Abstract
The understanding of the genetic mechanisms of livestock adaptation to environmental challenges is becoming an important research topic in this time of rapid climate change. New tools and approaches are now available to investigate this complex phenomenon. Low-cost high-throughput technologies have opened the genomic era to agricultural species. All major farm animals have been completely sequenced and HapMap projects are completed or in progress. Low, medium and high-density SNP panels are available or under construction. Molecular information on many thousand markers has initiated the era of population genomics, which is the application of genomic approaches to population genetics. The comparison of patterns of diversity along the genome in animals originating in different environments and new GIScience-based models able to associate molecular markers to environmental variables promise to discover genomic regions associated to traits important for adaptation and to pave the way to the identification of causative genes. Local breeds adapted to a sustainable production in extreme and harsh environments will play a fundamental role in this process.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
Covers the whole territory of states including parts of the Mediterranean states located north of 45th parallel.
References
Archibald, A.L., L. Bolund, C. Churcher, M. Fredholm, M.A. Groenen, B. Harlizius, K.T. Lee, D. Milan, J. Rogers, M.F. Rothschild, H. Uenishi, J. Wang, L.B. Schook and Swine Genome Sequencing Consortium, 2010. Pig genome sequence - analysis and publication strategy. BMC Genomics 11: 438.
Battisti, D.S. and R.L. Naylor, 2009. Historical warnings of future food insecurity with unprecedented seasonal heat. Science 323: 240-244.
Bonin, A., F. Nicole, F. Pompanon, C. Miaud and P. Taberlet, 2007. Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation. Conserv Biol 21: 697-708.
Bonin, A., P. Taberlet, C. Miaud and F. Pompanon, 2006. Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Ranatemporaria). Mol Biol Evol 23: 773-783
Buitkamp, J., P. Filmether, M.J. Stear and J.T. Epplen, 1996. Class I and class II major histocompatibility complex alleles are associated with faecal egg counts following natural, predominantly Ostertagia circumcincta infection. Parasitology Research 82: 693-696
Falloon, P. and R. Betts, 2010. Climate impacts on European agriculture and water management in the context of adaptation and mitigation - the importance of an integrated approach. Science of Total Environment 408: 5667-5687.
FAO, 2007. The state of the world’s animal genetic resources for food and agriculture. FAO, Rome, Italy.
Flori L, Fritz S, Jaffrèzic F, Boussaha M, Gut I, Heath S, Foulley JL and Gautier M, 2009. The genome response to artificial selection: a case study in dairy Cattle. Plos ONE 4: e6595.
Gautier, M., L. Flori, A. Riebler, F. Jaffrezic, D. Laloe, I. Gut, K. Moazami-Goudarzi and J.L. Foulley, 2009. A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics 10: 550.
Grossman, S.R., I. Shylakhter, E.K. Karlsson, E.H. Byrne, S. Morales, G. Frieden, E. Hostetter, E. Angelino, M. Garber, O. Zuk, E.S. Lander, S.F. Schaffner and P.C. Sabeti, 2010. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327: 883-886.
Harris, E.E. and D. Meyer, 2006. The molecular signature of selection underlying human adaptations. Yearbook of Physical Anthropology 49: 89-130.
Hayes, B.J., S. Lien, H. Nilsen, H.G. Olsen, P. Berg, S. Maceachern, S. Potter and T.H.E. Meuwissen, 2008. The origin of selection signatures on bovine chromosome 6. Animal Genetics 39: 105-111.
Hayes, B.J., P.J. Bowman, A.J. Chamberlain and M.E. Goddard, 2009. Genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92: 433-443.
International Sheep Genomics Consortium, A.L. Archibald, N.E. Cockett, B.P. Dalrymple, T. Faraut, J.W. Kijas, J.F. Maddox, J.C. McEwan, V. Hutton Oddy, H.W. Raadsma, C. Wade, J. Wang, W. Wang and X. Xun, 2010. The sheep genome reference sequence: a work in progress. Anim Genet 41: 449-453.
