Skip to main content
×
Home
    • Aa
    • Aa

Recent advances in cattle functional genomics and their application to beef quality

  • J.-F. Hocquette (a1), S. Lehnert (a2), W. Barendse (a2), I. Cassar-Malek (a1) and B. Picard (a1)...
Abstract
Abstract

The advent of high-throughput DNA sequencing techniques, array technology and protein analysis has increased the efficiency of research in bovine muscle physiology, with the ultimate objective of improving beef quality either by breeding or rearing factors. For genetic purposes, polymorphisms in some key genes have been reported for their association with beef quality traits. The sequencing of the bovine genome has dramatically increased the number of available gene polymorphisms. The association of these new polymorphisms with the variability in beef quality (e.g. tenderness, marbling) for different breeds in different rearing systems will be a very important issue. For rearing purposes, global gene expression profiling at the mRNA or protein level has already shown that previously unsuspected genes may be associated either with muscle development or growth, and may lead to the development of new molecular indicators of tenderness or marbling. Some of these genes are specifically regulated by genetic and nutritional factors or differ between different beef cuts. In recognition of the potential economic benefits of genomics, public institutions in association with the beef industry are developing livestock genomics projects around the world. From the scientific, technical and economical points of view, genomics is thus reshaping research on beef quality.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Recent advances in cattle functional genomics and their application to beef quality
      Available formats
      ×
      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your Dropbox account. Find out more about sending content to Dropbox.

      Recent advances in cattle functional genomics and their application to beef quality
      Available formats
      ×
      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your Google Drive account. Find out more about sending content to Google Drive.

      Recent advances in cattle functional genomics and their application to beef quality
      Available formats
      ×
Copyright
Corresponding author
* E-mail: hocquet@clermont.inra.fr
Linked references
Hide All

This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

L Andersson and M Georges 2004. Domestic-animal genomics: deciphering the genetics of complex traits. Natural Revue Genetique 5, 202-212.

W Barendse 2005. The transition from quantitative trait loci to diagnostic test in cattle and other livestock. Australian Journal of Experimental Agriculture 45, 831-836.

W Barendse , R Bunch , M Thomas , S Armitage , S Baud and N Donaldson 2004. The TG5 thyroglobulin gene test for a marbling quantitative trait loci evaluated in feedlot cattle. Australian Journal Experimental Agriculture 44, 669-674.

W Barendse , RJ Bunch and BE Harrison 2005. The leptin C73T missense mutation is not associated with marbling and fatness traits in a large gene mapping experiment in Australian cattle. Animal Genetics 36, 86-88.

W Barendse , RJ Bunch , BE Harrison and MB Thomas 2006. The growth hormone GH1:c.457C>G mutation is associated with relative fat distribution in intra-muscular and rump fat in a large sample of Australian feedlot cattle. Animal Genetics 37, 211-214.

J Bouley , C Chambon and B Picard 2004a. Mapping of proteins in bovine skeletal muscle using two-dimensional gel electrophoresis and mass spectrometry. Proteomics 4, 1811-1824.

J Bouley , B Meunier , C Chambon , S De Smet , JF Hocquette and B Picard 2005. Proteomic analysis of bovine skeletal muscle hypertrophy. Proteomics 5, 490-500.

A Brazma , P Hingamp , J Quackenbush , G Sherlock , P Spellman , C Stoeckert , J Aach , W Ansorge , CA Ball , HC Causton , T Gaasterland , P Glenisson , FCP Holstege , IF Kim , V Markowitz , JC Matese , H Parkinson , A Robinson , U Sarkans , S Schulze-Kremer , J Stewart , R Taylor , J Vilo and M Vingron 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 29, 365-371.

FC Buchanan , CJ Fitzsimmons , AG van Kessel , TD Thue , DC Winkelman-Sim and S Schmutz 2002. Association of a missense mutation in the bovine leptin gene with carcass fat content and leptin mRNA levels. Genetics Selection Evolution 34, 105-116.

