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Food, fibre and pharmaceuticals from animals
REVIEW (Open Access)

Application of gene expression studies in livestock production systems: a European perspective

I. Cassar-Malek A C , B. Picard A , C. Bernard B and J.-F. Hocquette A
+ Author Affiliations
- Author Affiliations

A INRA, UR1213, Unité de Recherches sur les Herbivores, Centre de Clermont-Ferrand/Theix, Saint-Genès-Champanelle 63122, France.

B Institut de l’Elevage, Service Aptitudes et Sélection des Races Allaitantes, 149 rue de Bercy, Paris Cedex 12, 75595, France.

C Corresponding author. Email: isabelle.cassar-malek@clermont.inra.fr

Australian Journal of Experimental Agriculture 48(7) 701-710 https://doi.org/10.1071/EA08018
Submitted: 7 January 2008  Accepted: 30 March 2008   Published: 20 June 2008

Abstract

In the context of sustainable agriculture and animal husbandry, understanding animal physiology remains a major challenge in the breeding and production of livestock, especially to develop animal farming systems that respond to the new and diversified consumer demand. Physiological processes depend on the expression of many genes acting in concert. Considerable effort has been expended in recent years on examining the mechanisms controlling gene expression and their regulation by biological and external factors (e.g. genetic determinants, nutritional factors, and animal management). Two main strategies have been developed to identify important genes. The first one has focussed on the expression of candidate genes for key physiological pathways at the level of both the transcripts and proteins. An original strategy has emerged with the advent of genomics that addresses the same issues through the examination of the molecular signatures of all genes and proteins using high-throughput techniques (e.g. transcriptomics and proteomics). In this review, the application of the gene expression studies in livestock production systems is discussed. Some practical examples of genomics applied to livestock production systems (e.g. to optimise animal nutrition, meat quality or animal management) are presented, and their outcomes are considered. In the future, integration of the knowledge gained from these studies will finally result in optimising livestock production systems through detection of desirable animals and their integration into accurate breeding programs or innovative management systems.


References


Barendse W (2005) The transistion from quantitative trait loci to diagnostic test in cattle and other livestock. Australian Journal of Experimental Agriculture 45, 831–836.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Bauchart C, Rémond D, Chambon C, Patureau-Mirand M, Savary-Auzeloux I, Reynes C (2006) Small peptides (<5 kDa) found in ready-to- eat beef meat. Meat Science 74, 658–666.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Bendixen E, Taylor R, Hollung K, Hildrum K, Picard B, Bouley J (2005a) Proteomics, an approach towards understanding the biology of meat quality. In ‘Indicators of milk and beef quality’. (Eds JF Hocquette, S Gigli) pp. 81–94. EAAP Publication 112. (Wageningen Academic Publishers: Wageningen, The Netherlands).

Bendixen E, Hedegaard J, Horn P (2005b) Functional genomics in farm animals – microarray analysis. Meat Science 71, 128–137.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Bernabucci U, Ronchi B, Basirico L, Pirazzi D, Rueca F, Lacetera N, Nardone A (2004) Abundance of mRNA of apolipoprotein B100, apolipoprotein E and microsomal triglyceride transfer protein in liver from periparturient cows. Journal of Dairy Science 87, 2881–2888.
CAS | PubMed |
open url image1

Bernard C, Cassar-Malek I, Hocquette JF (2006) EP06300943.5 Genomic marker for meat tenderness. 12 September 2006.

