A genome-wide scan for signatures of directional selection in domesticated pigs
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- 作者：Sunjin Moon (1) (12) (2)
Tae-Hun Kim (3)
Kyung-Tai Lee (3)
Woori Kwak (4) (5)
Taeheon Lee (1)
Si-Woo Lee (3)
Myung-Jick Kim (6)
Kyuho Cho (7)
Namshin Kim (8)
Won-Hyong Chung (8)
Samsun Sung (5)
Taesung Park (9)
Seoae Cho (5)
Martien AM Groenen (10)
Rasmus Nielsen (11)
Yuseob Kim (2)
Heebal Kim (1) (4) (5)
1. Department of Agricultural biotechnology ; Seoul National University ; Seoul ; 151-921 ; Republic of Korea
12. Current address ; Department of Genome Sciences ; University of Washington ; Seattle ; WA ; USA
2. Department of Life Science and Division of EcoScience ; Ewha Womans University ; Seoul ; 120-750 ; Republic of Korea
3. Animal Genomics and Bioinformatics Division ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
4. Interdisciplinary Program in Bioinformatics ; Seoul National University ; Seoul ; 151-747 ; Republic of Korea
5. C&K Genomics ; Seoul National University Research Park ; Seoul ; 151-919 ; Republic of Korea
6. Animal Genetic Resources Station ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
7. Swine Science Division ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
8. Korean Bioinformation Center ; Korea Research Institute of Bioscience and Biotechnology ; Daejeon ; 305-806 ; Republic of Korea
9. Department of Statistics ; Seoul National University ; Seoul ; Republic of Korea
10. Animal Breeding and Genomics Centre ; Wageningen University ; De Elst 1 ; 6708 WD ; Wageningen ; The Netherlands
11. Department of Integrative Biology and Department of Statistics ; University of California Berkeley ; Berkeley ; CA ; 94820 ; USA - 关键词：Pig ; Domestication ; Selective sweep ; Directional selection ; Quantitative traits
- 刊名：BMC Genomics
- 出版年：2015
- 出版时间：December 2015
- 年：2015
- 卷：16
- 期：1
- 全文大小：3,246 KB
- 参考文献：1. Amaral, AJ, Ferretti, L, Megens, H-J, Crooijmans, RPMA, Nie, H, Ramos-Onsins, SE (2011) Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA. PLoS One 6: pp. e14782 CrossRef
2. Akey, JM, Ruhe, AL, Akey, DT, Wong, AK, Connelly, CF, Madeoy, J (2010) Tracking footprints of artificial selection in the dog genome. Proc Natl Acad Sci U S A 107: pp. 1160-5 CrossRef
3. Rubin, CJ, Megens, HJ, Martinez Barrio, A, Maqbool, K, Sayyab, S, Schwochow, D (2012) Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A 109: pp. 19529-36 CrossRef
4. Wilkinson, S, Lu, ZH, Megens, HJ, Archibald, AL, Haley, C, Jackson, IJ (2013) Signatures of diversifying selection in European pig breeds. PLoS Genet 9: pp. e1003453 CrossRef
5. Purugganan, MD, Fuller, DQ (2009) The nature of selection during plant domestication. Nature 457: pp. 843-8 CrossRef
6. Andersson, L, Georges, M (2004) Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet 5: pp. 202-12 CrossRef
7. Groenen, MA, Archibald, AL, Uenishi, H, Tuggle, CK, Takeuchi, Y, Rothschild, MF (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491: pp. 393-8 622" target="_blank" title="It opens in new window">CrossRef
8. Yi, X, Liang, Y, Huerta-Sanchez, E, Jin, X, Cuo, ZXP, Pool, JE (2010) Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude. Science 329: pp. 75-8 6/science.1190371" target="_blank" title="It opens in new window">CrossRef
9. Sabeti, PC (2006) Positive Natural Selection in the Human Lineage. Science 312: pp. 1614-20 6/science.1124309" target="_blank" title="It opens in new window">CrossRef
10. Lewontin, RC, Krakauer, J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: pp. 175-95
11. Akey, JM (2009) Constructing genomic maps of positive selection in humans: where do we go from here?. Genome Res 19: pp. 711-22 6652.108" target="_blank" title="It opens in new window">CrossRef
12. Maynard-Smith, J, Haigh, J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23: pp. 23-35 6672300014634" target="_blank" title="It opens in new window">CrossRef