RD Canales , Y Luo , JC Willey , B Austermiller , CC Barbacioru , C Boysen , K Hunkapiller , RV Jensen , CR Knight , KY Lee , Y Ma , B Maqsodi , A Papallo , EH Peters , K Poulter , PL Ruppel , RR Samaha , L Shi , W Yang , L Zhang and FM Goodsaid 2006. Evaluation of DNA microarray results with quantitative gene expression platforms. Nature Biotechnology 24, 1115-1122.

KD Childs , DW Goad , MF Allan , D Pomp , C Krehbiel , RD Geisert , JB Morgan and JR Malayer 2002. Differential expression of NAT1 translational repressor during development of bovine intramuscular adipocytes. Physiological Genomics 10, 49-56.

B Cox , T Kislinger and A Emili 2005. Integrating gene and protein expression data: pattern analysis and profile mining. Methods 35, 303-314.

R Dalbies-Tran and P Mermillod 2003. Use of heterologous complementary DNA array screening to analyse bovine oocyte transcriptome and its evolution during in vitro maturation. Biology of Reproduction 68, 252-261.

C Diez-Tascón , OM Keane , T Wilson , A Zadissa , DL Hyndman , DB Baird , JC McEwan and AM Crawford 2005. Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep. Physiological Genomics 21, 59-69.

L Donaldson , T Vuocolo , C Gray , Y Strandberg , A Reverter , S McWilliam , Y Wang , K Byrne and R Tellam 2005. Construction and validation of a bovine innate immune microarray. BMC Genomics 6, 135.

U Dorroch , T Goldammer , RM Brunner , SR Kata , C Kühn , JE Womack and M Schwerin 2001. Isolation and characterization of hepatic and intestinal expressed sequence tags potentially involved in trait differentiation between cows of different metabolic type. Mammalian Genome 12, 528-537.

RD Drinkwater , Y Li , I Lenane , GP Davis , RP Shorthose , BE Harrison , K Richardson , D Ferguson , R Stevenson , J Renaud , I Loxton , RJ Hawken , MB Thomas , S Newman , DJS Hetzel and W Barendse 2006. Detecting quantitative trait loci affecting beef tenderness on bovine chromosome 7 near calpastatin and lysyl oxidase. Australian Journal of Experimental Agriculture 46, 159-164.

AL Drobyshev , M Hrabé de Anegelis and J Beckers 2003. Artefacts and reliability of DNA microarrays expression profiling data. Current Genomics 4, 615-621.

A Eggen and JF Hocquette 2004. Genomic approaches to economic trait loci and tissue expression profiling: application to muscle biochemistry and beef quality. Meat Science 66, 1-9.

A Everts-van der Wind , DM Larkin , CA Green , JS Elliott , CA Olmstead , R Chiu , JE Schein , MA Marra , JE Womack and HA Lewin 2005. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proceedings of the National Academy of Sciences of the United States of America 102, 18526-18531.

A Fadiel , I Anidi and KD Eichenbaum 2005. Farm animal genomics and informatics: an update. Nucleic Acids Research 33, 6308-6318.

JP Garnier , R Klont and G Plastow 2003. The potential impact of current animal research on the meat industry and consumer attitudes towards meat. Meat Science 63, 79-88.

Y Geay , D Bauchart , JF Hocquette and J Culioli 2001. Effect of nutritional factors on biochemical, structural and metabolic characteristics of muscles in ruminants; consequences on dietetic value and sensorial qualities of meat. Reproduction Nutrition Development 41, 1-26, Erratum, 377.

T Hanai , H Hamada and M Okamoto 2006. Application of bioinformatics for DNA microarray data to bioscience, bioengineering and medical fields. Journal of Biosciences and Bioengineering 101, 377-384.

B Harlizius , R van Wijk and JWM Merks 2004. Genomics for food safety and sustainable animal production. Journal of Biotechnology 113, 33-42.

RJ Hawken , WC Barris , SM McWilliam and BP Dalrymple 2004. An interactive bovine in silico SNP database (IBISS). Mammalian Genome 15, 819-827.

