Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding
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Objective: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. Methods: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios. Results: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. Conclusion: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.
Abstract
Objective: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. Methods: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios. Results: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. Conclusion: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.
참고문헌 (50)
- Giuffra E, "The origin of the domestic pig : independent domestication and subsequent introgression", Genetics, 154, pp.1785~1791 (2000)
- Veirano Fréchou R, "The state of the world’s animal genetic resources for food and agriculture", Acta Paediatr, 81, pp.21~24 (2007)
- Enard D, "Genome-wide signals of positive selection in human evolution", Genome Res, 24, pp.885~895 (2014)
- Frantz LAF, "Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes", Nat Genet, 47, pp.1141~1148 (2015)[DOI]
- Grossman SR, "A composite of multiple signals distinguishes causal variants in regions of positive selection", Science, 327, pp.883~886 (2010)[DOI]
- Lewontin RC, "Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms", Genetics, 74, pp.175~195 (1973)
- Tajima F, "Evolutionary relationship of DNA sequences in finite populations", Genet, 105, pp.437~460 (1983)
- Rubin C, "Whole-genome resequencing reveals loci under selection during chicken domestication", Nature, 464, pp.587~591 (2010)[DOI]
- Salas A, "The natural selection that shapes our genomes", Forensic Sci Int Genet, 39, pp.57~60 (2019)[DOI]
- Zhao P, "Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization", GigaScience, 7 (2018)[DOI]
- Rubin C, "Strong signatures of selection in the domestic pig genome", Proc Nat Acad Sci USA, 109, pp.19529~19536 (2012)[DOI]
- Kim J, "The genome landscape of indigenous African cattle", Genome Biol, 18, pp.34~ (2017)[DOI]
- Axelsson E, "The genomic signature of dog domestication reveals adaptation to a starch-rich diet", Nature, 495, pp.360~364 (2013)[DOI]
- Alberto FJ, "Convergent genomic signatures of domestication in sheep and goats", Nat Commun, 9, pp.813~ (2018)[DOI]
- Zhang Z, "Whole-genome resequencing reveals signatures of selection and timing of duck domestication", GigaScience, 7 (2018)[DOI]
- Li M, "Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars", Nat Genet, 45, pp.1431~1438 (2013)[DOI]
- Zhang X, "Polymorphism of the retinol-binding protein 4 gene(RBP4)and its association with carcass and meat quality traits in swine", Turk J Vet Anim Sci, 39, pp.395~400 (2015)[DOI]
- Ding YY, "Functional and association studies of the cholesteryl ester transfer protein(CETP)gene in a Wannan Black pig model", Anim Genet, 46, pp.702~706 (2015)[DOI]
- Xiaoling Ding, "Polymorphism, Expression of Natural Resistance-associated Macrophage Protein 1 Encoding Gene (NRAMP1) and Its Association with Immune Traits in Pigs", Animal Bioscience, 27(8), pp.1189~1195 (2014), 아세아·태평양축산학회[DOI]
- Tian M, "MicroRNA-21 and microRNA-214 play important role in reproduction regulation during porcine estrous", Anim Sci J, 89, pp.1398~1405 (2018)[DOI]
- Patel RK, "NGS QC Toolkit : A toolkit for quality control of next generation sequencing data", PLoS One, 7, pp.e30619~ (2012)[DOI]
- Li H, "Fast and accurate short read alignment with Burrows-Wheeler transform", Bioinformatics, 25, pp.1754~1760 (2009)[DOI]
- Li H, "The Sequence alignment", map format and SAMtools, 2009, pp.25, 2078~2099
