Detection of selection signatures in Limousin cattle using whole‐genome resequencing
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Summary: Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole‐genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi‐allelic SNPs and 92 229 indels located on autosomes were fixed for the alternative allele in all sequenced animals, including the previously reported missense deleterious F94L mutation in MSTN. We performed a whole‐genome screen to discover genomic regions with excess homozygosity, using the pooled heterozygosity score and identified 171 different candidate selective sweeps. In total, 68 candidate genes were found in only 57 of these regions, indicating that a large fraction of the genome under selection might lie in non‐coding regions and suggesting that a majority of adaptive mutations might be regulatory in nature. Many QTL were found within candidate selective sweep regions, including QTL associated with shear force or carcass weight. Among the putative selective sweeps, we located genes (MSTN, NCKAP5, RUNX2) that potentially contribute to important phenotypes in Limousin. Several candidate regions and genes under selection were also found in previous genome‐wide selection scans performed in Limousin. In addition, we were able to pinpoint candidate causative regulatory polymorphisms in GRIK3 and RUNX2 that might have been under selection. Our results will contribute to improved understanding of the mechanisms and targets of artificial selection and will facilitate the interpretation of GWASs performed in Limousin.
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GRIK3 has been targeted in modern human evolution and in multiple domestication events, including in dogs, sheep, yaks, and across multiple cattle breeds.
“This gene has been targeted in modern human evolution and in multiple domestication events, including in dogs, sheep, yaks, and across multiple cattle breeds [16, 19, 20].”
From Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle (2021) · cites this paper as [19]
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Cites
Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.-H., Pagès, F., Trajanoski, Z., & Galon, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp101 · Cited by 6,280 · see citing works
Otto, F., Thornell, A., Crompton, T., Denzel, A., Gilmour, K. C., Rosewell, I. R., Stamp, G., Beddington, R. S. P., Mundlos, S., Olsen, B. R., et al. (1997) · Cell · doi:10.1016/s0092-8674(00)80259-7 · Cited by 2,813 · see citing works
Proceedings of the National Academy of Sciences, USA.
Ochoa, S. (1996) · Current Biology · doi:10.1016/s0960-9822(09)00431-x · Cited by 2,783 · see citing works
Predicting Deleterious Amino Acid SubstitutionsPreprint
Ng, P. C., & Henikoff, S. (2001) · Genome Research · doi:10.1101/gr.176601 · Cited by 2,667 · see citing works
Double muscling in cattle due to mutations in the myostatin gene
McPherron, A. C., & Lee, S.-J. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.23.12457 · Cited by 2,039 · see citing works
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Sandelin, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh012 · Cited by 1,763 · see citing works
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
McLaren, W. M., Yates, B., Ríos, D., Chen, Y., Flicek, P., & Cunningham, F. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq330 · Cited by 1,586 · see citing works
A deletion in the bovine myostatin gene causes the double–muscled phenotype in cattle
Grobet, L., Royo Martin, L. J., Poncelet, D., Pirottin, D., Brouwers, B., Riquet, J., Schoeberlein, A., Dunner, S., Ménissier, F., Massabanda, J., et al. (1997) · Nature Genetics · doi:10.1038/ng0997-71 · Cited by 1,556 · see citing works
Mutations in <i>myostatin</i> ( <i>GDF8</i> ) in Double-Muscled Belgian Blue and Piedmontese Cattle
Kambadur, R., Sharma, M., Smith, T. P. L., & Bass, J. J. (1997) · Genome Research · doi:10.1101/gr.7.9.910 · Cited by 1,204 · see citing works
Whole-genome resequencing reveals loci under selection during chicken domestication
Rubin, C.-J., Zody, M. C., Eriksson, J., Meadows, J. R. S., Sherwood, E., Webster, M. T., Jiang, L., Ingman, M., Sharpe, T., Ka, S., et al. (2010) · Nature · doi:10.1038/nature08832 · Cited by 1,138 · see citing works
