A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs

English version

Autoři: In-Cheol Cho ^aff001; Hee-Bok Park ^aff002; Jin Seop Ahn ^aff003; Sang-Hyun Han ^aff004; Jae-Bong Lee ^aff005; Hyun-Tae Lim ^aff006; Chae-Kyoung Yoo ^aff007; Eun-Ji Jung ^aff008; Dong-Hwan Kim ^aff003; Wu-Sheng Sun ^aff003; Yuliaxis Ramayo-Caldas ^aff010; Sang-Geum Kim ^aff001; Yong-Jun Kang ^aff001; Yoo-Kyung Kim ^aff004; Hyun-Sook Shin ^aff001; Pil-Nam Seong ^aff001; In-Sul Hwang ^aff012; Beom-Young Park ^aff012; Seongsoo Hwang ^aff012; Sung-Soo Lee ^aff013; Youn-Chul Ryu ^aff014; Jun-Heon Lee ^aff015; Moon-Suck Ko ^aff001; Kichoon Lee ^aff016; Göran Andersson ^aff017; Miguel Pérez-Enciso ^aff018; Jeong-Woong Lee ^aff003
Působiště autorů: National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea ^aff001; Department of Animal Resources Science, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea ^aff002; Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea ^aff003; Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea ^aff004; Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Republic of Korea ^aff005; Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea ^aff006; Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea ^aff007; Bio-Medical Science Co., Ltd., Gimpo, Republic of Korea ^aff008; Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea ^aff009; Génétique Animale et Biologie Intégrative (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France ^aff010; Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, Spain ^aff011; National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea ^aff012; National Institute of Animal Science, Rural Development Administration, Namwon, Republic of Korea ^aff013; Division of Biotechnology, SARI, Jeju National University, Jeju, Republic of Korea ^aff014; Division of Animal and Dairy Science, Chungnam National University, Deajeon, Republic of Korea ^aff015; Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States of America ^aff016; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden ^aff017; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Barcelona, Spain ^aff018; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain ^aff019; ICREA, Carrer de Lluís Companys, Barcelona, Spain ^aff020
Vyšlo v časopise: A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs. PLoS Genet 15(10): e32767. doi:10.1371/journal.pgen.1008279
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008279

Souhrn

Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western commercial breeds and Korean native pigs (KNPs) and a joint linkage-linkage disequilibrium analysis, we identified a 488.1-kb region on porcine chromosome 12 that affects both reddish meat color (a*) and IMF. In this critical region, only the MYH3 gene, encoding myosin heavy chain 3, was found to be preferentially overexpressed in the skeletal muscle of KNPs. Subsequently, MYH3-transgenic mice demonstrated that this gene controls both myofiber-type specification and adipogenesis in skeletal muscle. We discovered a structural variant in the promotor/regulatory region of MYH3 for which Q allele carriers exhibited significantly higher values of a* and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation and cotransfection assays showed that the structural variant in the 5′-flanking region of MYH3 abrogated the binding of the myogenic regulatory factors (MYF5, MYOD, MYOG, and MRF4). The allele distribution of MYH3 among pig populations worldwide indicated that the MYH3 Q allele is of Asian origin and likely predates domestication. In conclusion, we identified a functional regulatory sequence variant in porcine MYH3 that provides novel insights into the genetic basis of the regulation of myofiber type ratios and associated changes in IMF in pigs. The MYH3 variant can play an important role in improving pork quality in current breeding programs.

Klíčová slova:

Fibroblasts – Genome-wide association studies – Luciferase – Meat – Sequence motif analysis – Skeletal muscles – Swine – Variant genotypes

Zdroje

1. Fu W, O'Connor TD, Akey JM. Genetic architecture of quantitative traits and complex diseases. 2013; Curr Opin Genet Dev 23: 678–683. doi: 10.1016/j.gde.2013.10.008 24287334

2. Georges M. Mapping, fine mapping, and molecular dissection of quantitative trait Loci in domestic animals. 2007; Annu Rev Genomics Hum Genet 8: 131–162. doi: 10.1146/annurev.genom.8.080706.092408 17477823

3. Andersson L. Molecular consequences of animal breeding. 2013; Curr Opin Genet Dev 23: 295–301. doi: 10.1016/j.gde.2013.02.014 23601626

4. Kim DH, Seong PN, Cho SH, Kim JH, Lee JM, Jo C, et al. Fatty acid composition and meat quality traits of organically reared Korean native black pigs. 2009; Livest Sci 120: 96–102.

