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Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes: I-selection goals and criteria

  • F. Phocas (a1), C. Belloc (a2), J. Bidanel (a3), L. Delaby (a4), J. Y. Dourmad (a4), B. Dumont (a5), P. Ezanno (a2), L. Fortun-Lamothe (a6), G. Foucras (a7), B. Frappat (a8), E. González-García (a9), D. Hazard (a6), C. Larzul (a6), S. Lubac (a10), S. Mignon-Grasteau (a11), C. R. Moreno (a6), M. Tixier-Boichard (a1) and M. Brochard (a8)...


Agroecology uses natural processes and local resources rather than chemical inputs to ensure production while limiting the environmental footprint of livestock and crop production systems. Selecting to achieve a maximization of target production criteria has long proved detrimental to fitness traits. However, since the 1990s, developments in animal breeding have also focussed on animal robustness by balancing production and functional traits within overall breeding goals. We discuss here how an agroecological perspective should further shift breeding goals towards functional traits rather than production traits. Breeding for robustness aims to promote individual adaptive capacities by considering diverse selection criteria which include reproduction, animal health and welfare, and adaptation to rough feed resources, a warm climate or fluctuating environmental conditions. It requires the consideration of genotype×environment interactions in the prediction of breeding values. Animal performance must be evaluated in low-input systems in order to select those animals that are adapted to limiting conditions, including feed and water availability, climate variations and diseases. Finally, we argue that there is no single agroecological animal type, but animals with a variety of profiles that can meet the expectations of agroecology. The standardization of both animals and breeding conditions indeed appears contradictory to the agroecological paradigm that calls for an adaptation of animals to local opportunities and constraints in weakly artificialized systems tied to their physical environment.


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Ahlman, T, Berglund, B, Rydhmer, L and Strandberg, E 2011. Culling reasons in organic and conventional dairy herds and genotype by environment interaction for longevity. Journal of Dairy Science 94, 15681575.
Ahlman, T, Ljung, M, Rydhmer, L, Röcklinsberg, H, Strandberg, E and Wallenbeck, A 2014. Differences in preferences for breeding traits between organic and conventional dairy producers in Sweden. Livestock Science 162, 514.
Alhidary, IA, Shini, S, Al Jassim, RAM and Gaughan, JB 2012. Physiological responses of Australian Merino wethers exposed to high heat load. Journal of Animal Science 90, 212220.
Azoulay, Y, Druyan, S, Yadgary, L, Hadad, Y and Cahaner, A 2011. The viability and performance under hot conditions of featherless broilers versus fully feathered broilers. Poultry Science 90, 1929.
Becker, EW 2007. Micro-algae as a source of protein. Biotechnology Advances 25, 207210.
Bell, MJ, Potterton, SL, Graignon, J, Saunders, N, Wilcox, RH, Hunter, M, Goodman, JR and Garnsworthy, PC 2014. Variation in enteric methane emissions among cows on commercial dairy farms. Animal 8, 15401546.
Bell, MJ, Wall, E, Russell, G, Simm, G and Scott, AW 2011. The effect of improving cow productivity, fertility and longevity on the global warming potential of dairy systems. Journal of Dairy Science 94, 36623678.
Berman, A 2011. Invited review: are adaptations present to support dairy cattle productivity in warm climates? Journal of Dairy Science 94, 21472158.
Bloemhof, S, Kause, A, Knol, EF, Van Arendonk, JAM and Misztal, I 2012. Heat stress effects on farrowing rate in sows: genetic parameter estimation using within-line and crossbred models. Journal Animal Science 90, 21092119.
Boettcher, PJ, Fatehi, J and Schutz, MM 2003. Genotype×environment interactions in conventional versus pasture-based dairies in Canada. Journal of Dairy Science 86, 383389.
Brandt, H, Werner, DN, Baulain, U, Brade, W and Weissmann, F 2010. Genotype–environment interactions for growth and carcass traits in different pig breeds kept under conventional and organic production systems. Animal 4, 535544.
Carabano, MJ, Bachagha, K, Ramon, M and Diaz, C 2014. Modeling heat stress effect on Holstein cows under hot and dry conditions: selection tools. Journal of Dairy Science 97, 78897904.
de Haas, Y, Windig, JJ, Calus, MPL, Dijkstra, J, de Haan, M, Bannink, A and Veerkamp, RF 2011. Genetic parameters for predicted methane production and potential for reducing enteric emissions through genomic selection. Journal of Dairy Science 94, 61226134.