13. Giuffra, E, Kijas, JM, Amarger, V, Carlborg, O, Jeon, JT, Andersson, L (2000) The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154: pp. 1785-91
14. Larson, G, Dobney, K, Albarella, U, Fang, M, Matisoo-Smith, E, Robins, J (2005) Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307: pp. 1618-21 6/science.1106927" target="_blank" title="It opens in new window">CrossRef
15. Wu, GS, Yao, YG, Qu, KX, Ding, ZL, Li, H, Palanichamy, MG (2007) Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biol 8: pp. R245 6/gb-2007-8-11-r245" target="_blank" title="It opens in new window">CrossRef
16. Amaral, AJ, Megens, HJ, Crooijmans, RPMA, Heuven, HCM, Groenen, MAM (2008) Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179: pp. 569-79 CrossRef
17. Bosse, M, Megens, HJ, Frantz, LAF, Madsen, O, Larson, G, Paudel, Y (2014) Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nat Commun 5: pp. 4392 CrossRef
18. Jones G. Genetic aspects of domestication, common breeds and their origin. In The Genetics of the Pig. Edited by Rothschild MF, Ruvinsky A. CAB International, Wallingford, UK; 1998:17-50.
19. Darwin C. The variation of animals and plants under domestication. John Murray, London. 1868.
20. Wiener, P, Wilkinson, S (2011) Deciphering the genetic basis of animal domestication. Proc Biol Sci Royal Soc 278: pp. 3161-70 6" target="_blank" title="It opens in new window">CrossRef
21. Sabeti, PC, Varilly, P, Fry, B, Lohmueller, J, Hostetter, E, Cotsapas, C (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449: pp. 913-8 6250" target="_blank" title="It opens in new window">CrossRef
22. Innan, H, Kim, Y (2008) Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 179: pp. 1713-20 6835" target="_blank" title="It opens in new window">CrossRef
23. Kim, Y, Gulisija, D (2010) Signatures of recent directional selection under different models of population expansion during colonization of new selective environments. Genetics 184: pp. 571-85 CrossRef
24. Voight, BF, Kudaravalli, S, Wen, X, Pritchard, JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4: pp. e72 CrossRef
25. Kim, TH, Kim, KS, Choi, BH, Yoon, DH, Jang, GW, Lee, KT (2005) Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 83: pp. 2255-63
26. Rubin, CJ, Zody, MC, Eriksson, J, Meadows, JR, Sherwood, E, Webster, MT (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: pp. 587-91 CrossRef
27. Qanbari, S, Pausch, H, Jansen, S, Somel, M, Strom, TM, Fries, R (2014) Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genet 10: pp. e1004148 CrossRef
28. Axelsson, E, Ratnakumar, A, Arendt, ML, Maqbool, K, Webster, MT, Perloski, M (2013) The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495: pp. 360-4 CrossRef
29. Alexander, DH, Lange, K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12: pp. 246 6/1471-2105-12-246" target="_blank" title="It opens in new window">CrossRef
30. Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MA, Bender, D (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: pp. 559-75 6/519795" target="_blank" title="It opens in new window">CrossRef
31. Moltke, I, Albrechtsen, A (2014) RelateAdmix: a software tool for estimating relatedness between admixed individuals. Bioinformatics 30: pp. 1027-8 652" target="_blank" title="It opens in new window">CrossRef
32. Ottoni, C, Flink, LG, Evin, A, Georg, C, Cupere, B, Neer, W (2013) Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol Biol Evol 30: pp. 824-32 61" target="_blank" title="It opens in new window">CrossRef
33. Kijas, JW, Lenstra, JA, Hayes, B, Boitard, S, Porto Neto, LR, San Cristobal, M (2012) Genome-wide analysis of the world鈥檚 sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol 10: pp. e1001258 CrossRef
34. Hu, ZL, Park, CA, Wu, XL, Reecy, JM (2013) Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res 41: pp. D871-9 CrossRef