Bernard C, Cassar-Malek I, Le Cunff M, Dubroeucq H, Renand G, Hocquette JF (2007) New indicators of beef sensory quality revealed by expression of specific genes. Journal of Agricultural and Food Chemistry 55, 5229–5237.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Bernard L, Leroux C, Chilliard Y (2008) Expression and nutritional regulation of lipogenic genes in the ruminant lactating mammary gland. Advances in Experimental Medicine and Biology 606, 67–108.
CAS | PubMed |
open url image1

Bonnet M, Leroux C, Faulconnier Y, Hocquette JF, Bocquier F, Martin P, Chilliard Y (2000) Lipoprotein lipase activity and mRNA are up-regulated by refeeding in adipose tissue and cardiac muscle of sheep. The Journal of Nutrition 130, 749–756.
CAS | PubMed |
open url image1

Bonnet M, Faulconnier Y, Leroux C, Jurie C, Cassar-Malek I, Bauchart D, Boulesteix P, Pethick D, Hocquette JF, Chilliard Y (2007) Glucose-6-phosphate dehydrogenase and leptin are related to marbling differences among Limousin and Angus or Japanese Black × Angus steers. Journal of Animal Science 85, 2882–2894.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Bouley J, Chambon C, Picard B (2004) Mapping of bovine skeletal muscle proteins using two-dimensional gel electrophoresis and mass spectrometry. Proteomics 4, 1811–1824.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Bouley J, Meunier B, Chambon C, De Smet S, Hocquette JF, Picard B (2005) Proteomic analysis of bovine skeletal muscle hypertrophy. Proteomics 5, 490–500.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Byrne KA, Wang YH, Lehnert SA, Harper GS, McWilliam SM, Bruce HL, Reverter A (2005) Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction. Journal of Animal Science 83, 1–12.
CAS | PubMed |
open url image1

Cassar-Malek I, Bernard C, Jurie C, Barnola I, Gentes G, Dozias D, Micol D, Hocquette JF (2005) Pasture-based beef production systems may influence muscle characteristics and gene expression. In ‘Indicators of milk and beef quality’. (Eds JF Hocquette, S Gigli) pp. 385–390. EAAP Publication 112. (Wageningen Academic Publishers: Wageningen, The Netherlands)

Cassar-Malek I, Passelaigue F, Bernard C, Léger J, Hocquette JF (2007) Target genes of myostatin loss-of-function in muscles of late bovine fetuses. BMC Genomics 8, 63.
Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Chadwick R (2004) Nutrigenomics, individualism and public health. The Proceedings of the Nutrition Society 63, 161–166.
Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Chaze T, Bouley J, Chambon C, Barboiron C, Picard B (2006) Mapping of alkaline proteins in bovine skeletal muscle. Proteomics 6, 2571–2575.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Chaze T, Meunier B, Chambon C, Jurie C, Picard B (2008) In vivo proteome dynamics during early bovine myogenesis Proteomics in press , open url image1

Cheon Y, Nara TY, Band MR, Beever JE, Wallig MA, Nakamura MT (2005) Induction of overlapping genes by fasting and a peroxisome proliferator in pigs: evidence of functional PPARalpha in non proliferating species. The American Journal of Physiology 288, R1525–R1535.
CAS |
open url image1

Chevalet C, Hocquette JF, Sellier P, Monget P (2007) AGENAE-GENANIMAL: the French Research program in animal genomics. In ‘Energy and protein metabolism and nutrition’. (Eds I Ortigues-Marty, N Miraux, W Brand-Williams) pp. 311–312. EAAP Publication 124. (Wageningen Academic Publishers: Wageningen, The Netherlands).

Childs KD, Goad DW, Allan MF, Pomp D, Krehbiel C, Geisert RD, Morgan JB, Malayer JR (2002) Differential expression of NAT1 translational repressor during development of bovine intramuscular adipocytes. Physiological Genomics 10, 49–56.
CAS | PubMed |
open url image1

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. Nature Genetics 38, 813–818.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Cogburn LA, Wang X, Carre W, Rejto L, Aggrey SE, Duclos MJ, Simon J, Porter TE (2004) Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways. Comparative and Functional Genomics 5, 253–261.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Fadiel A, Anidi I, Eichenbaum KD (2005) Farm animal genomics and informatics: an update. Nucleic Acids Research 33, 6308–6318.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Fox Keller E (2002) ‘The century of the gene.’ (Harvard University Press: Cambridge, MA) 192 pp.

