References
- Ennis S. Linkage disequilibrium as a tool for detecting signatures of natural selection. In: Collins AR, editor. Linkage disequilibrium and association mapping. Totowa, NJ, USA: Humana Press; 2007. p. 59-70.
- Smith JM, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res 1974;23:23-35. https://doi.org/10.1017/S0016672300014634
- Barton NH. Linkage and the limits to natural selection. Genetics 1995;140:821-41.
- Durrett R, Schweinsberg J. Approximating selective sweeps. Theor Popul Biol 2004;66:129-38. https://doi.org/10.1016/j.tpb.2004.04.002
- Pennings PS, Hermisson J. Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genet 2006;2:e186. https://doi.org/10.1371/journal.pgen.0020186
- Przeworski M, Coop G, Wall JD. The signature of positive selection on standing genetic variation. Evolution 2005;59:2312-23. https://doi.org/10.1111/j.0014-3820.2005.tb00941.x
- Wang Z, Chen Q, Yang Y, et al. A genome‐wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data. Anim Genet 2014;45:808-16. https://doi.org/10.1111/age.12229
- Kim H, Song KD, Kim HJ, et al. Exploring the genetic signature of body size in Yucatan miniature pig. PloS One 2015;10:e0121732. https://doi.org/10.1371/journal.pone.0121732
- Kim J, Cho S, Caetano-Anolles K, Kim H, Ryu Y-C. Genomewide detection and characterization of positive selection in Korean Native Black Pig from Jeju Island. BMC Genet 2015;16:3. https://doi.org/10.1186/1471-2164-16-3
- Amaral AJ, Ferretti L, Megens H-J, et al. Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PloS One 2011;6:e14782. https://doi.org/10.1371/journal.pone.0014782
- Li M, Tian S, Yeung CK, et al. Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication. Sci Rep 2014;4:4678.
- Ramensky V, Bork P, Sunyaev S. Human non‐synonymous SNPs: server and survey. Nucleic Acids Res 2002;30:3894-900. https://doi.org/10.1093/nar/gkf493
- Bergman I-M, Rosengren JK, Edman K, Edfors I. European wild boars and domestic pigs display different polymorphic patterns in the Toll-like receptor (TLR) 1, TLR2, and TLR6 genes. Immunogenetics 2010;62:49-58. https://doi.org/10.1007/s00251-009-0409-4
- Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. https://www.bioinformatics.babraham. ac.uk/projects/fastqc/
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114-20. https://doi.org/10.1093/bioinformatics/btu170
- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357-9. https://doi.org/10.1038/nmeth.1923
- Li H, Handsaker B, Wysoker A, et al. The sequence alignment/ map format and SAMtools. Bioinformatics 2009;25:2078-9. https://doi.org/10.1093/bioinformatics/btp352
- McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-303. https://doi.org/10.1101/gr.107524.110
- Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics 2011;27:2156-8. https://doi.org/10.1093/bioinformatics/btr330
- Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000;155:945-59.
- Bindea G, Mlecnik B, Hackl H, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009;25:1091-3. https://doi.org/10.1093/bioinformatics/btp101
- Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 2003;31:3812-4. https://doi.org/10.1093/nar/gkg509
- Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen‐2. Curr Protoc Hum Genet 2013;76:7.20.1-41.
- Cingolani P, Platts A, Wang LL, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012;6:80-92. https://doi.org/10.4161/fly.19695
- Ambruosi B, Accogli G, Douet C, et al. Deleted in malignant brain tumor 1 is secreted in the oviduct and involved in the mechanism of fertilization in equine and porcine species. Reproduction 2013;146:119-33. https://doi.org/10.1530/REP-13-0007
- Teijeiro JM, Roldan ML, Marini PE. Molecular identification of the sperm selection involved porcine sperm binding glycoprotein (SBG) as deleted in malignant brain tumors 1 (DMBT1). Biochimie 2012;94:263-7. https://doi.org/10.1016/j.biochi.2011.10.008
- Chen P. Genetic improvement of lean growth rate and reproductive traits in pigs [Retrospective Theses and Dissertations]. Ames, IA, USA: Iowa State University; 2002.
- Subha G. Role of biochemical factors and mineral supplementation in livestock ration for maintenance of their fertility and healthy reproductive status: a review. Res J Chem Sci ISSN 2013;3:102-6.
- Mayorga LS, Tomes CN, Belmonte SA. Acrosomal exocytosis, a special type of regulated secretion. IUBMB life 2007;59:286-92. https://doi.org/10.1080/15216540701222872
- Groenen MA, Archibald AL, Uenishi H, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012;491:393-8. https://doi.org/10.1038/nature11622
- Corominas J, Ramayo-Caldas Y, Puig-Oliveras A, et al. Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition. BMC Genomics 2013;14:843. https://doi.org/10.1186/1471-2164-14-843