Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, Kao RR, et al. Revealing the history of sheep domestication using retrovirus integrations. Science. 2009;324:532–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, et al. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol. 2012;10:e1001258.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei C, Wang H, Liu G, Wu M, Cao J, Liu Z, et al. Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. BMC Genomics. 2015;16:194.
Article
PubMed
PubMed Central
Google Scholar
Chen SY, Duan ZY, Sha T, Xiangyu J, Wu SF, Zhang YP. Origin, genetic diversity, and population structure of Chinese domestic sheep. Gene. 2006;376:216–23.
Article
CAS
PubMed
Google Scholar
China national commission of animal genetic resources. Animal genetic resources in China: Sheep and Goats. 1st ed. Beijing: China Agriculture Press; 2011.
Olson DM, Dinerstein E, Wikramanayake ED, Burgess ND, Powell GVN, Underwood EC, et al. Terrestrial ecoregions of the world: a new map of life on earth. Bioscience. 2001;51:933–8.
Article
Google Scholar
Karell P, Ahola K, Karstinen T, Valkama J, Brommer JE. Climate change drives microevolution in a wild bird. Nat Commun. 2011;2:208.
Article
PubMed
PubMed Central
Google Scholar
Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Barrio AM, et al. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science. 2014;345:1074–9107.
Article
CAS
PubMed
Google Scholar
Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010;464:587–91.
Article
CAS
PubMed
Google Scholar
Fang M, Larson G, Ribeiro HS, Li N, Andersson L. Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet. 2009;5:e1000341.
Article
PubMed
PubMed Central
Google Scholar
Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013;495:360–4.
Article
CAS
PubMed
Google Scholar
Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS, Axelsson J, et al. Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet. 2013;9:e1003211.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet. 2013;45:1431–8.
Article
CAS
PubMed
Google Scholar
Gou X, Wang Z, Li N, Qiu F, Xu Z, Yan D, et al. Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. Genome Res. 2014;24:1308–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang GD, Fan RX, Zhai W, Liu F, Wang L, Zhong L, et al. Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau. Genome Biol Evol. 2014;6:2122–8.
Article
PubMed
PubMed Central
Google Scholar
Qu Y, Zhao H, Han N, Zhou G, Song G, Gao B, et al. Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau. Nat Commun. 2013;4:2071.
PubMed
Google Scholar
Fan WL, Ng CS, Chen CF, Lu MY, Chen YH, Liu CJ, et al. Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol Evol. 2013;5:1376–92.
Article
PubMed
PubMed Central
Google Scholar
Yang S, Li X, Li K, Fan B, Tang Z. A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds. BMC Genet. 2014;15:7.
Article
PubMed
PubMed Central
Google Scholar
Wang C, Wang H, Zhang Y, Tang Z, Li K, Liu B. Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs. Mol Ecol Resour. 2015;15:414–24.
Article
CAS
PubMed
Google Scholar
Kawahara-Miki R, Tsuda K, Shiwa Y, Arai-Kichise Y, Matsumoto T, Kanesaki Y, et al. Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics. 2011;12:103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, et al. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics. 2011;12:559.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee KT, Chung WH, Lee SY, Choi JW, Kim J, Lim D, et al. Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC Genomics. 2013;14:519.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liao X, Peng F, Forni S, McLaren D, Plastow G, Stothard P. Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection. Genome. 2013;56:592–8.
Article
CAS
PubMed
Google Scholar
Choi JW, Liao X, Stothard P, Chung WH, Jeon HJ, Miller SP, et al. Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. PLoS One. 2014;9:e101127.
Article
PubMed
PubMed Central
Google Scholar
Bautista DM, Siemens J, Glazer JM, Tsuruda PR, Basbaum AI, Stucky CL, et al. The menthol receptor TRPM8 is the principal detector of environmental cold. Nature. 2007;448:204–8.
Article
CAS
PubMed
Google Scholar
Fariello MI, Servin B, Tosser-Klopp G, Rupp R, Moreno C, International Sheep Genomics Consortium, et al. Selection signatures in worldwide sheep populations. PLoS One. 2014;9:e103813.
Article
PubMed
PubMed Central
Google Scholar
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Modi D, Godbole G. HOXA1O signals on the highway through pregnancy. J Reprod Immunol. 2009;83:72–8.
Article
CAS
PubMed
Google Scholar
Murthi P, Hiden U, Rajaraman G, Liu H, Borg AJ, Coombes F, et al. Novel homeobox genes are differentially expressed in placental microvascular endothelial cells compared with macrovascular cells. Placenta. 2008;29:624–30.
Article
CAS
PubMed
Google Scholar
Taylor HS, Arici A, Olive D, Igarashi R. HOXA1O is expressed in response to sex steroids at the time of implantation in the human endometrium. J Clin Invest. 1998;101:1379–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Taylor HS, Vanden Heuvel GB, Igarashi P. A conserved Hox axis in the mouse and human female reproductive system: late establishment and persistent adult expression of the Hoxa cluster genes. Biol Reprod. 1997;57:1338–45.