5. Buckingham M, Rigby PW. Gene regulatory networks and transcriptional mechanisms that control myogenesis. 2014; Dev Cell 28: 225–238. doi: 10.1016/j.devcel.2013.12.020 24525185

6. Hausman GJ, Basu U, Wei S, Hausman DB, Dodson MV. Preadipocyte and adipose tissue differentiation in meat animals: influence of species and anatomical location. 2014; Annu Rev Anim Biosci 2: 323–351. doi: 10.1146/annurev-animal-022513-114211 25384146

7. Cho IC, Park HB, Yoo CK, Lee GJ, Lim HT, Lee JB, et al. QTL analysis of white blood cell, platelet and red blood cell-related traits in an F2 intercross between Landrace and Korean native pigs. 2011; Anim Genet 42: 621–626. doi: 10.1111/j.1365-2052.2011.02204.x 22035003

8. Cho IC, Yoo CK, Lee JB, Jung EJ, Han SH, Lee SS, et al. Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. 2015; Genet Sel Evol 47: 7. doi: 10.1186/s12711-014-0080-6 25888076

9. Luo W, Cheng D, Chen S, Wang L, Li Y, Ma X, et al. Genome-wide association analysis of meat quality traits in a porcine Large White x Minzhu intercross population. 2012; Int J Biol Sci 8: 580–595. doi: 10.7150/ijbs.3614 22532790

10. Xiong X, Liu X, Zhou L, Yang J, Yang B, Ma H, et al. Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs. 2015; Mamm Genome 26: 181–190. doi: 10.1007/s00335-015-9558-y 25678226

11. Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, et al. (2009) Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. 2009; PLoS One 4: e6524. doi: 10.1371/journal.pone.0006524 19654876

12. Ledur MC, Navarro N, Perez-Enciso M. Large-scale SNP genotyping in crosses between outbred lines: how useful is it? 2010; Heredity 105: 173–182. doi: 10.1038/hdy.2009.149 19844266

13. Druet T, Georges M. A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. 2010; Genetics 184: 789–798. doi: 10.1534/genetics.109.108431 20008575

14. Schiaffino S, Reggiani C. Fiber types in mammalian skeletal muscles. 2011; Physiol Rev 91: 1447–1531. doi: 10.1152/physrev.00031.2010 22013216

15. Spiegelman BM, Puigserver P, Wu Z. Regulation of adipogenesis and energy balance by PPARgamma and PGC-1. 2000; Int J Obes Relat Metab Disord 24 Suppl 4: S8–10.

16. Ahmadian M, Suh JM, Hah N, Liddle C, Atkins AR, Downes M, et al. PPARgamma signaling and metabolism: the good, the bad and the future. 2013; Nat Med 19: 557–566. doi: 10.1038/nm.3159 23652116

17. Merkestein M, Laber S, McMurray F, Andrew D, Sachse G, Sanderson J, et al. FTO influences adipogenesis by regulating mitotic clonal expansion. 2015; Nat Comm 6: 6792.

18. Karim L, Takeda H, Lin L, Druet T, Arias JA, Baurain D, et al. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. 2011; Nat Genet 43: 405–413. doi: 10.1038/ng.814 21516082

19. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L et al. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. 2003; Nature 425: 832–836. doi: 10.1038/nature02064 14574411

20. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. 2015; Nucleic Acids Res 43(W1): W39–49. doi: 10.1093/nar/gkv416 25953851

21. Thomas-Chollier M, Hufton A, Heinig M, O'Keeffe S, Masri NE, Roider HG et al. Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. 2011; Nat Protoc 6: 1860–1869. doi: 10.1038/nprot.2011.409 22051799

22. Mathelier A, Fornes O, Arenillas DJ, Chen CY, Denay G, Lee J, et al. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. 2016; Nucleic Acids Res 44: D110–115. doi: 10.1093/nar/gkv1176 26531826

23. Messeguer X, Escudero R, Farré D, Núñez O, Martínez J, Albà MM, et al. PROMO: detection of known transcription regulatory elements using species-tailored searches. 2002; Bioinformatics 18: 333–334. doi: 10.1093/bioinformatics/18.2.333 11847087

