title: Genome-wide detection of selective signature in Chinese Holstein.
abstract: Selective signatures in whole genome can help us understand the mechanisms of selection and target causal variants for breeding program. In present study, we performed Extended Haplotype Homozygosity (EHH) tests to identify significant core regions harboring such signals in Chinese Holstein, and then verified the biological significance of these identified regions based on commonly-used bioinformatics analyses. Results showed a total of 125 significant regions in entire genome containing some of important functional genes such as LEP, ABCG2, CSN1S1, CSN3 and TNF based on the Gene Ontology database. Some of these annotated genes involved in the core regions overlapped with those identified in our previous GWAS as well as those involved in a recently constructed candidate gene database for cattle, further indicating these genes under positive selection maybe underlie milk production traits and other important traits in Chinese Holstein. Furthermore, in the enrichment analyses for the second level GO terms and pathways, we observed some significant terms over represented in these identified regions as compared to the entire bovine genome. This indicates that some functional genes associated with milk production traits, as reflected by GO terms, could be clustered in core regions, which provided promising evidence for the exploitability of the core regions identified by EHH tests. Findings in our study could help detect functional candidate genes under positive selection for further genetic and breeding research in Chinese Holstein.
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Ministry of Agriculture, China Agricultural University, Beijing, China.
authors.forename: Dunfei
authors.initials: D
authors.lastname: Pan
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhang
authors.forename: Jicai
authors.initials: J
authors.lastname: Jiang
authors.forename: Li
authors.initials: L
authors.lastname: Jiang
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Liu
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D005260:Female; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics; D006239:Haplotypes; D006720:Homozygote; D008297:Male; D058977:Molecular Sequence Annotation; D012641:Selection, Genetic
references.citation: PLoS One. 2009 Aug 12;4(8):e6595
references.pmid: 19672461
references.citation: Am J Hum Genet. 2007 Nov;81(5):1084-97
references.pmid: 17924348
references.citation: Nat Rev Genet. 2003 Feb;4(2):99-111
references.pmid: 12560807
references.citation: Science. 2001 Jul 20;293(5529):455-62
references.pmid: 11423617
references.citation: Proc Natl Acad Sci U S A. 2004 Jul 20;101(29):10667-72
references.pmid: 15249682
references.citation: BMC Genomics. 2009 Apr 24;10:184
references.pmid: 19393059
references.citation: PLoS Biol. 2006 Mar;4(3):e72
references.pmid: 16494531
references.citation: J Anim Breed Genet. 2006 Apr;123(2):89-96
references.pmid: 16533362
references.citation: Anim Genet. 2009 Dec;40(6):832-51
references.pmid: 19508288
references.citation: Anim Genet. 2010 Aug;41(4):377-89
references.pmid: 20096028
references.citation: Nat Rev Genet. 2004 Mar;5(3):202-12
references.pmid: 14970822
references.citation: Nat Genet. 2003 Dec;35(4):311-3
references.pmid: 14634648
references.citation: Science. 2009 Apr 24;324(5926):528-32
references.pmid: 19390050
references.citation: Genome Res. 2002 Dec;12(12):1805-14
references.pmid: 12466284
references.citation: Genome Res. 2002 May;12(5):785-94
references.pmid: 11997345
references.citation: Nature. 2002 Oct 24;419(6909):832-7
references.pmid: 12397357
references.citation: J Dairy Res. 2004 May;71(2):182-7
references.pmid: 15190946
references.citation: Br J Nutr. 1985 May;53(3):637-48
references.pmid: 2998449
references.citation: Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11525-30
references.pmid: 12172007
references.citation: Science. 2010 Feb 12;327(5967):883-6
references.pmid: 20056855
references.citation: Bioinformatics. 2003 May 1;19(7):891-2
references.pmid: 12724301
references.citation: PLoS One. 2010 Oct 27;5(10):e13661
references.pmid: 21048968
references.citation: Hum Mol Genet. 2005 Jul 15;14(14):2075-87
references.pmid: 15944197
references.citation: BMC Genet. 2007 Oct 25;8:74
references.pmid: 17961247
references.citation: Genetics. 1973 May;74(1):175-95
references.pmid: 4711903
references.citation: Genome Res. 2007 Apr;17(4):520-6
references.pmid: 17351134