A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population |
Guo, Tianfu
(State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University)
Gao, Jun (State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) Yang, Bin (State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) Yan, Guorong (State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) Xiao, Shijun (State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) Zhang, Zhiyan (State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) Huang, Lusheng (State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) |
1 | Nishimura D, Sakai H, Sato T, et al. Roles of ADAM8 in elimination of injured muscle fibers prior to skeletal muscle regeneration. Mech Dev 2015;135:58-67. https://doi.org/10.1016/j.mod.2014.12.001 DOI |
2 | Brooke MH, Kaiser KK. Muscle fiber types: how many and what kind? Arch Neurol 1970; 23:369-79. https://doi.org/10.1001/archneur.1970.00480280083010 DOI |
3 | Sosnicki A. Histopathological observation of stress myopathy in M. longissimus in the pig and relationships with meat quality, fattening and slaughter traits. J Anim Sci 1987;65:584-96. https://doi.org/10.2527/jas1987.652584x DOI |
4 | Swatland HJ, Cassens RG. Observations on the postmortem histochemistry of myofibers from stress susceptible pigs. J Anim Sci 1973;37:885-91. https://doi.org/10.2527/jas1973.374885x DOI |
5 | Franck M, Figwer P, Godfraind C, Poirel MT, Khazzaha A, Ruchoux MM. Could the pale, soft, and exudative condition be explained by distinctive histological characteristics? J Anim Sci 2007;85:746-53. https://doi.org/10.2527/jas.2006-190 DOI |
6 | Rehfeldt C, Fiedler I, Dietl G, Ender K. Myogenesis and postnatal skeletal muscle cell growth as influenced by selection. Livest Prod Sci 2000;66:177-88. https://doi.org/10.1016/S0301-6226(00)00225-6 DOI |
7 | Hu ZL, Fritz ER, Reecy JM. Animalqtldb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Res 2007;35(Suppl 1):D604-9. https://doi.org/10.1093/nar/gkl946 DOI |
8 | Nii M, Hayashi T, Mikawa S, et al. Quantitative trait loci mapping for meat quality and muscle fiber traits in a Japanese wild boar Large White intercross. J Anim Sci 2005;83:308-15. https://doi.org/10.2527/2005.832308x DOI |
9 | Liang JJ, Wang W, Sorensen D, et al. Cellular prion protein regulates its own alpha-cleavage through ADAM8 in skeletal muscle. J Biol Chem 2012;287:16510-20. https://doi.org/10.1074/jbc.M112.360891 DOI |
10 | Wechsler-Reya RJ, Elliott KJ, Prendergast GC. A role for the putative tumor suppressor Bin1 in muscle cell differentiation. Mol Cell Biol 1998;18:566-75. https://doi.org/10.1128/ MCB.18.1.566 DOI |
11 | Muller AJ, Baker JF, DuHadaway JB, et al. Targeted disruption of the murine Bin1/Amphiphysin II gene does not disable endocytosis but results in embryonic cardiomyopathy with aberrant myofibril formation. Mol Cell Biol 2003;23:4295-306. https://doi.org/10.1128/MCB.23.12.4295-4306.2003 DOI |
12 | Johann B, Nasim V, Marie M, et al. Altered splicing of the BIN1 muscle-specific exon in humans and dogs with highly progressive centronuclear myopathy. PLoS Genet 2013;9:e1003430. https://doi.org/10.1371/journal.pgen.1003430 DOI |
13 | Fugier C, Klein AF, Hammer C, et al. Misregulated alternative splicing of BIN1 is associated with T tubule alterations and muscle weakness in myotonic dystrophy. Nat Med 2011;17:720-5. https://doi.org/10.1038/nm.2374 DOI |
14 | Yuan M, Zhao YH, Wang YS, et al. The apoptosis induced by FAM105A through Bcl-2 family and caspase dependent pathway. J Xiamen Univ 2011;50:1065-9. |
15 | Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA 2008;299:1335-44. https://doi.org/10.1001/jama.299.11.1335 DOI |
16 | Guo YY. Genome-wide association study on muscle fiber and eye muscle area traits in swine [Ph.D. Thesis]. Jizhong, China: Shanxi Agricultural University; 2015. |
17 | Wimmers K, Fiedler I, Hardge T, Murani E, Schellander K, Ponsuksili S. QTL for microstructural and biophysical muscle properties and body composition in pigs. BMC Genet 2006;7:15. https://doi.org/10.1186/1471-2156-7-15 |
18 | Estelle J, Gil F, Vazquez JM, et al. A quantitative trait locus genome scan for porcine muscle fiber traits reveals overdominance and epistasis. J Anim Sci 2008;86:3290-9. https://doi.org/10.2527/jas.2008-1034 DOI |
19 | Li WB, Ren J, Zhu WC, et al. Mapping QTL for porcine muscle fibre traits in a White Duroc x Erhualian F2 resource population. J Anim Breed Genet 2009;126:468-74. https://doi.org/10.1111/j.1439-0388.2009.00805.x DOI |
20 | Li N. Genome-wide association studies for pig meat traits and exploration of major genes [Ph.D. Thesis]. Beijing, China: China Agricultural University; 2016. |
21 | Yang GC, Ren J, Li SJ, et al. Genome-wide identification of QTL for age at puberty in gilts using a large intercross population between White Duroc Erhualian. Genet Sel Evol 2008;40:529-39. https://doi.org/10.1051/gse:2008019 DOI |
22 | Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009;5:e1000529. https://doi.org/10.1371/journal.pgen.1000529 DOI |
23 | 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 DOI |
24 | 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 DOI |
25 | Delaneau O, Howie B, Cox AJ, Zagury JF, Marchini J. Haplotype estimation using sequencing reads. Am J Hum Genet 2013;93:687-96. https://doi.org/10.1016/j.ajhg.2013.09.002 DOI |
26 | Zhou X, Carbonetto P, Stephens M. Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet 2013;9:e1003264. https://doi.org/10.1371/journal.pgen.1003264 DOI |
27 | Storey JD. The positive false discovery rate: a Bayesian interpretation and the q-value. Ann Statist 2003;31:2013-35. https://doi.org/10.1214/aos/1074290335 DOI |
28 | Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Statist 2001;29:1165-88. https://doi.org/10.1214/aos/1013699998. DOI |
29 | Rebai A, Goffinet B, Mangin B. Approximate thresholds of interval mapping tests for QTL detection. Genetics 1994;138:235-40. DOI |