Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Miguel Carneiro; Carl Johan Rubin; Federica Di Palma; Frank W. Albert; Jessica Alföldi; Alvaro Martinez Barrio; Gerli Pielberg; Nima Rafati; Shumaila Sayyab; Jason Turner-Maier; Shady Younis; Sandra Afonso; Bronwen Aken; Joel M. Alves; Daniel Barrell; Gerard Bolet; Samuel Boucher; Hernán A. Burbano; Rita Campos; Jean L. Chang; Veronique Duranthon; Luca Fontanesi; Herve Garreau; David Heiman; Jeremy Johnson; Rose G. Mage; Ze Peng; Guillaume Queney; Claire Rogel-Gaillard; Magali Ruffier; Steve Searle; Rafael Villafuerte; Anqi Xiong; Sarah Young; Karin Forsberg-Nilsson; Jeffrey M. Good; Eric S. Lander; Nuno Ferrand; Kerstin Lindblad-Toh; Leif Andersson

doi:10.1126/science.1253714

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Miguel Carneiro, Carl Johan Rubin, Federica Di Palma, Frank W. Albert, Jessica Alföldi, Alvaro Martinez Barrio, Gerli Pielberg, Nima Rafati, Shumaila Sayyab, Jason Turner-Maier, Shady Younis, Sandra Afonso, Bronwen Aken, Joel M. Alves, Daniel Barrell, Gerard Bolet, Samuel Boucher, Hernán A. Burbano, Rita Campos, Jean L. ChangVeronique Duranthon, Luca Fontanesi, Herve Garreau, David Heiman, Jeremy Johnson, Rose G. Mage, Ze Peng, Guillaume Queney, Claire Rogel-Gaillard, Magali Ruffier, Steve Searle, Rafael Villafuerte, Anqi Xiong, Sarah Young, Karin Forsberg-Nilsson, Jeffrey M. Good, Eric S. Lander, Nuno Ferrand, Kerstin Lindblad-Toh, Leif Andersson

Genetics, Cell Biology and Development (CBS)

Research output: Contribution to journal › Article › peer-review

288 Scopus citations

Abstract

The genetic changes underlying the initial steps of animal domestication are still poorly understood.We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits.We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

Original language	English (US)
Pages (from-to)	1074-1079
Number of pages	6
Journal	Science
Volume	345
Issue number	6200
DOIs	https://doi.org/10.1126/science.1253714
State	Published - Aug 29 2014

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Carneiro, M., Rubin, C. J., Palma, F. D., Albert, F. W., Alföldi, J., Barrio, A. M., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J. M., Barrell, D., Bolet, G., Boucher, S., Burbano, H. A., Campos, R., ... Andersson, L. (2014). Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science, 345(6200), 1074-1079. https://doi.org/10.1126/science.1253714

Carneiro, M, Rubin, CJ, Palma, FD, Albert, FW, Alföldi, J, Barrio, AM, Pielberg, G, Rafati, N, Sayyab, S, Turner-Maier, J, Younis, S, Afonso, S, Aken, B, Alves, JM, Barrell, D, Bolet, G, Boucher, S, Burbano, HA, Campos, R, Chang, JL, Duranthon, V, Fontanesi, L, Garreau, H, Heiman, D, Johnson, J, Mage, RG, Peng, Z, Queney, G, Rogel-Gaillard, C, Ruffier, M, Searle, S, Villafuerte, R, Xiong, A, Young, S, Forsberg-Nilsson, K, Good, JM, Lander, ES, Ferrand, N, Lindblad-Toh, K & Andersson, L 2014, 'Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication', Science, vol. 345, no. 6200, pp. 1074-1079. https://doi.org/10.1126/science.1253714

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abstract = "The genetic changes underlying the initial steps of animal domestication are still poorly understood.We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits.We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.",

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AU - Alföldi, Jessica

AU - Barrio, Alvaro Martinez

AU - Pielberg, Gerli

AU - Rafati, Nima

AU - Sayyab, Shumaila

AU - Turner-Maier, Jason

AU - Younis, Shady

AU - Afonso, Sandra

AU - Aken, Bronwen

AU - Alves, Joel M.

AU - Barrell, Daniel

AU - Bolet, Gerard

AU - Boucher, Samuel

AU - Burbano, Hernán A.

AU - Campos, Rita

AU - Chang, Jean L.

AU - Duranthon, Veronique

AU - Fontanesi, Luca

AU - Garreau, Herve

AU - Heiman, David

AU - Johnson, Jeremy

AU - Mage, Rose G.

AU - Peng, Ze

AU - Queney, Guillaume

AU - Rogel-Gaillard, Claire

AU - Ruffier, Magali

AU - Searle, Steve

AU - Villafuerte, Rafael

AU - Xiong, Anqi

AU - Young, Sarah

AU - Forsberg-Nilsson, Karin

AU - Good, Jeffrey M.

AU - Lander, Eric S.

AU - Ferrand, Nuno

AU - Lindblad-Toh, Kerstin

AU - Andersson, Leif

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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

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