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds
The Bovine HapMap Consortium, Gibbs, R. A., Taylor, J. F., Van Tassell, C. P., Barendse, W., Eversole, K. A., Gill, C. A., Green, R. D., Hamernik, D. L., Kappes, S. M., et al. (2009) · Science · doi:10.1126/science.1167936 · Cited by 868 · see citing works
Evidence for Two Independent Domestications of Cattle
Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M., & Cunningham, P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.7.2757 · Cited by 812 · see citing works
Runx2, an inducer of osteoblast and chondrocyte differentiation
Komori, T. (2018) · Histochemistry and Cell Biology · doi:10.1007/s00418-018-1640-6 · Cited by 468 · see citing works
Lasky-Su, J. A., Neale, B. M., Franke, B., Anney, R., Zhou, K., Maller, J., Vásquez, A. A., Chen, W., Asherson, P. J., Buitelaar, J. K., et al. (2008) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.30867 · Cited by 388 · see citing works
Journal of Animal Breeding and Genetics
(2010) · Journal of Animal Breeding and Genetics · doi:10.1111/(issn)1439-0388 · Cited by 292 · see citing works
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond
Hu, Z., Fritz, E., & Reecy, J. M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl946 · Cited by 234 · see citing works
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder
Wang, K.-S., Liu, X.-F., & Aragam, N. (2010) · Schizophrenia Research · doi:10.1016/j.schres.2010.09.002 · Cited by 204 · see citing works
Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle
Xu, L., Bickhart, D. M., Cole, J. B., Schroeder, S., Song, J., Tassell, C. P. V., Sonstegard, T. S., & Liu, G. E. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu333 · Cited by 202 · see citing works
Selection for complex traits leaves little or no classic signatures of selection
Kemper, K. E., Saxton, S. J., Bolormaa, S., Hayes, B. J., & Goddard, M. E. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-246 · Cited by 134 · see citing works
Detection of selective sweeps in cattle using genome-wide SNP data
Ramey, H. R., Decker, J. E., McKay, S., Rolf, M. M., Schnabel, R. D., & Taylor, J. F. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-382 · Cited by 126 · see citing works
Influence of breed and early management on ease of handling and open-field behaviour of cattle
Boivin, X., Neindre, P. L., Chupin, J. M., et al. (1992) · Applied Animal Behaviour Science · doi:10.1016/s0168-1591(05)80024-3 · Cited by 123 · see citing works
Knüppel, R., Dietze, P., LEHNBERG, W., Frech, K., & Wingender, E. (1994) · Journal of Computational Biology · doi:10.1089/cmb.1994.1.191 · Cited by 109 · see citing works
Gutiérrez‐Gil, B., Arranz, J. J., & Wiener, P. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00167 · Cited by 104 · see citing works
Effects of the myostatin F94L substitution on beef traits1
Esmailizadeh, A., Bottema, C. D. K., Sellick, G. S., Verbyla, A. P., Morris, C. A., Cullen, N. G., & Pitchford, W. S. (2008) · Journal of Animal Science · doi:10.2527/jas.2007-0589 · Cited by 99 · see citing works
Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds
Boitard, S., Boussaha, M., Capitan, A., Rocha, D., & Servin, B. (2016) · Genetics · doi:10.1534/genetics.115.181594 · Cited by 86 · see citing works
Self-citationPurfield, D. C., Evans, R. D., & Berry, D. P. (2019) · BMC Genomics · doi:10.1186/s12864-019-6071-9 · Cited by 83 · see citing works
Effect of myostatin F94L on carcass yield in cattle
Sellick, G. S., Pitchford, W. S., Morris, C. A., Cullen, N. G., Crawford, A. M., Raadsma, H. W., & Bottema, C. D. K. (2007) · Animal Genetics · doi:10.1111/j.1365-2052.2007.01623.x · Cited by 75 · see citing works
Szmatoła, T., Gurgul, A., Jasielczuk, I., Ząbek, T., Ropka‐Molik, K., Litwińczuk, Z., & Bugno‐Poniewierska, M. (2019) · Animals · doi:10.3390/ani9121024 · Cited by 72 · see citing works
A novel method for improved accuracy of transcription factor binding site prediction
Khamis, A. M., Motwalli, O., Oliva, R., Janković, B. R., Medvedeva, Y. A., Ashoor, H., Essack, M., Gao, X., & Bajić, V. B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky237 · Cited by 55 · see citing works
Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle
Shen, J., Hanif, Q., Cao, Y., Yu, Y., Lei, C., Zhang, G., & Zhao, Y. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00094 · Cited by 53 · see citing works
Identification of large selective sweeps associated with major genes in cattle
Druet, T., Pérez-Pardal, L., Charlier, C., & Gautier, M. (2013) · Animal Genetics · doi:10.1111/age.12073 · Cited by 49 · see citing works
Valente, T. S., Baldi, F. S., Sant’Anna, A. C., de Albuquerque, L. G., & da Costa, M. J. R. P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0156956 · Cited by 44 · see citing works
Allais, S., Levéziel, H. H., Hocquette, J.-F. J.-F., Rousset, S., Denoyelle, C., Journaux, L., & Renand, G. (2014) · Journal of Animal Science · doi:10.2527/jas.2014-7868 · Cited by 42 · see citing works
Self-citationGenome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa
Zwane, A. A., Schnabel, R. D., Hoff, J. L., Choudhury, A., Makgahlela, M. L., Maiwashe, A., van Marle-Köster, E., & Taylor, J. F. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00273 · Cited by 41 · see citing works
Identification of genome‐wide selection signatures in the L imousin beef cattle breed
Gurgul, A., Szmatoła, T., Ropka‐Molik, K., Jasielczuk, I., Pawlina‐Tyszko, K., Semik, E., & Bugno‐Poniewierska, M. (2015) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12196 · Cited by 31 · see citing works
Alexander, L. J., Kuehn, L. A., Smith, T. P. L., et al. (2009) · Journal of Animal Science · doi:10.2527/jas.2008-1531 · Cited by 26 · see citing works
Detection of selection signatures for agonistic behaviour in cattle
Eusebi, P. G., Cortés, O., Carleos, C., Dunner, S., & Cañon, J. (2018) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12325 · Cited by 25 · see citing works
Survey of allele specific expression in bovine muscle
Guillocheau, G., Hou, A. E., Meersseman, C., Esquerré, D., Rebours, E., Letaief, R., Simao, M., Hypolite, N., Bourneuf, E., Bruneau, N., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-40781-6 · Cited by 22 · see citing works
Self-citationAn Association of GRIK3 Ser310Ala Functional Polymorphism with Personality Traits
Minelli, A., Scassellati, C., Bonvicini, C., Pérez, J., & Gennarelli, M. (2009) · Neuropsychobiology · doi:10.1159/000202827 · Cited by 20 · see citing works
Jiang, E., Kang, Z., Wang, X., Liu, Y., Liu, X., Wang, Z., Li, X., & Lan, X. (2019) · Animal Biotechnology · doi:10.1080/10495398.2019.1671858 · Cited by 18 · see citing works
Association of RUNX2 and TNFSF11 genes with production traits in a paternal broiler line
Grupioni, N. V., Stafuzza, N. B., Carvajal, A. B., et al. (2017) · Genetics and Molecular Research · doi:10.4238/gmr16019443 · Cited by 11 · see citing works
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Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle
Eusebi, P. G., Sevane, N., O’Rourke, T., Pizarro, M., Boeckx, C., & Dunner, S. (2021) · BMC Genomics · doi:10.1186/s12864-021-07505-5 · Cited by 24 · see citing works
- Authors
- Mariadassou, M., Ramayo‐Caldas, Y., Charles, M., Féménia, M., Renand, G., & Rocha, D.
- Affiliations
- Université Paris-Saclay (FR)
- AgroParisTech (FR)
- Corresponding author
- Rocha, D.
- Venue
- Animal Genetics
- Publisher
- Wiley
- Published
- 2020-07-20
- Volume
- 51
- Issue
- 5
- Pages
- 815-819
- ISSN
- 0268-9146 (ISSN-L)
- 1365-2052
- OpenAlex
- W3045057304
- Cited by
- 21
- References
- 41
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 9 · 2023: 3 · 2022: 2 · 2021: 3
- FWCI
- 1.17
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Animal Genetics (publishedVersion, other-oa)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- Agence Nationale de la Recherche (ANR‐05‐GANI‐005, ANR‐05‐GANI‐017‐01, ANR‐09‐GENM‐011)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- Limousin cattle, selective breeding, selective sweeps, whole-genome resequencing, myostatin, regulatory polymorphisms, quantitative trait loci, shear force, carcass weight, Runx2, GRIK3, beef cattle
- MeSH terms
- Whole Genome Sequencing, Animals, Cattle, France, Male, Selection, Genetic, Polymorphism, Single Nucleotide, INDEL Mutation
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