Delaby, L, Faverdin, P, Michel, G, Disenhaus, C and Peyraud, JL 2009. Effect of different feeding strategies on lactation performance of Holstein and Normande dairy cows. Animal 3, 891905.
Delaby, L and Fiorelli, JL 2014. Elevages laitiers à bas intrants: entre traditions et innovations. INRA. Productions Animales 27, 123134.
De Verdal, H, Mignon-Grasteau, S, Bastianelli, D, Même, N, Le Bihan-Duval, E and Narcy, A 2013a. Reducing the environmental impact of poultry breeding by genetic selection. Journal of Animal Science 91, 613622.
De Verdal, H, Narcy, A, Bastianelli, D, Chapuis, H, Meme, N, Urvoix, S, Le Bihan-Duval, E and Mignon-Grasteau, S 2011. Improving the efficiency of feed utilization in poultry by selection. 2. Genetic parameters of excretion traits and correlations with anatomy of the gastro-intestinal tract and digestive efficiency. BMC Genetics 12, 10.
De Verdal, H, Narcy, A, Bastianelli, D, Meme, N, Urvoix, S, Collin, A, Le Bihan-Duval, E and Mignon-Grasteau, S 2013b. Genetic variability of metabolic characteristics in chickens selected for their ability to digest wheat. Journal of Animal Science 91, 26052615.
Dumont, B, Fortun-Lamothe, L, Jouven, M, Thomas, M and Tichit, M 2013. Prospects from agroecology and industrial ecology for animal production in the 21st century. Animal 7, 10281043.
Dumont, B, González-García, E, Thomas, M, Fortun-Lamothe, L, Ducrot, C, Dourmad, JY and Tichit, M 2014. Forty research issues for the redesign of animal production systems in the 21st century. Animal 8, 13821393.
Ellis, S 2004. Review: the cattle major histocompatibility complex: is it unique? Veterinary Immunology and Immunopathology 102, 18.
FAO 2006. Livestock’s long shadow: environmental issues and options. LEAD, FAO, Rome, Italy.
Flori, L, Gao, Y, Laloë, D, Lemonnier, G, Leplat, JJ, Teillaud, A, Cossalter, AM, Laffitte, J, Pinton, P, de Vaureix, C, Bouffaud, M, Mercat, MJ, Lefevre, F, Oswald, IP, Bidanel, JP and Rogel-Gaillard, C 2011. Immunity traits in pigs: substantial genetic variation and limited covariation. PLoS One 6, e22717.
Friggens, NC, Ingvartsen, KL and Emmans, GC 2004. Prediction of body lipid change in pregnancy and lactation. Journal of Dairy Science 87, 9881000.
Fulkerson, WJ, Davison, TM, Garcia, SC, Hough, G, Goddard, ME, Dobos, R and Blockey, M 2008. Holstein-Friesian dairy cows under a predominantly grazing system: interaction between genotype and environment. Journal of Dairy Science 91, 826839.
Gavojdian, D, Kusza, S and Javor, A 2014. Implications of genotype by environment interactions in dairy sheep welfare. Animal Science and Biotechnologies 47, 289295.
González-García, E, Gozzo de Figuereido, V, Foulquie, D, Jousserand, E, Autran, P, Camous, S, Tesniere, A, Bocquier, F and Jouven, M 2014. Circannual body reserves dynamics and metabolic profile in Romane ewes reared in a pastoral system. Domestic Animal Endocrinology 46, 3748.
Haile-Mariam, M, Carrick, MJ and Goddard, ME 2008. Genotype by environment interaction for fertility, survival, and milk production traits in Australian dairy cattle. Journal of Dairy Science 91, 48404853.
Hammami, H, Bormann, J, M’hamdi, N, Montaldo, HH and Gengler, N 2013. Evaluation of heat stress effects on production traits and somatic cell score of Holsteins in a temperate environment. Journal of Dairy Science 96, 18441855.
Harinder, P, Makkar, S, Tran, G, Heuzé, V and Ankers, P 2014. Review: state-of-the-art on use of insects as animal Feed. Animal Feed Science adn Techology 197, 133.
Herrero, M, Havlik, P, Valin, H, Notenbaert, A, Rufino, MC, Thornton, PK, Blümmel, M, Weiss, F, Grace, D and Obersteiner, M 2013. Biomass use, production, feed efficiencies, and greenhouse gas emissions from global livestock systems. Proceedings of the National Academy of Sciences of the USA 110, 2088820893.
Huisman, AE, Brown, DJ and Fogarty, NM 2016. Ability of sire breeding values to predict progeny bodyweight, fat and muscle using various transformations across environments in terminal sire sheep breeds. Animal Production Science 56, 95101.