24. Schaid DJ, Chen W, Larson NB. From genome-wide associations to candidate causal variants by statistical fine-mapping. 2018; Nat Rev Genet 19: 491–504. doi: 10.1038/s41576-018-0016-z 29844615

25. Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association. 2014; Genetics 198: 497–508. doi: 10.1534/genetics.114.167908 25104515

26. Hormozdiari F, van de Bunt M, Segrè AV, Li X, Joo JWJ, Bilow M, et al. Colocalization of GWAS and eQTL Signals Detects Target Genes. 2016; Am J Hum Genet 99: 1245–1260. doi: 10.1016/j.ajhg.2016.10.003 27866706

27. Pasaniuc B, Price AL. Dissecting the genetics of complex traits using summary association statistics. 2017; Nat Rev Genet 18: 117–127. doi: 10.1038/nrg.2016.142 27840428

28. Ahn KS, Kim YJ, Kim M, Lee BH, Heo SY, Kang MJ, et al. Resurrection of an alpha-1,3-galactosyltransferase gene-targeted miniature pig by recloning using postmortem ear skin fibroblasts. 2011; Theriogenology 75: 933–939. doi: 10.1016/j.theriogenology.2010.11.001 21196043

29. Do M, Jang WG, Hwang JH, Jang H, Kim EJ, Jeong EJ, et al. Inheritance of mitochondrial DNA in serially recloned pigs by somatic cell nuclear transfer (SCNT). 2012; Biochem Biophys Res Commun 424: 765–770. doi: 10.1016/j.bbrc.2012.07.031 22809505

30. Giuffra E, Kijas JM, Amarger V, Carlborg O, Jeon JT, Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. 2000; Genetics 154: 1785–1791. 10747069

31. Bosse M, Megens HJ, Madsen O, Frantz LA, Paudel Y, Crooijmans RP, et al. Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations. 2014; Mol Ecol 23: 4089–4102. doi: 10.1111/mec.12807 24863459

32. Frantz LA, Schraiber JG, Madsen O, Megens HJ, Cagan A, Bosse M, et al. (2015) Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes. Nat Genet 47: 1141–1148. doi: 10.1038/ng.3394 26323058

33. Ojeda A, Huang LS, Ren J, Angiolillo A, Cho IC, Soto H, et al. Selection in the making: a worldwide survey of haplotypic diversity around a causative mutation in porcine IGF2. 2008; Genetics 178: 1639–1652. doi: 10.1534/genetics.107.084269 18245828

34. Hu ZL, Park CA, Reecy JM. Developmental progress and current status of the Animal QTLdb. 2016; Nucleic Acids Res 44: D827–833. doi: 10.1093/nar/gkv1233 26602686

35. Schiaffino S, Reggiani C. Molecular diversity of myofibrillar proteins: gene regulation and functional significance. 1996; Physiol Rev 76: 371–423. doi: 10.1152/physrev.1996.76.2.371 8618961

36. Whalen RG, Schwartz K, Bouveret P, Sell SM, Gros F. Contractile protein isozymes in muscle development: identification of an embryonic form of myosin heavy chain. 1979; Proc Natl Acad Sci USA 76: 5197–5201. doi: 10.1073/pnas.76.10.5197 291935

37. Chong JX, Burrage LC, Beck AE, Marvin CT, McMillin MJ, Shively KM, et al. Autosomal-Dominant Multiple Pterygium Syndrome Is Caused by Mutations in MYH3. 2015; Am J Hum Genet 96: 841–849. doi: 10.1016/j.ajhg.2015.04.004 25957469

38. Toydemir RM, Rutherford A, Whitby FG, Jorde LB, Carey JC, Bamshad MJ. Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. 2006; Nat Genet 38: 561–565. doi: 10.1038/ng1775 16642020

39. Yoo CK, Park HB, Lee JB, Jung EJ, Kim BM, Kim HI, et al. QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs. 2014; Anim Genet 45: 589–592. doi: 10.1111/age.12166 24797173

40. Fujii J, Otsu K, Zorzato F, de Leon S, Khanna VK, Weiler JE, et al. Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. 1991; Science 253: 448–451. doi: 10.1126/science.1862346 1862346