D Henderson , M Thomas and Y Da 2005. Conference review: bovine genomics from academia to industry. Comparative Functional Genomics 6, 174-180.

JF Hocquette , I Ortigues-Marty , D Pethick , P Herpin and X Fernandez 1998. Nutritional and hormonal regulation of energy metabolism in skeletal muscles of meat-producing animals. Livestock Production Science 56, 115-143.

J Hu , C Mungall , A Law , R Papworth , JP Nelson , A Brown , I Simpson , S Leckie , DW Burt , AL Hillyard and AL Archibald 2001. The ARKdb: genome databases for farmed and other animals. Nucleic Acids Research 29, 106-110.

K Jensen , R Talbot , E Paxton , D Waddington and EJ Glass 2006. Development and validation of a bovine macrophage specific cDNA microarray. BMC Genomics 7, 224.

JT Jeon , JH Lee , KS Kim , CK Park and SJ Oh 2006. Application of DNA markers in animal industries. Australian Journal of Experimental Agriculture 46, 173-182.

ZH Jiang , T Kunej , JJ Michal , CT Gaskins , JJ Reeves , JR Busboom , P Dovc and RW Wright 2005. Significant associations of the mitochondrial transcription factor A promoter polymorphisms with marbling and subcutaneous fat depth in Wagyu ×  Limousin F-2 crosses. Biochemical and Biophysical Research Communications 334, 516-523.

JP Jin , J Wang and O Ogut 1998. Developmentally regulated muscle type-specific alternative splicing of the COOH-terminal variable region of fast skeletal muscle troponin T and an aberrant splicing pathway to encode a mutant COOH-terminus. Biochemical and Biophysical Research Communications 242, 540-544.

F Le Provost , A Lépingle and P Martin 1996. A survey of the goat genome transcribed in the lactating mammary gland. Mammalian Genome 7, 657-666.

SA Lehnert , YH Wang and KA Byrne 2004. Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue. Australian Journal Experimental Agriculture 44, 1127-1133.

SA Lehnert , KA Byrne , A Reverter , G Nattrass , PL Greenwood , YH Wang , NJ Hudson and GS Harper 2006. Gene expression profiling of bovine longissimus muscle in response and during recovery from severe chronic under nutrition. Journal of Animal Science, in press.

JJ Loor , HM Dann , RE Everts , R Oliveira , CA Green , NA Guretzky , SL Rodriguez-Zas , HA Lewin and JK Drackley 2005. Temporal gene expression profiling of liver from periparturient dairy cows reveals complex adaptive mechanisms in hepatic function. Physiological Genomics 23, 217-226.

FM McCarthy , N Wang , GB Magee , B Nanduri , ML Lawrence , EB Camon , DG Barrell , DP Hill , ME Dolan , WP Williams , DS Luthe , SM Bridges and SC Burgess 2006. AgBase: a functional genomics resource for agriculture. BMC Genomics 7, 229.

K McGuire and EJ Glass 2005. The expanding role of microarrays in the investigation of macrophage responses to pathogens. Veterinary Immunology and Immunopathology 105, 259-275.

KG Meade , E Gormley , SD Park , T Fitzsimons , GJ Rosa , E Costello , J Keane , PM Coussens and DE MacHugh 2006. Gene expression profiling of peripheral blood mononuclear cells (PBMC) from Mycobacterium bovis infected cattle after in vitro antigenic stimulation with purified protein derivative of tuberculin (PPD). Veterinary Immunology Immunopathology 113, 73-89.

B Meunier , J Bouley , I Piec , C Bernard , B Picard and JF Hocquette 2005. Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis. Analytical Biochemistry 340, 226-230.

B Meunier , E Dumas , I Piec , M Hébraud , D Béchet and JF Hocquette 2007. Assessment of hierarchical clustering methodologies for proteomic data mining. Journal of Proteome Research, in press.

JJ Michal , ZW Zhang , CT Gaskins and Z Jiang 2006. The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu ×  Limousin F2 crosses. Animal Genetics 37, 400-402.