Huquet, B, Leclerc, H and Ducrocq, V 2012. Modelling and estimation of genotype by environment interactions for production traits in French dairy cattle. Genetics Selection Evolution 44, 114.
IFOAM 2014. Organic Animal Husbandry across the world: Towards an Action Plan for development and strengthening of Organic Animal Husbandry. In Proceedings of the IAHA-Preconference and Workshop, IFOAM 18th Organic World Congress, 12 to 15 October, Istanbul, Turkey.
Kadowaki, H, Suzuki, E, Kojima-Shibata, C, Suzuki, K, Okamura, T, Onodera, W, Kojima-Shibata, C and Kano, H 2012. Selection for resistance to swine mycoplasmal pneumonia over 5 generations in Landrace pigs. Livesock Science 147, 2026.
Kearney, JF, Schutz, MM, Boettcher, PJ and Weigel, KA 2004. Genotype×environment interaction for grazing vs. confinement. II. Health and reproduction traits. Journal of Dairy Science 87, 510516.
Lamont, SJ, Pinard-van der Laan, MH, Cahaner, A, Van Der Poel, JJ and Parmentier, HK 2003. Selection for disease resistance: direct selection on the immune response. In Poultry genetics, breeding and biotechnology (ed. WM Muir and SE Aggrey), pp. 399418. CABI, Wallingord.
Lawrence, AB. and Wall, E 2014. Selection for environmental fit from existing domesticated species. Revue Scientifique et Technique-Office International des Epizooties 33, 171179.
Leenhouwers, JI, Ten Napel, J, Hanenberg, EHAT and Merks, JWM 2011. Breeding replacement gilts for organic pig herds. Animal 5, 615621.
Littlejohn, MD, Henty, KM, Tiplady, K, Johnson, T, Harland, C, Lopdell, T, Sherlock, RG, Li, W, Lukefahr, SD, Shanks, BC, Garrick, DJ, Snell, RG, Spelman, RJ and Davis, SR 2014. Functionally reciprocal mutations of the prolactin signaling pathway define hairy and slick cattle. Nature Communications 5, 5861.
Mark, T 2004. Applied genetic evaluations for production and functional traits in dairy cattle. Journal of Dairy Science 87, 26412652.
Martin, C, Morgavi, DP and Doreau, M 2010. Methane mitigation in ruminants: from microbe to the farm scale. Animal 4, 351365.
McLaren, A, Brotherstone, S, Lambe, NR, Conington, J, Mrode, R and Bunger, L 2015. The effects of different farm environments on the performance of Texel sheep. Animal 9, 16241634.
Morris, CA 2007. A review of genetic resistance to disease in Bos taurus cattle. Veterinary Journal 174, 481491.
Morris, CA, Baker, RL, Hickey, SM, Johnson, DL, Cullen, NG and Wilson, JA 1993. Evidence of genotype by environment interaction for reproductive and maternal traits in beef cattle. Animal Production 56, 6983.
Mulder, HA, Veerkamp, RF, Ducro, BJ, van Arendonk, JAM and Bijma, P 2006. Optimization of dairy cattle breeding programs for different environments with genotype by environment interaction. Journal Dairy Science 89, 17401752.
Nauta, WJ, Baars, T, Groen, AF, Veerkamp, RF and Roep, D 2001. Animal breeding in organic farming. Discussion paper. Retrieved on 21 September 2015 from
N’Dri, AL, Mignon-Grasteau, S, Sellier, N, Tixier-Boichard, M and Beaumont, C 2007a. Interactions between the naked neck gene, sex, and fluctuating ambient temperature on heat tolerance, growth, body composition, meat quality, and sensory analysis of slow growing meat-type broilers. Livestock Science 110, 3345.
N’Dri, AL, Sellier, N, Tixier-Boichard, M, Beaumont, C and Mignon-Grasteau, S 2007b. Genotype by environment interactions in relation to growth traits in slow growing chickens. Genetics. Selection and Evolution 39, 513528.
Pabiou, T, Nilforooshan, M, Laloë, D, Hjerpe, E and Venot, E 2014. Across Country Genetic Parameters in Beef Cattle for Interbeef Weaning Weight Genetic Evaluation. In Proceedings 10thWorld Congress of Genetics Applied to Livestock Production, 17 to 22 August, Vancouver, BC, Canada.
