Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs |
Wu, Xudong
(College of Animal Science and Technology, Anhui Agricultural University)
Zhou, Ren (College of Animal Science and Technology, Anhui Agricultural University) Zhang, Wei (College of Animal Science and Technology, Anhui Agricultural University) Cao, Bangji (College of Animal Science and Technology, Anhui Agricultural University) Xia, Jing (College of Animal Science and Technology, Anhui Agricultural University) Wang, Caiyun (College of Animal Science and Technology, Anhui Agricultural University) Zhang, Xiaodong (College of Animal Science and Technology, Anhui Agricultural University) Chu, Mingxing (Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences) Yin, Zongjun (College of Animal Science and Technology, Anhui Agricultural University) Ding, Yueyun (College of Animal Science and Technology, Anhui Agricultural University) |
1 | Ma X, Guan L, Xuan J, et al. Effect of polymorphisms in the CAMKMT gene on growth traits in Ujumqin sheep. Anim Genet 2016;47:618-22. https://doi.org/10.1111/age.12455 DOI |
2 | Meng Q, Wang K, Liu X, et al. Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies. Asian-Australas J Anim Sci 2017;30:462-9. https://doi.org/10.5713/ajas.16.0548 DOI |
3 | Maldonado L, Brait M, Begum S, et al. GULP1, a potential tumor suppressor gene in ovarian tumors and its utility as a biomarker. Cancer Res 2010;70:4891. https://doi.org/10.1158/1538-7445.Am10-4891 DOI |
4 | Bao X, Zeng Y, Wei S, et al. Developmental changes of Col3a1 mRNA expression in muscle and their association with intramuscular collagen in pigs. J Genet Genomics 2007;34: 223-8. https://doi.org/10.1016/s1673-8527(07)60023-x DOI |
5 | Luhrig S, Kolb S, Mellies N, Nolte J. The novel BTB-kelch protein, KBTBD8, is located in the Golgi apparatus and translocates to the spindle apparatus during mitosis. Cell Div 2013;8:3. https://doi.org/10.1186/1747-1028-8-3 DOI |
6 | Do C, Yang C, Choi J, et al. The outcomes of selection in a closed herd on a farm in operation. Asian-Australas J Anim Sci 2015;28:1244-51. https://doi.org/10.5713/ajas.14.0962 DOI |
7 | Tang GQ, Xuea J, Lian MJ, et al. Inbreeding and genetic diversity in three imported swine breeds in china using pedigree data. Asian-Australas J Anim Sci 2013;26:755-65. https://doi.org/10.5713/ajas.2012.12645 DOI |
8 | Zhang W, Yang M, Wang YL, et al. Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding. Asian-Australas J Anim Sci 2020;33:712-21. https://doi.org/10.5713/ajas.19.0289 DOI |
9 | Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet 2006;15:789-95. https://doi.org/10.1093/hmg/ddi493 DOI |
10 | Chen H, Huang T, Zhang Z, et al. Genome-wide association studies and meta-analysis reveal novel quantitative trait loci and pleiotropic loci for swine head-related traits. J Anim Sci 2017;95:2354-66. https://doi.org/10.2527/jas.2016.1137 DOI |
11 | Avila-Arcos MC, McManus KF, Sandoval K, et al. Population history and gene divergence in native Mexicans inferred from 76 human exomes. Mol Biol Evol 2020;37:994-1006. https://doi.org/10.1093/molbev/msz282 DOI |
12 | Gorlov IF, Kolosov YA, Shirokova NV, et al. GDF9 gene polymorphism and its association with litter size in two Russian sheep breeds. Rend Lincei Sci Fis Nat 2018;29:61-6. https://doi.org/10.1007/s12210-017-0659-2 DOI |
13 | Maselli V, Polese G, Larson G, et al. A dysfunctional sense of smell: the irreversibility of olfactory evolution in freeliving pigs. Evol Biol 2014;41:229-39. https://doi.org/10.1007/s11692-013-9262-3 DOI |