41. Brooke MH, Kaiser KK. Muscle fiber types: how many and what kind? 1970; Arch Neurol 23:369–379. doi: 10.1001/archneur.1970.00480280083010 4248905

42. Aulchenko YS, de Koning DJ, Haley C. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. 2007; Genetics 177: 577–585. doi: 10.1534/genetics.107.075614 17660554

43. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. 2015; GigaScience 4:7. doi: 10.1186/s13742-015-0047-8 25722852

44. Falconer DS, Mackay TFC. Introduction to Quantitative Genetics, 4th Ed., Longman Group Ltd., 1996.

45. Perez-Enciso M, Misztal I. Qxpak.5: old mixed model solutions for new genomics problems. 2001; BMC Bioinformatics 12: 202.

46. Knudsen S. Promoter2.0: for the recognition of PolII promoter sequences. 1999; Bioinformatics 15: 356–361. doi: 10.1093/bioinformatics/15.5.356 10366655

47. Sargolzaei M, Chesnais JP, Schenkel FS. A new approach for efficient genotype imputation using information from relatives. 2014; BMC Genomics 15: 478. doi: 10.1186/1471-2164-15-478 24935670

48. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. 2009; Clin Chem 55: 611–622. doi: 10.1373/clinchem.2008.112797 19246619

49. Daou N, Lecolle S, Lefebvre S, della Gaspera B, Charbonnier F, Chanoine C, et al. A new role for the calcineurin/NFAT pathway in neonatal myosin heavy chain expression via the NFATc2/MyoD complex during mouse myogenesis. 2013; Development 140: 4914–4925. doi: 10.1242/dev.097428 24301466

50. Li T, Xu D, Zuo B, Lei M, Xiong Y, Chen H, et al. Ectopic overexpression of porcine DGAT1 increases intramuscular fat content in mouse skeletal muscle. 2013; Transgenic Res 22: 187–194. doi: 10.1007/s11248-012-9633-z 22826105

51. Liu Y, Chakroun I, Yang D, Horner E, Liang J, Aziz A, et al. Six1 regulates MyoD expression in adult muscle progenitor cells. 2013; PLoS One 28: e67762.

52. Lin J, Wu H, Tarr PT, Zhang CY, Wu Z, Boss O, Michael LF, et al. Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres. 2002; Nature 418: 797–801. doi: 10.1038/nature00904 12181572

53. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. 2001; Methods 25: 402–408. doi: 10.1006/meth.2001.1262 11846609

54. Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, et al. Analyses of pig genomes provide insight into porcine demography and evolution. 2012, Nature 491: 393–398. doi: 10.1038/nature11622 23151582

55. Rubin CJ, Megens HJ, Martinez Barrio A, Maqbool K, Sayyab S, Schwochow D et al. Strong signatures of selection in the domestic pig genome. 2012; Proc Natl Acad Sci USA 109: 19529–19536. doi: 10.1073/pnas.1217149109 23151514

56. Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Megens HJ, Silió L et al. Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs. 2013; BMC Genomics 14: 148. doi: 10.1186/1471-2164-14-148 23497037

57. Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, et al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. 2015; Nat Genet 47: 217–225. doi: 10.1038/ng.3199 25621459

58. Bianco E, Nevado B, Ramos-Onsins SE, Perez-Enciso M. A deep catalog of autosomal single nucleotide variation in the pig. 2015; PLoS One 10: e0118867. doi: 10.1371/journal.pone.0118867 25789620

59. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. 2009. Bioinformatics 25: 1754–1760. doi: 10.1093/bioinformatics/btp324 19451168

60. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. 2010; Genome Res 20: 1297–1303. doi: 10.1101/gr.107524.110 20644199

61. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. 2009; Bioinformatics 25:2078–2079. doi: 10.1093/bioinformatics/btp352 19505943

62. Quinlan AR. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. 2014; Curr Protoc Bioinformatics 47:11 12 11–34. doi: 10.1002/0471250953.bi1112s47 25199790

63. Ferretti L, Raineri E, Ramos-Onsins S. Neutrality tests for sequences with missing data. 2012; Genetics 191: 1397–1401. doi: 10.1534/genetics.112.139949 22661328

64. Guirao-Rico S, Ramirez O, Ojeda A, Amills M, Ramos-Onsins S. Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations. 2018; Heredity 120: 63–76. doi: 10.1038/s41437-017-0002-9 29234173