CA Morris , NG Cullen , SM Hickey , PM Dobbie , BA Veenvliet , TR Manley , WS Pitchford , ZA Kruk , CDK Bottema and T Wilson 2006. Genotypic effects of calpain 1 and calpastatin on the tenderness of cooked M. longissimus dorsi steaks from Jersey ×  Limousin, Angus and Herefrod-cross cattle. Animal Genetics 37, 411-414.

JD Nkrumah , C Li , JB Basarab , S Guercio , Y Meng , B Murdoch , C Hansen and SS Moore 2004. Association of a single nucleotide polymorphism in the bovine leptin gene with feed intake, feed efficiency, growth, feeding behaviour, carcass quality and body composition. Canadian Journal of Animal Science 84, 211-219.

M Oishi , Y Taniguchi , K Nishimura , T Yamada and Y Sasaki 2000. Characterisation of gene expression in bovine adipose tissue before and alter fattening. Animal Genetics 31, 166-170.

M Pfister-Genskow , C Myers , LA Childs , JC Lacson , T Patterson , JM Betthauser , PJ Goueleke , RW Koppang , G Lange , P Fisher , SR Watt , EJ Forsberg , Y Zheng , GH Leno , RM Schultz , B Liu , C Chetia , X Yang , I Hoeschele and KJ Eilertsen 2005. Identification of differentially expressed genes in individual bovine preimplantation embryos produced by nuclear transfer: Improper reprogramming of genes required for development. Biology of Reproduction 72, 546-555.

B Picard , L Lefaucheur , C Berri and MJ Duclos 2002. Muscle fibre ontogenesis in farm animal species. Reproduction Nutrition Development 42, 415-431.

GS Plastow , D Carrion , M Gil , JA Garcia-Regueiro , MFI Furnols , M Gispert , MA Oliver , A Velarde , MD Guardia , M Hortos , MA Rius , C Sarraga , I Diaz , A Valero , A Sosnicki , R Klont , S Dornan , JM Wilkinson , G Evans , C Sargent , G Davey , D Connolly , B Houeix , CM Maltin , HE Hayes , V Anandavijayan , A Foury , N Geverink , M Cairns , RE Tilley , P Mormede and SC Blott 2005. Quality pork genes and meat production. Meat Science 70, 409-421, Special Issue.

EJ Pollak 2005. Application and impact of new genetic technologies on beef cattle breeding: a ‘real world’ perspective. Australian Journal of Experimental Agriculture 45, 739-748.

JK Potts , SE Echternkamp , TPL Smith and JM Reecy 2003. Characterization of gene expression in double-muscled and normal-muscled bovine embryos. Animal Genetics 34, 438-444.

A Reverter , W Barris , N Moreno-Sánchez , S McWilliam , YH Wang , GS Harper , SA Lehnert and BP Dalrymple 2005. Construction of gene interaction and regulatory networks in bovine skeletal muscle from expression data. Australian Journal of Experimental Agriculture 45, 821-829.

A Reverter , NJ Hudson , Y Wang , SH Tan , W Barris , KA Byrne , SM McWilliam , CD Bottema , A Kister , PL Greenwood , GS Harper , SA Lehnert and BP Dalrymple 2006. A gene co-expression network for bovine skeletal muscle inferred from microarray data. Physiological Genomics, in press.

P Schlee , R Graml , O Rottmann and F Pirchner 1994. Influence of growth-hormone genotypes on breeding values of Simmental bulls. Journal of Animal Breeding and Genetics 111, 253-256.

R Shields 2006. The emperor's new clothes revisited. Trends in Genetics 22, 463.

M Sievertzon , P Nilsson and J Lundeberg 2006. Improving reliability and performance of DNA microarrays. Expert Review of Molecular Diagnostics 6, 481-492.

SL Smith , RE Everts , XC Tian , F Du , LY Sung , SL Rodriguez-Zas , BS Jeong , JP Renard , HA Lewin and X Yang 2005. Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning. Proceedings of the National Academy of Sciences of the United States of America 102, 17582-17587.