14 | Novoselova TA, Meuwissen MPM, Jongbloed AW, Huirne RBM. Expected economic performance of genetic modification in pork production. NJAS-Wageningen J Life Sci 2013; 64-65:9-15. https://doi.org/10.1016/j.njas.2012.03.002 DOI |
15 | Muhammad H, Iqbal Z, Bashir Q. Genetic polymorphism among five species of Indus River carps on the basis of random amplified polymorphic DNA (RAPD) analysis. Rend Lincei Sci Fis Nat 2017;28:73-80. https://doi.org/10.1007/s12210-016-0576-9 DOI |
16 | Simino J, Shi G, Arnett D, Broeckel U, Hunt SC, Rao DC. Variants on chromosome 6p22.3 associated with blood pressure in the HyperGEN study: follow-up of FBPP quantitative trait loci. Am J Hypertens 2011;24:1227-33. https://doi.org/10.1038/ajh.2011.140 DOI |
17 | McQuillan R, Leutenegger A-L, Abdel-Rahman R, et al. Runs of homozygosity in european populations. Am J Hum Genet 2008;83:658. https://doi.org/10.1016/j.ajhg.2008.10.009 DOI |
18 | He SG, Di J, Han B, et al. Genome-wide scan for runs of homozygosity identifies candidate genes related to economically important traits in Chinese merino. Animals 2020;10:524. https://doi.org/10.3390/ani10030524 DOI |
19 | Bosse M, Megens HJ, Madsen O, et al. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet 2012;8:e1003100. https://doi.org/10.1371/journal.pgen.1003100 DOI |
20 | Marras G, Gaspa G, Sorbolini S, et al. Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim Genet 2015;46:110-21. https://doi.org/10.1111/age.12259 DOI |
21 | Szmatola T, Jasielczuk I, Semik-Gurgul E, et al. Detection of runs of homozygosity in conserved and commercial pig breeds in Poland. J Anim Breed Genet 2020. https://doi.org/10.1111/jbg.12482 DOI |
22 | Purcell S, Neale B, Todd-Brown K, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75. https://doi.org/10.1086/519795 DOI |
23 | Kim ES, Cole JB, Huson H, et al. Effect of artificial selection on runs of homozygosity in US Holstein cattle. PLoS One 2013;8:e80813. https://doi.org/10.1371/journal.pone.0080813 DOI |
24 | Metzger J, Karwath M, Tonda R, et al. Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC Genomics 2015;16:764. https://doi.org/10.1186/s12864-015-1977-3 DOI |
25 | Ding YY, Zhang W, Zhang MQ, et al. Functional and association studies of the cholesteryl ester transfer protein (CETP) gene in a Wannan Black pig model. Anim Genet 2015;46: 702-6. https://doi.org/10.1111/age.12370 DOI |
26 | Zhao G, Zhang T, Liu Y, et al. Genome-wide assessment of runs of homozygosity in Chinese Wagyu beef cattle. Animals 2020;10:1425. https://doi.org/10.3390/ani10081425 DOI |
27 | Zavarez LB, Utsunomiya YT, Carmo AS, et al. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Front Genet 2015;6:5. https://doi.org/10.3389/fgene.2015.00005 DOI |
28 | Li Q, Wang C, Yang J, et al. Genetic diversity analysis based on microsatellite markers in 5 Anhui local and 5 introduced pig breeds. Swine Prod 2018;3:67-72. |
29 | Woolliams J. Genetic contributions and inbreeding. Pages in 147-165 In: Oldenbroek K, editor. Utilization and conservation of farm animal genetic resources. Wageningen, the Netherlands: Wageningen Academic Publishers; 2007. pp. 147-65. |
30 | Purfield DC, Berry DP, McParland S, Bradley DG. Runs of homozygosity and population history in cattle. BMC Genet 2012;13:70. https://doi.org/10.1186/1471-2156-13-70 DOI |