- McKenna A, "The genome analysis toolkit : a MapReduce framework for analyzing next-generation DNA sequencing data", Genome Res, 20, pp.1297~1303 (2010)[DOI]
- Wang K, "ANNOVAR : functional annotation of genetic variants from high-throughput sequencing data", Nucleic Acids Res, 38, pp.e164~ (2010)[DOI]
- Yang J, "GCTA : A tool for genome-wide complex trait analysis", Am J Hum Genet, 88, pp.76~82 (2011)[DOI]
- Holsinger KE, "Genetics in geographically structured populations : defining, estimating and interpreting FST", Nat Rev Genet, 10, pp.639~650 (2009)[DOI]
- Purcell S, "PLINK : A tool set for whole-genome association and population-based linkage analyses", Am J Hum Genet, 81, pp.559~575 (2007)[DOI]
- Lee TH, "SNPhylo : A pipeline to construct a phylogenetic tree from huge SNP data", BMC Genomics, 15, pp.162~ (2014)[DOI]
- Drummond AJ, "Bayesian Phylogenetics with BEAUti and the BEAST 1. 7", Mol Biol Evol, 29, pp.1969~1973 (2012)[DOI]
- Browning BL, "A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals", Am J Hum Genet, 84, pp.210~223 (2009)[DOI]
- Pfeifer B, "PopGenome : an efficient Swiss army knife for population genomic analyses in R", Mol Biol Evol, 31, pp.1929~1936 (2014)[DOI]
- Huang DW, "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", Nat Protoc, 4, pp.44~57 (2009)[DOI]
- Reiner A, "Identifying differentially expressed genes using false discovery rate controlling procedures", Bioinformatics, 19, pp.368~375 (2003)[DOI]
- Davis TL, "Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases", PLoS Biol, 8, pp.e1000439~ (2010)[DOI]
- Prins BP, "Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6", Genome Biol, 19, pp.87~ (2018)[DOI]
- Park AC, "Deficits in col5a2 expression result in novel skin and adipose abnormalities and predisposition to aortic aneurysms and dissections", Am J Pathol, 187, pp.2300~2311 (2017)[DOI]
- Cheeseman IM, "KNL1 and the CENP-H", I, Mol Biol Cell, pp.2008, 19[DOI]
- Burbach BJ, "T-cell receptor signaling to integrins", Immunol Rev, 218, pp.65~81 (2007)[DOI]
- Zhao B, "The hippo pathway in organ size control, tissue regeneration and stem cell self-renewal", Nat Cell Biol, 13, pp.877~883 (2011)[DOI]
- Khanal RC, "Regulation of intestinal calcium transport", Ann Rev Nutr, 28, pp.179~196 (2008)[DOI]
- Aksanov O, "BBS4 directly affects proliferation and differentiation of adipocytes", Cell Mol Life Sci, 71, pp.3381~3392 (2014)[DOI]
- Wang Q, "Tristetraprolin inhibits macrophage IL-27-induced activation of antitumour cytotoxic T cell responses", Nat Commun, 8, pp.867~ (2017)[DOI]
- Richard AC, "Reduced monocyte and macrophage TNFSF15", TL1A expression is associated with susceptibility to inflammatory bowel disease, 2018, pp.14, e1007458~
- Koochakzadeh L, "Study of SH2D1A gene mutation in paediatric patients with B-cell lymphoma", Allergol Immunopathol, 43, pp.568~570 (2015)[DOI]
- Fischl H, "Paf1 has distinct roles in transcription elongation and differential transcript fate", Mol Cell, 65, pp.685~698 (2017)[DOI]
- Wang X, "Mst1 regulates post-infarction cardiac injury through the JNK-Drp1-mitochondrial fission pathway", Cell Mol Biol Lett, 23, pp.21~ (2018)[DOI]
- Glavey SV, "The sialyltransferase ST3GAL6 influences homing and survival in multiple myeloma", Blood, 124, pp.1765~1776 (2014)[DOI]
- Horiuchi N, "Detection of the nonsense mutation of OPA3 gene in Holstein Friesian cattle with dilated cardiomyopathy in japan", J Vet Med Sci, 77, pp.1281~1283 (2015)[DOI]
- Nishi A, "De novo non-synonymous TBL1XR1 mutation alters Wnt signaling activity", Sci Rep, 7, pp.2887~ (2017)[DOI]