Joost, S., A. Bonin, M.W. Bruford, L. Despres, C. Conord, G. Erhardt and P. Taberlet, 2007. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Molecular Ecology 16: 3955-3969
Joost, S., L. Colli, P.V. Baret, J.F. Garcia, P. J. Boettcher, M. Tixier-Boichard, P. Ajmone-Marsan and GLOBALDIV Consortium, 2010. Integrating geo-referenced multiscale and multidisciplinary data for the management of biodiversity in livestock genetic resources. Anim Genet 41 Suppl 1: 47-63.
Kolbehdari, D., Z. Wang, J.R. Grant, B. Murdoch, A. Prasad, Z. Xiu, E. Marques, P. Stothard and S.S. Moore, 2008. A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls. J Dairy Sci 91: 2844-2856.
Lappalainen, T., E. Salmela, P.M. Andersen, K. Dahlman-Wright, P. Sistonen, M.L. Savontaus, S. Schreiber, P. Lahermo and J. Kere, 2010. Genomic landscape of positive natural selection in Northern European populations. Eur J Hum Genet 18: 471-478.
Li, R., W. Fan, G. Tian, H. Zhu, L. He, J. Cai, Q. Huang, Q. Cai, B. Li, Y. Bai, Z. Zhang, Y. Zhang, W. Wang, J. Li, F. Wei, H. Li, M. Jian, J. Li, Z. Zhang, R. Nielsen, D. Li, W. Gu, Z. Yang, Z. Xuan, O.A. Ryder, F.C.-C. Leung, Y. Zhou, J. Cao, X. Sun, Y. Fu, X. Fang, X. Guo, B. Wang, R. Hou, F. Shen, B. Mu, P. Ni, R. Lin, W. Qian, G. Wang, C. Yu, W. Nie, J. Wang, Z. Wu, H. Liang, J. Min, Q. Wu, S. Cheng, J. Ruan, M. Wang, Z. Shi, M. Wen, B. Liu, X. Ren, H. Zheng, D. Dong, K. Cook, G. Shan, H. Zhang, C. Kosiol, X. Xie, Z. Lu, H. Zheng, Y. Li, C.C. Steiner, T.T.-Y. Lam, S. Lin, Q. Zhang, G. Li, J. Tian, T. Gong, H. Liu, D. Zhang, L. Fang, C. Ye, J. Zhang, W. Hu, A. Xu, Y. Ren, G. Zhang, M.W. Bruford, Q. Li, L. Ma, Y. Guo, N. An, Y. Hu, Y. Zheng, Y. Shi, Z. Li, Q. Liu, Y. Chen, J. Zhao, N. Qu, S. Zhao, F. Tian, X. Wang, H. Wang, L. Xu, X. Liu, T. Vinar, Y. Wang, T.-W. Lam, S.-M. Yiu, S. Liu, H. Zhang, D. Li, Y. Huang, X. Wang, G. Yang, Z. Jiang, J. Wang, N. Qin, L. Li, J. Li, L. Bolund, K. Kristiansen, G.K.-S. Wong, M. Olson, X. Zhang, S. Li, H. Yang, J. Wang and J. Wang, 2010. The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317
Luikart, G.H., P. England, D.A. Tallmon, S. Jordan and P. Taberlet, 2003. The power and promise of population genomics: from genotyping to genome-typing. Nature Rev Genet 4: 981-994.
Manolio, T.A., F.S. Collins, N.J. Cox, D.B. Goldstein, L.A. Hindorff, D.J. Hunter, M.I. McCarthy, E.M. Ramos, L.R. Cardon, A. Chakravarti, J.H. Cho, A.E. Guttmacher, A. Kong, L. Kruglyak, E. Mardis, C.N. Rotimi, M. Slatkin, D. Valle, A.S. Whittemore, M. Boehnke, A.G. Clark, E.E. Eichler, G. Gibson, J.L. Haines, T.F.C. Mackay, S.A. McCarroll and P.M. Visscher, 2009. Finding the missing heritability of complex diseases. Nature 461: 747-753.
MacEachern, S., B. Hayes, J. McEwan and M. Goddard, 2009. An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. BMC Genomics 10: 181.