31 | Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 2018;19:220-34. https://doi.org/10.1038/nrg.2017.109 DOI |
32 | Sell-Kubiak E, Czarniecki A, Strabel T. Challenges in inbreeding estimation of large populations based on Polish HolsteinFriesian cattle pedigree. J Appl Genet 2018;59:313-23. https://doi.org/10.1007/s13353-018-0441-x DOI |
33 | Gomez-Raya L, Rauw WM, Dunkeiberger JR, Dekkers JCM. Autozygosity and genetic differentiation of landrace and large white pigs as revealed by the genetic analyses of crossbreds. Front Genet 2019;10. https://doi.org/10.3389/fgene.2019.00739 DOI |
34 | Forutan M, Mahyari SA, Baes C, et al. Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genomics 2018;19:98. https://doi.org/10.1186/s12864-018-4453-z DOI |
35 | Mastrangelo S, Ciani E, Sardina MT, et al. Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds. Anim Genet 2018;49:71-81. https://doi.org/10.1111/age.12634 DOI |
36 | Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009;4:44-57. https://doi.org/10.1038/nprot.2008.211 DOI |
37 | Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F. Runs of homozygosity: current knowledge and applications in livestock. Anim Genet 2017;48:255-71. https://doi.org/10.1111/age.12526 DOI |
38 | Purfield DC, McParland S, Wall E, Berry DP. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One 2017;12:e0176780. https://doi.org/10.1371/journal.pone.0176780 DOI |
39 | Christensen OF, Nielsen B, Su G, et al. A bivariate genomic model with additive, dominance and inbreeding depression effects for sire line and three-way crossbred pigs. Genet Sel Evol 2019;51:45. https://doi.org/10.1186/s12711-019-0486-2 DOI |
40 | Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R, Hedrick PW. Conservation genetics in transition to conservation genomics. Trends Genet 2010;26:177-87. https://doi.org/10.1016/j.tig.2010.01.001 DOI |
41 | Ding X, Zhang X, Yang Y, et al. Polymorphism, expression of natural resistance-associated macrophage protein 1 encoding gene (NRAMP1) and Its association with immune traits in pigs. Asian-Australas J Anim Sci 2014;27:1189-95. https://doi.org/10.5713/ajas.2014.14017 DOI |
42 | Xu Z, Sun H, Zhang Z, et al. Assessment of autozygosity derived from runs of homozygosity in Jinhua pigs disclosed by sequencing data. Front Genet 2019;10:274. https://doi.org/10.3389/fgene.2019.00274 DOI |
43 | Abdelmohsen K, Srikantan S, Yang X, et al. Ubiquitin-mediated proteolysis of HuR by heat shock. EMBO J 2009;28:1271-82. https://doi.org/10.1038/emboj.2009.67 DOI |
44 | Zhang XD, Zhu HY, Zhou J, et al. Relationship between polymorphisms in exon 10 of FSHR gene and litter size in swine. Genet Mol Res 2015;14:8252-61. https://doi.org/10.4238/2015.July.27.13 DOI |
45 | Shi L, Wang L, Liu J, et al. Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population. J Anim Sci Biotechnol 2020;11:46. https://doi.org/10.1186/s40104-020-00447-0 DOI |
46 | China National Commission of Animal Genetic Resources. Animal genetic resources in China pigs. Beijing, China: China Agricultural Press; 2011. |
47 | Ding X, Ding Y, Zhang C, Huang L, He X, Yin Z et al. Polymorphisms and sequencing analysis in 5' upstream and intron 2 region of H-FABP gene in Anhui Wannan Black pig population. J Anim Vet Adv 2011;10:1568-72. DOI |
48 | Peripolli E, Metzger J, de Lemos MVA, et al. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics 2018;19:680. https://doi.org/10.1186/s12864-018-5060-8 DOI |
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