec P, Ducrocq V, Mattalia S, Fritz S, Boichard D, Ponsart C, Humblot P. 2010. Female fertility in French dairy breeds: current situation and strategies for improvement. Journal of Reproduction and Development 56 (Suppl. S), 15-21.
5. Barendse W. 2011. The effect of measurement error of phenotypes on genome wide association studies. BMC Genomics 12, 232.
6. Bewley J. 2010. Precision dairy farming: advanced analysis solutions for future profitability. The First North American Conference on Precision Dairy Management. March 2-5, 2010. Toronto, Canada. [cited 12 March 2012]. Available from URL:.
7. Botreau R, Veissier I, Perny P. 2009. Overall assessment of cow welfare: strategy adopted in Welfare Quality. Animal Welfare 18 (Sp. Iss. SI), 363-370.
8. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. 2001. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genetics 29, 365-371.
9. Charlier C, Coppieters W, Rollin F, Desmecht D, Agerholm JS, Cambisano N, Carta E, Dardano S, Dive M, Fasquelle C, Frennet JC, Hanset R, Hubin X, Jorgensen C, Karim L, Kent M, Harvey K, Pearce BR, Simon P, Tama N, Nie H, Vandeputte S, Lien S, Longeri M, Fredholm M, Harvey RJ, Georges M. 2008. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nature Genetics 40, 449-454.
10. th, 2011. [cited 12 March 2012]. Available from URL:.
11. FABRE. 2006. Sustainable farm animal breeding and reproduction - a vision for 2025. [cited 26 January 2012]. Available from URL:.
12. th Annual Meeting of the European Association for Animal Production, Heraklion 2010, p. 19.
13. th Annual Meeting - Riga, Latvia, 31 May-4 June, 2010. [cited 12 March 2012]. Available from URL:.
14. Friggens N, Sauvant D, Martin O. 2010. Towards operational definitions of robustness that rely on biology: nutrition. Inra Productions Animales 23, 43-52.
15. Frost AR, Schofield CP, Beaulah SA, Mottram TT, Lines JA, Wathes CM. 1997. A review of livestock monitoring and the need for integrated systems. Computers and Electronics in Agriculture 17, 139-159.
16. Gad A, Besenfelder U, Rings F, Ghanem N, Salilew-Wondim D, Hossain MM, Tesfaye D, Lonergan P, Becker A, Cinar U, Schellander K, Havlicek V, Hölker M. 2011. Effect of reproductive tract environment following controlled ovarian hyperstimulation treatment on embryo development and global transcriptome profile of blastocysts: implications for animal breeding and human assisted reproduction. Human Reproduction 26, 1693-1707.
17. Guyader-Joly C, Ponchon S, Gonzalez C, Marquant-Le Guienne B, Clément L, Dalbies-Tran R, Mermillod P, Humblot P. 2008. Identification of contrasted phenotypes in the bovine from repeated in vivo and in vitro embryo production following superovulation. Reproduction Fertility and Development 20, 131.
18. Herpin P. 2009. Quelles perspectives de recherche en productions animales. Cahiers Agricultures 18, 5-6.
19. th, 2011. [cited 12 March 2012]. Available from URL:.
20. Hocquette JF, Cassar-Malek I, Scalbert A, Guillou F. 2009. Contribution of Genomics to the understanding of physiological functions. Journal of Physiology and Pharmacology 60 (Suppl. 2), 5-16.
21. Hocquette JF, Gondret F, Baéza E, Médale F, Jurie C, Pethick DW. 2010. Intramuscular fat content in meat-producing animals: development, genetic and nutritional control, identification of putative markers. Animal 4, 303-319.
22. Hocquette JF, Legrand I, Jurie C, Pethick DW, Micol D. 2011b. Perception in France of the Australian system for the prediction of beef quality (Meat Standards Australia) with perspectives for the European beef sector. Animal Production Science 51, 30-36.
23. Hocquette JF, Meurice P, Brun JP, Jurie C, Denoyelle D, Bauchart D, Renand G, Nute GR, Picard B. 2011c. The challenge and limitations of combining data: a case study examining the relationship between intramuscular fat content and flavour intensity based on the BIF-BEEF database. Animal Production Science 51, 975-981.
24. Hrynaszkiewicz I. 2010. A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication. BMC Research Notes 3, 235.
25. Huber L. 2007. Validation and Qualification in Analytical Laboratories, 2nd edn. Interpharm Press Inc., Buffalo Grove, IL, US.
26. Hughes LM, Bao J, Hu Z-L, Honavar V, Reecy JM. 2008. Animal trait ontology: the importance and usefulness of a unified trait vocabulary for animal species. Journal of Animal Science 86, 1485-1491.