Article
CAS
PubMed
Google Scholar
Bagot CN, Troy PJ, Taylor HS. Alteration of maternal Hoxa10 expression by in vivo gene transfection affects implantation. Gene Ther. 2000;7:1378–84.
Article
CAS
PubMed
Google Scholar
Lim H, Ma L, Ma WG, Maas RL, Dey SK. Hoxa-10 regulates uterine stromal cell responsiveness to progesterone during implantation and decidualization in the mouse. Mol Endocrinol. 1999;13:1005–17.
Article
CAS
PubMed
Google Scholar
Nakao N, Ono H, Yamamura T, Anraku T, Takagi T, Higashi K, et al. Thyrotrophin in the pars tuberalis triggers photoperiodic response. Nature. 2008;452:317–22.
Article
CAS
PubMed
Google Scholar
Hodson DJ, Henderson HL, Townsend J, Tortonese DJ. Photoperiodic modulation of the suppressive actions of prolactin and dopamine on the pituitary gonadotropin responses to gonadotropin-releasing hormone in sheep. Biol Reprod. 2012;86:122.
Article
PubMed
Google Scholar
Zhang L, Mousel MR, Wu X, Michal JJ, Zhou X, Ding B, et al. Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep. PLoS One. 2013;8:e65942.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davis GH. Fecundity genes in sheep. Anim Reprod Sci. 2004;82-83:247–53.
Article
CAS
PubMed
Google Scholar
Davis GH. Major genes affecting ovulation rate in sheep. Genet Sel Evol. 2005;37 Suppl 1:S11–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar D, Joshi A, Naqvi SM, Kumar S, Mishra AK, Maurya VP, et al. Sperm motion characteristics of GarolexMalpura sheep evolved in a semi-arid tropical environment through introgression of FecB gene. Anim Reprod Sci. 2007;100:51–60.
Article
CAS
PubMed
Google Scholar
Abdoli R, Zamani P, Deljou A, Rezvan H. Association of BMPR-1B and GDF9 genes polymorphisms and secondary protein structure changes with reproduction traits in Mehraban ewes. Gene. 2013;524:296–303.
Article
CAS
PubMed
Google Scholar
Eghbalsaied S, Ghaedi K, Shahmoradi S, Pirestani A, Amini H, Saiedi T, et al. Presence of SNPs in GDF9 mRNA of Iranian Afshari Sheep. Int J Fertil Steril. 2012;5:225–30.
PubMed
PubMed Central
Google Scholar
Martínez-Royo A, Lahoz B, Alabart JL, Folch J, Calvo JH. Characterisation of the Melatonin Receptor 1A (MTNR1A) gene in the Rasa Aragonesa sheep breed: association with reproductive seasonality. Anim Reprod Sci. 2012;133:169–75.
Article
PubMed
Google Scholar
Mateescu RG, Lunsford AK, Thonney ML. Association between melatonin receptor 1A gene polymorphism and reproductive performance in Dorset ewes. J Anim Sci. 2009;87:2485–8.
Article
CAS
PubMed
Google Scholar
Mura MC, Luridiana S, Vacca GM, Bini PP, Carcangiu V. Effect of genotype at the MTNR1A locus and melatonin treatment on first conception in Sarda ewe lambs. Theriogenology. 2010;74:1579–86.
Article
CAS
PubMed
Google Scholar
McRae KM, McEwan JC, Dodds KG, Gemmell NJ. Signatures of selection in sheep bred for resistance or susceptibility to gastrointestinal nematodes. BMC Genomics. 2014;15:637.
Article
PubMed
PubMed Central
Google Scholar
Bonhomme M, Chevalet C, Servin B, Boitard S, Abdallah J, Blott S, et al. Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics. 2010;186:241–62.
Article
PubMed
PubMed Central
Google Scholar
Bierne N, Roze D, Welch JJ. Pervasive selection or is it…? Why are FST outliers sometimes so frequent? Mol Ecol. 2013;22:2061–4.
Article
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, et al. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol. 2011;12:R114.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
Google Scholar
Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, snpeff: Snps in the genome of drosophila melanogaster strain w(1118); iso-2; iso-3. Fly (Austin). 2012;6:80–92.
Article
CAS
Google Scholar
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073–81.
Article
CAS
PubMed
Google Scholar
Cockerham CC, Weir BS. Covariances of relatives stemming from a population undergoing mixed self and random mating. Biometrics. 1984;40:157–64.
Article
CAS
PubMed
Google Scholar
Weir BS, Hill WG. Estimating F-statistics. Annu Rev Genet. 2002;36:721–50.
Article
CAS
PubMed
Google Scholar
Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, et al. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res. 2015;43:W589–98.
Article
PubMed
PubMed Central
Google Scholar
Beissbarth T, Speed TP. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics. 2004;20:1464–5.
Article
CAS
PubMed
Google Scholar
da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
Article
CAS
Google Scholar
Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006;78:629–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 2015;43:D222–6.
Article
PubMed
Google Scholar
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45.
Article
CAS
PubMed
PubMed Central
Google Scholar