35. Niswender, CM, Conn, PJ (2010) Metabotropic glutamate receptors: physiology, pharmacology, and disease. Annu Rev Pharmacol Toxicol 50: pp. 295-322 6/annurev.pharmtox.011008.145533" target="_blank" title="It opens in new window">CrossRef
36. Li, M, Tian, S, Jin, L, Zhou, G, Li, Y, Zhang, Y (2013) Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet 45: pp. 1431-8 CrossRef
37. Knott, SA, Marklund, L, Haley, CS, Andersson, K, Davies, W, Ellegren, H (1998) Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics 149: pp. 1069-80
38. Huang, W, Sherman, BT, Lempicki, RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: pp. 44-57 CrossRef
39. Gratacos, M, Escaramis, G, Bustamante, M, Saus, E, Aguera, Z, Bayes, M (2010) Role of the neurotrophin network in eating disorders鈥?subphenotypes: body mass index and age at onset of the disease. J Psychiatr Res 44: pp. 834-40 6/j.jpsychires.2010.01.009" target="_blank" title="It opens in new window">CrossRef
40. Ramos, AM, Crooijmans, RP, Affara, NA, Amaral, AJ, Archibald, AL, Beever, JE (2009) Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4: pp. e6524 6524" target="_blank" title="It opens in new window">CrossRef
41. Ai, H, Huang, L, Ren, J (2013) Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers. PLoS One 8: pp. e56001 6001" target="_blank" title="It opens in new window">CrossRef
42. Wang, GD, Zhai, W, Yang, HC, Fan, RX, Cao, X, Zhong, L (2013) The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun 4: pp. 1860 CrossRef
43. O鈥機onnor, RM, Thakker, DR, Schmutz, M, Putten, H, Hoyer, D, Flor, PJ (2013) Adult siRNA-induced knockdown of mGlu7 receptors reduces anxiety in the mouse. Neuropharmacology 72: pp. 66-73 6/j.neuropharm.2013.03.028" target="_blank" title="It opens in new window">CrossRef
44. Sinisalo, A, Niemi, JK, Heinonen, M, Valros, A (2012) Tail biting and production performance in fattening pigs. Livest Sci 143: pp. 220-5 6/j.livsci.2011.09.019" target="_blank" title="It opens in new window">CrossRef
45. Meruvu, S, Hugendubler, L, Mueller, E (2011) Regulation of adipocyte differentiation by the zinc finger protein ZNF638. J Biol Chem 286: pp. 26516-23 6" target="_blank" title="It opens in new window">CrossRef
46. Li, H, Handsaker, B, Wysoker, A, Fennell, T, Ruan, J, Homer, N (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: pp. 2078-9 CrossRef
47. McKenna, A, Hanna, M, Banks, E, Sivachenko, A, Cibulskis, K, Kernytsky, A (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: pp. 1297-303 CrossRef
48. Nielsen, R, Korneliussen, T, Albrechtsen, A, Li, Y, Wang, J (2012) SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One 7: pp. e37558 CrossRef
49. Browning, SR, Browning, BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81: pp. 1084-97 6/521987" target="_blank" title="It opens in new window">CrossRef
50. Gutenkunst, RN, Hernandez, RD, Williamson, SH, Bustamante, CD (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5: pp. e1000695 695" target="_blank" title="It opens in new window">CrossRef
51. Hudson, RR (2002) Generating samples under a Wright鈥揊isher neutral model of genetic variation. Bioinformatics 18: pp. 337-8 CrossRef
52. Hudson, RR, Slatkin, M, Maddison, WP (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132: pp. 583-9
53. Cavalli-Sforza, L (1969) Human diversity. Proceedings of the 12th International Congress of Genetics: 1969; Tokyo. pp. 405-16
54. Sabeti, PC, Reich, DE, Higgins, JM, Levine, HZ, Richter, DJ, Schaffner, SF (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: pp. 832-7 CrossRef
55. Gautier, M, Vitalis, R (2012) rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics 28: pp. 1176-7 CrossRef - 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
- 出版者：BioMed Central
- ISSN：1471-2164
文摘
Background Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Results Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. Conclusions We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.