TPL Smith , WM Grosse , BA Freking , AJ Roberts , RT Stone , E Casas , JE Wray , J White , J Cho , JC Fahrenkrug , GL Bennett , MP Heaton , WW Laegreid , GA Rohrer , CG Chitko-McKown , G Pertea , I Holt , S Karamycheva , F Liang , J Quackenbush and JW Keele 2001. Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Research 11, 626-630.

TPL Smith , RM Thallman , E Casas , SD Shackelford , TL Wheeler and M Koohmaraie 2003. Theory and application of genome-based approaches to improve the quality and value of beef. Outlook on Agriculture 32, 253-265.

J Somers , C Smith , M Donnison , DN Wells , H Henderson , L McLeay and PL Pfeffer 2006. Gene expression profiling of individual bovine nuclear transfer blastocysts. Reproduction 131, 1073-1084.

SP Suchyta , S Sipkovsky , R Kruska , A Jeffers , A McNulty , MJ Coussens , RJ Tempelman , RJ Halgren , PM Saama , DE Bauman , YR Boisclair , JL Burton , RJ Collier , EJ DePeters , TA Ferris , MC Lucy , MA McGuire , JF Medrano , TR Overton , TP Smith , GW Smith , TS Sonstegard , JN Spain , DE Spiers , J Yao and PM Coussens 2003. Development and testing of a high-density cDNA microarray resource for cattle. Physiological Genomics 15, 158-164.

K Sudre , I Cassar-Malek , A Listrat , Y Ueda , C Leroux , C Jurie , C Auffray , G Renand , P Martin and JF Hocquette 2005a. Biochemical and transcriptomic analyses of two bovine skeletal muscles in Charolais bulls divergently selected for muscle growth. Meat Science 70, 267-277.

K Sudre , C Leroux , I Cassar-Malek and JF Hocquette 2005b. A collection of bovine cDNA probes for gene expression profiling in muscle. Molecular and Cellular Probes 19, 61-70.

CF Taylor , NW Paton , KL Garwood , PD Kirby , DA Stead , Z Yin , EW Deutsch , L Selway , J Walker , I Riba-Garcia , S Mohammed , MJ Deery , JA Howard , T Dunkley , R Aebersold , DB Kell , KS Lilley , P Roepstorff , JF Yates , A Brass , AJ Brown , P Cash , SJ Gaskell , SJ Hubbard and SG Oliver 2003. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nature Biotechnology 21, 247-254.

G Thaller , C Kühn , A Winter , A Ewald , O Bellmann , J Wegner , H Zühlke and R Fries 2003. DGAT1, a new positional and functional candidate gene for intramuscular fat deposition in cattle. Animal Genetics 34, 354-357.

CK Tuggle , JC Dekkers and JM Reecy 2006. Integration of structural and functional genomics. Animal Genetics 37, (suppl 1) 1-6.

YH Wang , KA Byrne , A Reverter , GS Harper , M Taniguchi , SM McWilliam , H Mannen , K Oyama and SA Lehnert 2005a. Transcriptional profiling of skeletal muscle tissue from two breeds of cattle. Mammalian Genome 16, 201-221.

YH Wang , A Reverter , H Mannen , M Taniguchi , GS Harper , K. Oyama , KA Byrne , A. Oka , S Tsuji and SA Lehnert 2005b. Transcriptional profiling of adult muscle in Japanese Black Cattle to identify genes involved with the development of intramuscular fat. Australian Journal of Experimental Agriculture 45, 809-820.

W Weckwerth , K Wenzel and O Fiehn 2004b. Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4, 78-83.

JE Womack 2006. The impact of sequencing the bovine genome. Australian Journal of Experimental Agriculture 46, 151-153.

Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

animal
  • ISSN: 1751-7311
  • EISSN: 1751-732X
  • URL: /core/journals/animal
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Keywords:

Metrics

Altmetric attention score

Full text views

Total number of HTML views: 20
Total number of PDF views: 134 *
Loading metrics...

Abstract views

Total abstract views: 326 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 19th September 2017. This data will be updated every 24 hours.