Greenfield RB, Cevana MJ, Donkin SS (2000) Changes in mRNA expression for gluconeogenic enzymes in liver of dairy cattle during the transition to lactation. Journal of Dairy Science 83, 1228–1236.
CAS | PubMed |
open url image1

Grobet L, Martin LJ, Poncelet D, Pirottin D, Brouwers B , et al. (1997) A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics 17, 71–74.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Gruffat D, Durand D, Chilliard Y, Williams P, Bauchart D (1997) Hepatic gene expression of apolipoprotein B100 during early lactation in underfed, high producing dairy cows. Journal of Dairy Science 80, 657–666.
CAS | PubMed |
open url image1

Hamelin M, Sayd T, Chambon C, Bouix J, Bibé B , et al. (2006) Proteomic analysis of ovine muscle hypertrophy. Journal of Animal Science 84, 3266–3276.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Heyman Y, Chavatte-Palmer P, Berthelot V, Fromentin G, Hocquette JF, Martignat L, Renard JP (2007) Assessing the quality of products from cloned animal: an integrative approach. Theriogenology 67, 134–141.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Hocquette JF (2005) Where are we in genomics? Journal of Physiology and Pharmacology 56, 37–70.
PubMed |
open url image1

Hocquette JF, Graulet B, Vermorel M, Bauchart D (2001) Weaning affects lipoprotein lipase activity and gene expression only in adipose tissues and in masseter but not in other muscles of the calf. The British Journal of Nutrition 86, 433–441.
CAS | PubMed |
open url image1

Hocquette JF, Cassar-Malek I, Listrat A, Picard B (2005) Current genomics in cattle and application to beef quality. In ‘Indicators of milk and beef quality’. (Eds JF Hocquette, S Gigli) pp. 65–79. EAAP Publication 112. (Wageningen Academic Publishers: Wageningen, The Netherlands)

Hocquette JF, Lehnert S, Barendse W, Cassar-Malek I, Picard B (2007) Recent advances in cattle functional genomics and their application to beef quality. Animal 1, 159–173.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Hollung K, Veiseth E, Jia X, Moslet Faergestad E, Ivar Hildrum K (2007) Application of proteomics to understand the molecular mechanisms behind meat quality. Meat Science 77, 97–104.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Jeong DW, Kim TS, Chung YW, Lee BJ, Kim IY (2002) Selenoprotein W is a glutathione-dependent antioxidant in vivo. FEBS Letters 517, 225–228.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Jurie C, Cassar-Malek I, Bonnet M, Leroux C, Bauchart D, Boulesteix P, Pethick DW, Hocquette JF (2007) Adipocyte fatty acid-binding protein and mitochondrial enzyme activities in muscles as relevant indicators of marbling in cattle. Journal of Animal Science 85, 2660–2669.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Lee SH, Park EW, Cho YM, Kim SK, Lee JH , et al. (2007) Identification of differentially expressed genes related to intramuscular fat development in the early and late fattening stages of hanwoo steers. Journal of Biochemistry and Molecular Biology 40, 757–764.
CAS | PubMed |
open url image1

Lehnert SA, Wang YH, Tan SH, Reverter A (2006) Gene expression-based approaches to beef quality research. Australian Journal of Experimental Agriculture 46, 165–172.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Lehnert SA, Reverter A, Byrne KA, Wang Y, Nattrass GS, Hudson NJ, Greenwood PL (2007) Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds. BMC Developmental Biology 7, 95.
Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Loor JJ, Dann HM, Janovick Guretzky NA, Everts RE, Oliveira R, Green CA, Litherland NB, Rodriguez-Zas SL, Lewin HA, Drackley JK (2006) Plane of nutrition prepartum alters hepatic gene expression and function in dairy cows as assessed by longitudinal transcript and metabolic profiling. Physiological Genomics 27, 29–41.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Morzel M, Terlouw C, Chambon C, Micol D, Picard B (2008) Muscle proteome and meat eating qualities of Longissimus thoracis of “Blonde d’Aquitaine” young bulls: a central role of HSP27 isoforms. Meat Science 78, 297–304.
CAS |
open url image1

