Article pp.133-142 du Vol.27 n°2 (2007)

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FOCUS : JSMTV

Genomics applied to the improvement

of farm animals: a survey of the research projects funded in the frame of the French programme

“AGENAE”

P. Sellier

1 – INTRODUCTION

The scientific scope and organisational features of the French research programme dealing with genomics of farm animals and called AGENAE – an acro- nym for “Analyse du Génome des Animaux d’Elevage” – were formerly presented by SELLIER et al. (2002) and SELLIER (2003). We now dispose of retro- spective information on the accomplishments of this programme for several years. This article intends to survey its state of achievement while putting spe- cial emphasis on the studies pertaining to the topic “muscle and meat”.

2 – BRIEF RECALL ON PARTNERSHIP, GOVERNANCE STRUCTURE AND FUNDING RESOURCES OF THE PROGRAMME AGENAE

The programme AGENAE is mainly piloted by a “Groupement d’Intérêt Sci- entifique” (GIS) established in May 2002 for a five-year period. The members of the GIS AGENAE, in its final form, are two State-supported research organisa- tions (INRA and CIRAD), on one hand, and four private associations represent- ing the main components of French animal industry, on the other hand (APIS GENE for cattle and small ruminants, CIPA for fish and shellfish, BIOPORC for pigs and AGENAVI for poultry). The programme AGENAE is also supported by a

“Réseau de Recherche et d’Innovation Technologique” devoted to animal genomics, set up in 2003 by the French Ministry in charge of research and called GENANIMAL. The network GENANIMAL plays, in particular, a major role for the financial support of the research projects selected in yearly calls for projects following the usual procedures of scientific evaluation by anonymous INRA, UR337 Station de Génétique Quantitative et Appliquée – F-78352 Jouy-en-Josas – France.

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referees. State funds allocated to GENANIMAL projects originated in the first two years from the “Fonds National de la Science” (FNS) for the “generic”

projects and from the “Fonds de la Recherche Technologique” (FRT) for the

“applied” projects, the latter also receiving funds from the involved industry partners. In the beginning of 2005, a new structure – “Agence Nationale de la Recherche” (ANR) – took place in France and replaced FNS and FRT in their role of financial support of research. Calls for GENANIMAL projects have there- fore been launched since 2005 by ANR that delegates to INRA the further man- agement of the programme for organisational aspects and allocation of funds to research teams.

It is also worth mentioning that, in the course of the initial stages of the programme AGENAE (years 2002 and 2003), a number of infrastructures were either established de novo or extended in order to supply researchers with a coordinated network of resources and equipments that makes possible an easy access to “high-throughput biology” facilities. Two of these infrastructures have a national vocation, namely the CRB GADIE (“Centre de Ressources Biologiques pour la Génomique des Animaux d’Intérêt Économique”) located in Jouy-en-Josas (for more details on the missions and activities of CRB GADIE, see the web site http://www-crb.jouy.inra.fr) and the bioinformatics platform SIGENAE located in Toulouse (http://www.inra.fr/agenae/SIGENAE.html). Other infrastructures, installed in various sites close to the research teams involved, have a local vocation. Most of them are platforms dedicated to either gene expression analyses (hybridisation of microarrays) or proteome analyses (two- dimensional gel electrophoresis and mass spectrometry device). Researchers can also make use of infrastructures and/or resources available in the national network of “génopoles”.

3 – A SURVEY OF THE “TARGETS” OF AGENAE PROJECTS (YEARS 2002-2006)

The distribution of the projects funded in the first five years of the AGENAE/

GENANIMAL programme is summarised in table 1 under two entries: the thematic field on one hand and the species (or group of species) on the other hand. It should be indicated that for few projects having received two or even three funding sets in the successive calls for projects, these different sets are counted as different “projects” for the needs of this survey. On the whole, 58 two- to four-year research projects have benefited from AGENAE/GENANI- MAL funds since 2002. About one-third of these projects tackle a generic question whereas the others refer to more applied objectives. The total amount of public and industry funds allocated to the 58 AGENAE-labelled projects is of the order of 15 millions euros.