27. Humblot P, Le Bourhis D, Fritz S, Colleau JJ, Gonzalez C, Guyader-Joly C, Malafosse A, Heyman Y, Amigues Y, Tissier M, Ponsart C. 2010. Reproductive technologies and genomic selection in cattle. Veterinary Medicine International Article ID 192787. doi:10.4061/2010/192787.
28. Hurtaud C, Bugeon J, Dameron O, Fatet A, Hue I, Meunier-Salaün MC, Reichstadt M, Valancogne A, Vernet J, Reecy J, Park C, Le Bail PY. 2011. ATOL: a new ontology for livestock. General Assembly and annual workshop of ICAR 2011. Bourg-en-Bresse, France, 22-24 June 2011. [cited 12 March 2012]. Available from URL:.
29. eme journées de la recherche équine, 177-185.
30. th Annual Conference of the IETS, p. 197 (abstract 193).
31. Ledoux D, Gatien J, Grimard B, Deloche MC, Fritz S, Lefebvre R, Humblot P, Ponsart C. 2011. Phenotyping pregnancy failure occurring within 90days following first postpartum insemination in Holstein cattle and relationship with fertility breeding value of bull fathers. Rencontres Recherches Ruminants 18, 339-342.
32. th, 2011. [cited 12 March 2012]. Available from URL.
33. Liao B-Y, Zhang J. 2008. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proceedings of the National Academy of Sciences of the United States of America 105, 6987-6992.
34. Mansouri-Attia N, Aubert J, Reinaud P, Giraud-Delville C, Taghouti G, Galio L, Everts RE, Degrelle S, Richard C, Hue I, Yang X, Tian XC, Lewin HA, Renard JP, Sandra O. 2009. Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation. Physiological Genomics 39, 14-27.
35. Monget P, Le Bail PY. 2009. Animal phenotyping: the new challenge? Rencontres Recherches Ruminants 16, 407-409.
36. Mormède P, Foury A, Terenina E, Knap P. 2011. Breeding for robustness: the role of cortisol. Animal 5, 651-657.
37. th, 2011. [cited 12 March 2012]. Available from URL:.
38. Ponsart C, Dalbies-Tran R, Hue I, Druart X, Duranthon V, Dupont J, Jammes H, Uzbekova S, Nuttinck F, Charpigny G, Joly C, Leguienne B, Salvetti P, Capitan A, Grimard B, Humblot P, Sandra O, Mermillod P. 2011c. Inputs from functional genomics on bovine female fertility. Rencontres Recherches Ruminants 18, 335-338.
39. th July 2008, Budapest, Hungary.
40. th, 2011. p. 27. [cited 12 March 2012]. Available from URL:.
41. Prache S, Martin B, Nozière P, Engel E, Besle JM, Ferlay A, Micol D, Cornu A, Cassar-Malek I, Andueza D. 2006. Diet authentication in herbivores using meat, milk and animal tissues composition. Rencontres Recherches Ruminants 13, 175-182.
42. Radhakrishnan R, Solomon M, Satyamoorthy K, Martin LE, Mark W Lingen MW. 2008. Tissue microarray - a high-throughput molecular analysis in head and neck cancer. Journal of Oral Pathology & Medicine 37, 166-176.
43. Reynolds CK, Crompton LA, Mills JAN. 2011. Improving the efficiency of energy utilisation in cattle. Animal Production Science 51, 6-12.
44. Scollan ND, Greenwood PL, Newbold CJ, Yáñez Ruiz DR, Shingfield KJ, Wallace RJ, Hocquette JF. 2011. Future research priorities for animal production in a changing world. Animal Production Science 51, 1-5.
45. Taylor CF. 2007. Standards for reporting bioscience data: a forward look. Drug Discovery Today 12, 527-533.
46. Taylor CF, Paton NW, Lilley KS, Binz P-A, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck A Jr, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR III, Hermjakob H. 2007. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology 25, 887-893.
47. Thelie A, Papillier P, Perreau C, Uzbekova S, Hennequet-Antier C, Dalbies-Tran R. 2009. Regulation of bovine oocyte-specific transcripts during in vitro oocyte maturation and after maternal-embryonic transition analyzed using a transcriptomic approach. Molecular Reproduction and Development 76, 773-782.
48. VanRaden PM, Olson KM, Wiggans GR, Cole JB, Tooker ME. 2011. Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss. Journal of Dairy Science 94, 5673-5680.
49. Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. 2011. Minimum Information About a Simulation Experiment (MIASE). PLoS Computational Biology 7, e1001122.
50. Watson R, Polkinghorne R, Thompson JM. 2008. Development of the Meat Standards Australia (MSA) prediction model for beef palatability. Australian Journal of Experimental Agriculture 48, 1368-1379.