Mullen AM, Stapleton PC, Corcoran D, Hamill RM, White A (2006) Understanding meat quality through the application of genomic and proteomic approaches. Meat Science 74, 3–16.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Ojha S, Kostrzynska M (2008) Examination of animal and zoonotic pathogens using microarrays. Veterinary Research 39, 4.
Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Ollier S, Robert-Granié C, Bernard L, Chilliard Y, Leroux C (2007) Mammary transcriptome analysis of food-deprived lactating goats highlights genes involved in milk secretion and programmed cell death. The Journal of Nutrition 137, 560–567.
CAS | PubMed |
open url image1

Renand G, Payet N, Levéziel H, Denoyelle C, Hocquette JF, Lepetit J, Rousset S, Dodelin V, Malafosse A (2007) Markers in DAGT1 and TG genes are not associated with intramuscular lipid content in the french beef breeds. In ‘Proceedings of the 53rd International Congress of Meat Science and Technology’. (Eds G Zhou, W Zhang) pp. 75–76. (China Agricultural University Press: Beijing)

Sayd T, Morzel M, Chambon C, Franck M, Figwer P, Larzul C, Le Roy P, Monin G, Cherel P, Laville E (2006) Proteome analysis of the sarcoplasmic fraction of pig semimembranosus muscle: implications on meat color development. Journal of Agricultural and Food Chemistry 54, 2732–2737.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Schwerin M, Kuehn C, Wimmers S, Walz C, Goldammer T (2006) Trait-associated expressed hepatic and intestine genes in cattle of different metabolic type-putative functional candidates for nutrient utilization. Journal of Animal Breeding and Genetics 123, 307–314.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Shirazi-Beechey S (2004) Transcriptional regulation of intestinal nutrient transporters. In ‘Molecular mechanisms controlling transmembrane transport. Topics in current genetics’. (Eds E Boles, R Kramer) pp. 1–22. (Springer Verlag: Berlin)

Sudre K, Leroux C, Pietu G, Cassar-Malek I, Petit E, Listrat A, Auffray C, Picard B, Martin P, Hocquette JF (2003) Transcriptome analysis of two bovine muscles during ontogenesis. Journal of Biochemistry 133, 745–756.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Sudre K, Cassar-Malek I, Listrat A, Ueda Y, Leroux C, Jurie C, Auffray C, Renand G, Martin P, Hocquette JF (2005) Biochemical and transcriptomic analyses of two bovine skeletal muscles in Charolais bulls divergently selected for muscle growth. Meat Science 70, 267–277.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Tsitsilonis OE, Stoeva S, Echner H, Balafas A, Margomenoua L, Katsoulasa HL, Troy DJ, Voelter W, Papamichail M, Lymberi P (2002) A skeletal muscle troponin T specific ELISA based on the use of an antibody against the soluble troponin T (16–31) fragment. Journal of Immunological Methods 268, 141–148.
Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Tuggle CK, Wang Y, Couture O (2007) Advances in swine transcriptomics. International Journal of Biological Sciences 3, 132–152.
CAS | PubMed |
open url image1

Wang YH, Reverter A, Mannen H, Taniguchi M, Harper GS, Oyama K, Byrne KA, Oka A, Tsuji S, Lehnert SA (2005) Transcriptional profiling of muscle tissue in growing Japanese Black cattle to identify genes involved with the development of intramuscular fat. Australian Journal of Experimental Agriculture 45, 809–820.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Wang YH, Reverter A, Kemp D, McWilliam SM, Ingham A, Davis CA, Moore RJ, Lehnert SA (2007) Gene expression profiling of Hereford Shorthorn cattle following challenge with Boophilus microplus tick larvae. Australian Journal of Experimental Agriculture 47, 1397–1407.
Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Yeh JY, Gu QP, Beilstein MA, Forsberg NE, Whanger PD (1997) Selenium influences tissue levels of selenoprotein W in sheep. The Journal of Nutrition 127, 394–402.
CAS | PubMed |
open url image1