With regard to the distribution of the projects by group of species, it appears that ruminants (23 projects, dealing with cattle with few exceptions) and aquatic species (16 projects, conducted mainly on rainbow trout) are by far the most represented. It should however be indicated that these two groups of species have benefited from a certain anteriority in getting support funds. The initial AGENAE projects dealing with fish were funded in 2002, i.e. prior to the imple-

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mentation of the GENANIMAL network by the French Ministry of Research, due to the availability of European funds from IFOP (“Institution Financière pour le Fonctionnement de la Pêche”). As for cattle, several applied research projects received FRT and APIS GENE funds in 2003 when the first call for projects was launched by the GENANIMAL network. Due to their later entry into the GIS AGENAE, the pig industry association BIOPORC and the poultry industry association AGENAVI brought their first contributions to funding of applied research projects only in 2004 and 2005, respectively.

Table 1

Distribution of the AGENAE projects funded over the years 2002-2006 by thematic field and by animal species.

Regarding the distribution of the projects by thematic field, table 1 shows that particular attention has been paid to three grand physiological functions, i.e. reproduction, growth and immunity. Emphasis put on these three topics is however variable, to some extent, according to the species involved. The 15 projects pertaining to the reproductive function are essentially devoted to cattle reproduction (8 projects, most of them having to do with the concern caused by the reduction of fertility currently observed in high-yield milking cows) and to fish reproduction (5 projects). The thematic field “immunity and health status” is investigated under different aspects in all species (10 projects, often relating to genomics of immune response and host-pathogen interactions) but that this topic is strongly predominant among the projects dealing with pigs

Species or group of species

Cattle and small ruminants

Pigs

Chicken and other avian

species

Rainbow trout and other

aquatic species

“Multi- species”

Reproduction: gamete fertility (female and male), sex determination, embryo development

8 – – 5 2

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Meat production: growth,

body composition, meat quality 6 1 2 3 –

Immunity, health status, food safety (microbiological aspects)

3 3 1 3 –

Lactation, milk composition 1 – –

Nutrition – – – 1 –

Stress, adaptation – – – 1 –

“Multi-trait” 2 – 1 – –

Genetic abnormalities 1 – – – –

“Generic” activities and studies:

genomic resources, methodologies and tools, avian stem cells, hormone receptors, etc.

2 – 4 3 5

(a) Cattle and pigs for both projects.

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can be pointed out. As for the thematic field “growth and meat production”, that is specifically investigated in a total of 12 projects about which more details are given below, it is covered by at least one project in all groups of species, with a particular attention paid to this topic in ruminants and, to a lesser extent, in aquatic and avian species.

The 14 projects mentioned in table 1 under the item “generic activities and studies” greatly differ in terms of objective and content. Most of them relate to the basic work that is the prerequisite to further studies in the field of genomics:

sequencing of ESTs (expressed sequence tags) from normalised multi-tissue cDNA libraries in cattle, pigs, chicken and rainbow trout, high-resolution physi- cal mapping – e.g. by use of the whole-genome radiation hybrid panel ChickRH6 (MORISSON et al., 2005) –, detection of single nucleotide polymor- phisms (SNP), development of bioinformatics methods and tools, etc. This item also encompasses a number of projects having a fundamental scope, e.g.

those devoted to functional genomics of avian stem cells, comparative genomics of nuclear receptors of hormones or search for vectors enabling expression of genes coding for interferent RNA or microRNA, as well as projects aiming to develop innovative methods that could be an aid to animal breeding practice (e.g. technology for genotyping of bovine embryos).

4 – THE AGENAE PROJECTS PERTAINING TO MUSCLE AND MEAT PRODUCTION

The interest of genomic approaches for a deeper understanding of the variation in muscle characteristics and meat quality was analysed and discussed by RENANDet al. (2003) and EGGEN and HOCQUETTE (2004). As mentioned above, among the 58 projects funded so far in the frame of AGENAE, a dozen of generic or applied research projects are related to the “muscle and meat” field.

A brief description of the objectives and approaches of each of these projects is done below.

4.1 Cattle

The applied project “QUALVIGENE” was selected in the first GENANIMAL call for projects in 2003 and has benefited from additional funds in 2005 and 2006. The general objective of this large-scale study is to detect and/or to vali- date genes implied in the variation of meat quality in the three main French beef breeds (Charolais, Limousin and Blonde d’Aquitaine). One of the products expected from the achievement of this project is the setting up of a large phe- notypic database that is due to incorporate not only beef traits usually recorded (growth rate, carcass weight and composition) but also – which is encountered much more scarcely and confers a particular originality to the project – a large set of measures relating to muscle characteristics and meat quality, e.g. biochemical and biophysical traits and sensory evaluation of meat by taste panels.