Phocas, F, Agabriel, J, Dupont-Nivet, M, Geurden, I, Médale, F, Mignon-Grasteau, S, Gilbert, H and Dourmad, JY 2014. Le phénotypage de l’efficacité alimentaire et de ses composantes, une nécessité pour accroître l’efficience des productions animales. INRA Productions Animales 27, 235248.
Phocas, F, Belloc, C, Delaby, L, Dourmad, JY, Ducrot, C, Dumont, B, Ezanno, P, Foucras, G, Gonzales-Garcia, E, Hazard, D, Lamothe, L, Larzul, C, Mignon-Grasteau, S, Moreno, CR, Tixier-Boichard, M, Brochard, M, Bidanel, J, Frappat, B and Lubac, S 2015. Outils et leviers pour favoriser le développement d’une génétique animale adaptée aux enjeux de l’agroécologie. Rapport de l’étude no. SSP-2014-061 commanditée par le Ministère de l’Agriculture, l’Alimentation et la Forêt, septembre 2015. 120 p. Available at
Pinard-van der Laan, MH, Lillehoj, HS and Zhu, JJ 2003. Genetic resistance and transmission of avian parasites. In Poultry genetics, breeding and biotechnology (ed. WM Muir and SE Aggrey), pp. 313326. CABI, Wallingford.
Pinares-Patiño, CS, Hickey, SM, Young, EA, Dodds, KG, MacLean, S, Molano, G, Sandoval, E, Kjestrup, H, Harland, R, Hunt, C, Pickering, NK and McEwan, JC 2013. Heritability estimates of methane emissions from sheep. Animal 7, 316321.
Rauw, WM, Kanis, E, Noordhuizen-Stassen, EN and Grommers, FJ. 1998. Undesirable side effects of selection for high production efficiency in farm animals: a review. Livestock Production Science 56, 1533.
Renaudeau, D, Huc, E and Noblet, J 2007. Acclimation to high ambient temperature in Large White and Caribbean Creole growing pigs. Journal of Animal Science 85, 779790.
Robertson, A 1959. The sampling variance of the genetic correlation coefficient. Biometrics 15, 469485.
Rupp, R, Bergonier, D, Dion, S, Hygoneng, MC, Aurel, MR, Robert-Granié, C and Foucras, G 2009. Response to somatic cell count-based selection for mastitis resistance in a divergent selection experiment in sheep. Journal of Dairy Science 92, 12031219.
Strandberg, E, Brotherstone, S, Wall, E and Coffey, MP 2009. Genotype by environment interaction for first-lactation female fertility traits in UK dairy cattle. Journal of Dairy Science 92, 34373446.
Thompson-Crispi, KA, Hine, B, Quinton, M, Miglior, F and Mallard, BA 2012b. Short communication: association of disease incidence and adaptive immune response in Holstein dairy cows. Journal of Dairy Science 95, 38883893.
Thompson-Crispi, KA, Sewalem, A, Miglior, F and Mallard, BA 2012a. Genetic parameters of adaptive immune response traits in Canadian Holsteins. Journal of Dairy Science 95, 401409.
Thornton, PK 2010. Livestock production: recent trends, future prospects. Philosophical Transactions of the Royal Society B 365, 28532867.
Wallenbeck, A, Gustafson, G and Rydhmer, L 2009a. Sow performance and maternal behaviour in organic and conventional herds. Acta Agriculturae Scandinavica 59, 181191.
Wallenbeck, A, Rydhmer, L and Lundeheim, N 2009b. G×E interactions for growth and carcass leanness: re-ranking of boars in organic and conventional pig production. Livestock Science 123, 154160.
Wallenbeck, A, Rydhmer, L, Röcklinsberg, H, Ljung, M, Strandberg, E and Ahlman, T 2015. Preferences for pig breeding goals among organic and conventional farmers in Sweden. Organic Agriculture 5, 1–12.
Warner, CM, Meeker, DL and Rothschild, MF 1986. Genetic control of immune responsiveness: a review of Its use as a tool for selection for disease resistance. Journal of Animal Science 64, 394406.
Wilkie, B and Mallard, B 1999. Selection for high immune response: an alternative approach to animal health maintenance? Veterinary Immunology and Immunopathology 72, 231235.
Yin, T, Bapst, B, Borstel, UUV, Simianer, H and König, S 2012. Genetic parameters for Gaussian and categorical traits in organic and low input dairy cattle herds based on random regression methodology. Livestock Science 147, 159169.
Zerjal, T, Gourichon, D, Rivet, B and Bordas, A 2013. Performance comparison of laying hens segregating for the frizzle gene under thermoneutral and high ambient temperatures. Poultry Science 92, 14741485.



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