McKay, S.D., R.D. Schnabel, B.M. Murdoch, L.K. Matukumalli, J. Aerts, W. Coppieters, D. Crews, E. Dias Neto, C.A. Gill, C. Gao, H. Mannen, Z. Wang, C.P. Van Tassell, J.L. Williams, J.F. Taylor and S.S. Moore, 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genet 9: 37.
Müller, C., W. Cramer, W.L. Hare and H. Lotze-Campen, 2011. Climate change risks for African agriculture. Proc Natl Acad Sci USA 108: 4313-4315.
Nardone, A., 1992. Cattle resources in the Mediterranean area. Livestock in the Mediterranean cereal production systems. EAAP Publications no. 49, Pudoc Scientific Publishers, Wageningen, the Netherlands.
Oleksyk, T.K., M.W. Smith and S.J. O’Brien, 2010. Genome-wide scans for footprints of natural selection. Philos Trans R Soc Lond B Biol Sci 365: 185-205.
Pariset, L., S. Joost, P. Ajmone Marsan, A. Valentini and Econogene Consortium, 2009. Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genet. 10: 7.
Parisod, C. and S. Joost, 2010. Divergent selection in trailing- versus leading-edge populations of Biscutellalaevigata. Ann Bot 105: 655-660.
Poncet, B.N., D. Herrmann, F. Gugerli, P. Taberlet, R. Holderegger, L. Gielly, D. Rioux, W. Thuiller, S. Aubert and S. Manel, 2010. Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol Ecol 19: 2896-2907.
Porter, V., 2007. Cattle, a handbook to the breeds of the world. Crowood Press, Marlborough, UK.
Ross-Gillespie, A., M.J. O’Riain and L.F. Keller, 2007. Viral epizootic reveals inbreeding depression in a habitually inbreeding mammal. Evolution 61: 2268-2273.
Rubin, C.-J., M.C. Zody, J. Eriksson, J.R.S. Meadows, E. Sherwood, M.T. Webster, L. Jiang, M. Ingman, T. Sharpe, S. Ka, F. Hallbook, F. Besnier, O. Carlborg, B. Bed’hom, M. Tixier-Boichard, P. Jensen, P. Siegel, K. Lindblad-Toh and L. Andersson, 2010. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-591.
Stella, A., P. Ajmone-Marsan, B. Lazzari and P. Boettcher, 2010. identification of selection signatures in cattle breeds selected for dairy production. Genetics 185: 1451-1461.
Taberlet, P., A. Valentini, H.R. Rezaei, S. Naderi, F. Pompanon, R. Negrini and P. Ajmone-Marsan, 2008. Are cattle, sheep and goats endangered species? Molecular Ecology 17: 275-284.
The Bovine Hapmap Consortium, 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: 528-532.
The Bovine Genome Sequencing and Analysis Consortium, C.G. Elsik, R.L. Tellam and K.C. Worley, 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.
VanRaden, P.M., C.P. Van Tassell, G.R. Wiggans, T.S. Sonstegard, R.D. Schnabel, J.F. Taylor and F.S. Schenkel, 2009. Invited review: reliability of genomic predictions for North American Holstein bulls. J Dairy Sci 92: 16-24.
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2012 Wageningen Academic Publishers
About this chapter
Cite this chapter
Marsan, P.A., Colli, L., Nicolazzi, E.L., Negrini, R., Zjalic, M., Rosati, A. (2012). New approaches to investigate the genetic basis of animal adaptation to different environments. In: Casasús, I., Rogošiç, J., Rosati, A., Štokoviç, I., Gabiña, D. (eds) Animal farming and environmental interactions in the Mediterranean region. EAAP – European Federation of Animal Sciences, vol 131. Wageningen Academic Publishers, Wageningen. https://doi.org/10.3920/978-90-8686-741-7_1
Download citation
DOI: https://doi.org/10.3920/978-90-8686-741-7_1
Publisher Name: Wageningen Academic Publishers, Wageningen
Online ISBN: 978-90-8686-741-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)