In parallel, a genomic library consisting of DNA of all recorded animals and their two parents is stored for further microsatellite and SNP genotyping needs (e.g.

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MIRANDA et al., 2002). The family structure of the sample of animals follows that of the routine procedure implemented for progeny-testing of artificial insemina- tion (AI) bulls in each of the three involved breeds. The study comprises a total of about 3 400 feedlot-recorded young bulls sired by 114 different AI bulls and slaughtered at 17 months of age on average. This large data set enables to perform a variety of genetic analyses (e.g. RENAND et al., 2006a, 2006b), including those aiming at validating in French beef breeds the practical interest of genetic polymorphisms that have been found to influence meat production traits in various cattle populations (e.g. for calpastatin, thyroglobulin and leptin genes). As beef tenderness is a major concern, one of the tasks of this project will be devoted to the detection of protein markers of this trait through comparing the proteome profiles of animals giving the most tender or the toughest meat.

The applied project “MUGENE” was selected in 2004 and is due to investi- gate an integrated approach – combining genetics, genomics and muscle biology – for monitoring beef quality according to growth capacity and rearing conditions of animals. This study lies on two Charolais lines divergently selected for muscle growth in a feedlot context (RENAND et al., 1998). Animals from both lines are raised in two different systems of meat production, either young bulls intensively fed and slaughtered at 15-19 months of age or pasture- fed steers slaughtered at 30 months of age. The aim of this project is to assess the joint influence of the genetic merit for muscle growth capacity and the sys- tem of beef production on post mortem maturation and ultimate quality of meat, including sensory quality traits. Body composition traits and adipose tissue properties are also investigated. Tools formerly developed, i.e. muscle cDNA library (SUDRE et al., 2004) and muscle proteome maps (BOULEY et al., 2004), are being used for the comparative study of muscle transcriptome and proteome in the four experimental treatments (HOCQUETTE et al., 2006).

The generic project “MUSCLON”, selected in 2006, refers to a subject that completely differs from the preceding ones since it tackles the question of muscle tissue development in cloned cattle issued from somatic cell nuclear trans- fer technology. The objective of this three-year project is (1) to characterise biochemical and histological properties of muscle of cloned animals, during the foetal period and until 18 months of age, comparatively to those of animals issued from sexual reproduction, (2) to carry out functional genomics studies in order to explore the molecular mechanisms underlying the delayed muscle differentiation that seemingly occurs in somatic clones according to preliminary observations, and (3) to see whether similar mechanisms are also displayed in the offspring of cloned animals.

4.2 Sheep

One of the applied projects selected in 2004 is conducted in the ovine species (“TEXEL BELGE”). The general purpose is to take benefit from the original model of muscular hypertrophy offered by the Belgian Texel population (LAVILLE

et al., 2004) for investigating the expression of genes controlling muscle devel- opment in sheep and relating this expression with carcass characteristics and ultimate meat quality (HAMELIN et al., 2006). In another part of the project, it is intended to conduct on a real scale and to evaluate an operation of marker- assisted introgression of the involved QTL into a “meaty” strain of the Lacaune breed. It can incidentally be noted that CLOP et al. (2006) reported a quite novel

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mechanism for explaining the way in which muscle hypertrophy exhibited by Belgian Texel sheep is genetically determined. The point mutation responsible for this phenotype creates an “illegitimate” target site for microRNAs within a gene that does not contain it in its normal form. The gene involved is the well- known myostatin (GDF8) gene whose translation is disrupted by the above mutation. The absence of myostatin causes muscular hypertrophy as this has been found, through more classical polymorphisms of the same gene (point mutation or deletion), for the double-muscling phenotype in cattle.

4.3 Pigs

The applied project “BIOMARK”, selected in 2004, is designed for performing the fine mapping of several quantitative trait loci that are in segregation in French commercial pig populations, with the perspective of possible implemen- tation of marker-assisted selection schemes in pigs. The main traits concerned by this three-year project are postweaning daily gain, backfat thickness, carcass tissue composition and a number of pork quality traits (colour, ultimate pH, water-holding capacity, intramuscular fat content). The 8-10 chromosomal regions covered by this fine mapping study have been chosen from previously published data on QTL influencing pork production traits (BIDANEL and ROTH- SCHILD, 2002; MILAN et al., 2002). Regarding animal resources, the study relies on around 100 informative families that originate from most of breeds and lines currently used in France.

