publication . Article . Preprint . Other literature type . 2014

Selection signatures in worldwide Sheep populations

Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; San Cristobal, Magali; Boitard, Simon; Drögemüller, Cord; The International Sheep Genomics Consortium, ISGC;
Open Access English
  • Published: 15 Aug 2014
  • Publisher: Public Library of Science
Abstract
<jats:p>The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinp...
Subjects
free text keywords: 590 Animals (Zoology), 630 Agriculture, 610 Medicine & health, holstein cattle, artificial selection, genotype data, adult height, coat color, gene, genone, breed, missense mutation, receptor, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], Research Article, Biology and Life Sciences, Agriculture, Animal Management, Animal Breeding, Animal Production, Computational Biology, Genome Analysis, Evolutionary Biology, Evolutionary Processes, Natural Selection, Population Genetics, Haplotypes, Genetics, Animal Genetics, Genomics, holstein cattle;artificial selection;missense mutation;genotype data;adult height;coat color;gene;genone;breed;receptor, International HapMap Project, Linkage disequilibrium, Biology, Genetic diversity, World wide, Genome
Communities
Agricultural and Food Sciences
Socio-economic impact of digitalisation in rural areas
58 references, page 1 of 4

1. Andersson L (2012) How selective sweeps in domestic animals provide new insight into biological mechanisms. J Intern Med 271: 1-14.

2. Zeder MA (2008) Domestication and early agriculture in the mediterranean basin: Origins, diffusion, and impact. Proceedings of the National Academy of Sciences 105: 11597-11604. [OpenAIRE]

3. Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, et al. (2009) A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS One 4: e4668. [OpenAIRE]

4. Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, et al. (2012) Genomewide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol 10: e1001258.

5. Garcia-Ga´mez E, Reverter A, Whan V, McWilliam SM, Arranz JJA, et al. (2011) Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep. PLoS ONE 6: e21158.

6. Moradi MH, Nejati-Javaremi A, Moradi-Shahrbabak M, Dodds KG, McEwan JC (2012) Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genet 13: 10.

7. Becker D, Tetens J, Brunner A, Burstel D, Ganter M, et al. (2010) Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene. PLoS One 5: e8689.

8. Zhang L, Mousel MR, Wu X, Michal JJ, Zhou X, et al. (2013) Genome-Wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee Sheep. PLoS One 8: e65942.

9. Excoffer L, Hofer T, Foll M (2009) Detecting loci under selection in a hierarchically structured population. Heredity (Edinb) 103: 285-98. [OpenAIRE]

10. Bonhomme M, Chevalet C, Servin B, Boitard S, Abdallah J, et al. (2010) Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics 186: 241-62. [OpenAIRE]

11. Bierne N, Roze D, Welch JJ (2013) Pervasive selection or is it? why are fst outliers sometimes so frequent? Molecular Ecology 22: 2061-2064. [OpenAIRE]

12. Gnther T, Coop G (2013) Robust identification of local adaptation from allele frequencies. Genetics 195: 205-220. [OpenAIRE]

13. Fariello MI, Boitard S, Naya H, SanCristobal M, Servin B (2013) Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics 193: 929-41. [OpenAIRE]

14. Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195. [OpenAIRE]

15. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-59.

58 references, page 1 of 4
Abstract
<jats:p>The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinp...
Subjects
free text keywords: 590 Animals (Zoology), 630 Agriculture, 610 Medicine & health, holstein cattle, artificial selection, genotype data, adult height, coat color, gene, genone, breed, missense mutation, receptor, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], Research Article, Biology and Life Sciences, Agriculture, Animal Management, Animal Breeding, Animal Production, Computational Biology, Genome Analysis, Evolutionary Biology, Evolutionary Processes, Natural Selection, Population Genetics, Haplotypes, Genetics, Animal Genetics, Genomics, holstein cattle;artificial selection;missense mutation;genotype data;adult height;coat color;gene;genone;breed;receptor, International HapMap Project, Linkage disequilibrium, Biology, Genetic diversity, World wide, Genome
Communities
Agricultural and Food Sciences
Socio-economic impact of digitalisation in rural areas
58 references, page 1 of 4

1. Andersson L (2012) How selective sweeps in domestic animals provide new insight into biological mechanisms. J Intern Med 271: 1-14.

2. Zeder MA (2008) Domestication and early agriculture in the mediterranean basin: Origins, diffusion, and impact. Proceedings of the National Academy of Sciences 105: 11597-11604. [OpenAIRE]

3. Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, et al. (2009) A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS One 4: e4668. [OpenAIRE]

4. Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, et al. (2012) Genomewide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol 10: e1001258.

5. Garcia-Ga´mez E, Reverter A, Whan V, McWilliam SM, Arranz JJA, et al. (2011) Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep. PLoS ONE 6: e21158.

6. Moradi MH, Nejati-Javaremi A, Moradi-Shahrbabak M, Dodds KG, McEwan JC (2012) Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genet 13: 10.

7. Becker D, Tetens J, Brunner A, Burstel D, Ganter M, et al. (2010) Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene. PLoS One 5: e8689.

8. Zhang L, Mousel MR, Wu X, Michal JJ, Zhou X, et al. (2013) Genome-Wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee Sheep. PLoS One 8: e65942.

9. Excoffer L, Hofer T, Foll M (2009) Detecting loci under selection in a hierarchically structured population. Heredity (Edinb) 103: 285-98. [OpenAIRE]

10. Bonhomme M, Chevalet C, Servin B, Boitard S, Abdallah J, et al. (2010) Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics 186: 241-62. [OpenAIRE]

11. Bierne N, Roze D, Welch JJ (2013) Pervasive selection or is it? why are fst outliers sometimes so frequent? Molecular Ecology 22: 2061-2064. [OpenAIRE]

12. Gnther T, Coop G (2013) Robust identification of local adaptation from allele frequencies. Genetics 195: 205-220. [OpenAIRE]

13. Fariello MI, Boitard S, Naya H, SanCristobal M, Servin B (2013) Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics 193: 929-41. [OpenAIRE]

14. Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195. [OpenAIRE]

15. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-59.

58 references, page 1 of 4
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publication . Article . Preprint . Other literature type . 2014

Selection signatures in worldwide Sheep populations

Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; San Cristobal, Magali; Boitard, Simon; Drögemüller, Cord; The International Sheep Genomics Consortium, ISGC;