4.4 Poultry

Increasing use of poultry meat for processing has led since some years to pay greater attention to the genetic control of technological quality of meat, defined as the ability to be stored and further processed into meat products (DEBUT et al., 2003; LE BIHAN-DUVAL, 2004). One of the applied projects selected in 2005 (“QUALVIVOL”) is intended to decipher genetic variation in technological quality of broiler meat using both positional and functional genomics, know- ing that very few QTL findings are so far available in this respect (HOCKING, 2005). This three-year project aims to identify molecular markers (microsatellites or SNP) associated with meat quality in a commercial population through trans- posing and refining the QTL findings previously obtained in experimental lines and exploiting gene expression data resulting from the study of muscle transcriptome. Particular emphasis is put in this project on the detection of genetic polymorphisms responsible for the joint variation in muscle glycolytic potential and ultimate pH of meat (LE BIHAN-DUVAL et al., 2006).

The purpose of the generic project “eQTL” selected in 2004 is to evaluate the interest of an approach called eQTL (expression quantitative trait locus) for identifying genes responsible for variability of quantitative traits (JANSEN and NAP, 2001). This original method consists of performing a genetic linkage analysis, similar to that used for detection of QTL, using gene expression data resulting from transcriptome analyses instead of performance records. This methodological project refers to the field of broiler meat production because the traits studied for testing the eQTL method deal with growth and fatness of chicken. The animals concerned by this project originate from two divergent

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selection experiments (lines selected upward and downward for either average daily gain or abdominal fat content).

The applied project “GENECAN”, selected in 2006, is included under the item “multi-trait” in table 1. It consists of a genome scan designed to search for QTL contributing to genetic variation in a number of traits of interest for the production of overfed mule ducks, including those relating to quality of products (“foie gras” and “magret”). The design of this experiment is original since it should be taken into account that the mule duck is an inter-generic hybrid resulting from the cross between a Muscovy drake and a common female duck (BRUN et al., 2005).

One can also mention here the applied project “RESISAL” that was selected in 2005 and is directly linked with the microbiological quality of chicken meat.

This project indeed aims at identifying genetic factors underlying host resistance/sensitivity to Salmonella carrier state by use of differential gene expression analysis. Candidate genes and QTL have formerly been reported for this trait by BEAUMONT et al. (2003) and TILQUIN et al. (2005) among others. The immune response mechanisms implied in resistance will also be investigated.

Results could lead to define new criteria of selection that would be of interest for breeding schemes in chicken and further in other avian species.

4.5 Fish

Investigations on the genetic determination of muscle hyperplasic development and muscle fibre typology in rainbow trout have been conducted in the frame of a research project selected in the 2002 call for fish projects. A repertoire of muscle-specific transcripts was defined starting from the rainbow trout multi-tissue cDNA library developed for the needs of the “fish” community inter- ested in the programme AGENAE. This repertoire has been used for in situ hybridisation assays in order to follow the changes in gene expression patterns in the course of myogenesis and to characterise the stages of differentiation and diversification of muscle fibres in embryos (CHAUVIGNE et al., 2005) and larvae (CHAUVIGNE et al., 2006).

Two other projects, selected in 2003 for the first one and in 2005 for the second one, are related to each other since both of them deal with variation in adi- posity of the rainbow trout. The first project concerns the molecular bases of the genetic and nutritional control of fat deposition. Regarding the variation of genetic origin, the project rests on two lines resulting from divergent selection for intramuscular fat content. The variation of nutritional origin concerns the dietary energy concentration using two diets more or less rich in lipids. Differential analyses of gene expression in animals from each of the four line x diet combi- nations are performed in muscle, liver and abdominal fat. In addition of this transcriptomic approach, liver proteome is also investigated (KOLDITZ et al., 2006). As for the second project (“GFAT”), it aims at evaluating the effects of genome ploidy state (diploids vs. triploids) and dietary fat concentration on the expression of genes implied in lipid metabolism of adipose tissue and liver, during the consecutive phases of storage and mobilisation of body fat reserves that occur in the course of the reproductive life of farmed rainbow trout.

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5 – CONCLUSION

This rapid survey of the AGENAE/GENANIMAL projects funded in the period 2002-2006 shows the great thematic diversity of the generic and applied research works that have been financially supported in the frame of this large French programme devoted to farm animal genomics. It also reveals that the research projects pertaining to animal growth, meat production and quality of meat products in several species represent a significant proportion of the 58 projects that are in progress or are going to be implemented in the near future.

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