Аннотация (русский):
Livni is one of the Russian local pig breeds. We previously reported that this breed was more distinct from Duroc breed than from Landrace and the Large White breeds, which participated in the Livni breed creation. The aim of the study was to determine the SNP-based genetic signatures in fat-type Livni breed shared with commercial Landrace and the Large White breeds, and ones that are affected by putative selection. The genome-wide SNP genotyping was carried out using the Porcine GGP HD BeadChip, which contains ~ 80 000 SNPs. Obtained breed relationship and admixture results indicated the insignificant participation of the Landrace and the Large White breeds in the formation of the modern allelofund of Livni pigs. 238 candidate genes were found in the genomic regions with selection signatures, 182 genes with described functions were identified. In the Livni and Landrace breeds, 35 common genes were detected which formed one cluster with enrichment coefficient = 4.94 and predominant HOXD genes. In the Livni and Large White breeds, the largest amounts of common genes were detected (62 in average), which formed two clusters. Cluster 1, with enrichment coefficient = 2.11, was characterized with genes involved in glucose metabolism. Cluster 2, with enrichment coefficient = 1.60, demonstrated helicase genes. Annotated clusters were not determined for the Livni breed. However, 50 candidate genes were specific to Livni pigs and associated with various growth, carcass and reproductive traits, essential for thermoregulation. Results revealed common SNP-based genetic signatures and breeding effects in indigenous Livni compared with Landrace and Large White breeds.

Ключевые слова:
Livni breed, animal genetic resources, SNPs, pig, carcass, traits

1. Hulsegge I, Calus M, Hoving-Bolink R, Lopes M, Megens H-J, Oldenbroek K. Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs. Genetics Selection Evolution. 2019;51. https://doi.org/10.1186/s12711-019-0502-6

2. Ianni A, Bennato F, Martino C, Odoardi M, Sacchetti A, Martino G. Qualitative attributes of commercial pig meat from an Italian native breed: the Nero d’Abruzzo. Foods. 2022;11(9). https://doi.org/10.3390/foods11091297

3. Zhao Q, Oyelami FO, Qadri QR, Sun H, Xu Z, Wang Q, et al. Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation. BMC Genomics. 2021;22. https://doi.org/10.1186/s12864-021-07476-7

4. Zhao Q, López-Cortegano E, Oyelami FO, Zhang Z, Ma P, Wang Q, et al. Conservation priorities analysis of Chinese indigenous pig breeds in the Taihu Lake region. Frontiers in Genetics. 2021;12. https://doi.org/10.3389/fgene.2021.558873

5. Panda R, Pawankar KN, Laishram M, Debbarma A. The relevance of pig breeds from North Eastern India towards pork production - A review. International Journal of Advances in Agricultural Science and Technology. 2018;5(7):124-132.

6. Touma S, Shimabukuro H, Arakawa A, Oikawa T. Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region. Asian-Australasian Journal of Animal Sciences. 2019;32(4):501-507. https://doi.org/10.5713/ajas.18.0378

7. Muñoz M, Bozzi R, García F, Núñez Y, Geraci C, Crovetti A, et al. Diversity across major and candidate genes in European local pig breeds. PLoS One. 2018;13(11). https://doi.org/10.1371/journal.pone.0207475

8. Dadousis C, Muñoz M, Óvilo C, Fabbri MC, Araújo JP, Bovo S, et al. Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data. Scientific Reports. 2022;12. https://doi.org/10.1038/s41598-022-10698-8

9. Halimani TE, Mapiye O, Marandure T, Januarie D, Imbayarwo-Chikosi VE, Dzama K. Domestic free-range pig genetic resources in Southern Africa: Progress and prospects. Diversity. 2020;12(2). https://doi.org/10.3390/d12020068

10. Osei-Amponsah R, Skinner BM, Adjei DO, Bauer J, Larson G, Affara NA, et al. Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis. BMC Genomics. 2017;18. https://doi.org/10.1186/s12864-017-3536-6

11. Grossi DA, Jafarikia M, Brito LF, Buzanskas ME, Sargolzaei M, Schenkel FS. Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs. BMC Genetics. 2017;18. https://doi.org/10.1186/s12863-017-0473-y

12. Willson HE, de Oliveira HR, Schinckel AP, Grossi D, Brito LF. Estimation of genetic parameters for pork quality, novel carcass, primal-cut and growth traits in Duroc pigs. Animals. 2020;10(5). https://doi.org/10.3390/ani10050779

13. Cortés O, Martinez AM, Cañon J, Sevane N, Gama LT, Ginja C, et al. Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information. Heredity. 2016;117:14-24. https://doi.org/10.1038/hdy.2016.21

14. Scarpa R, Drucker AG, Anderson S, Ferraes-Ehuan N, Gómez V, Risopatrón CR, et al. Valuing genetic resources in peasant economies: The case of “hairless” creole pigs in Yucatan. Ecological Economics. 2003;45(3):427-443. https://doi.org/10.1016/S0921-8009(03)00095-8

15. Koziner AB, Shtakelberg ER. 3Pigs. In: Dmitriev NG, Ernst LK, editors. Animal genetic resources of the USSR. Rome: FAO and UNEP; 1989. pp. 104-153.

16. Traspov A, Deng W, Kostyunina O, Ji J, Shatokhin K, Lugovoy S, et al. Population structure and genome characterization of local pig breeds in Russia, Belorussia, Kazakhstan and Ukraine. Genetics Selection Evolution. 2016;48. https://doi.org/10.1186/s12711-016-0196-y

17. Development of pig farming in the Russian Federation [Internet]. [cited 2023 Aug 15]. Available from: https://mcx.gov.ru/upload/iblock/22e/22e03f3b762d95fc0b037b9eeede1198.pdf

18. Pavlova SV, Kozlova NA, Myshkina MS, Schavlikova TN. Genetic resources of domestic pig-breeding in Russian Federation as of January 1, 2022. Pigbreeding. 2022;(5):9-11. (In Russ.). https://doi.org/10.37925/0039-713X-2022-5-9-11

19. Yearbook on breeding work in pig husbandry in establishment of the Russian Federation for 2021 [Internet]. [cited 2023 Aug 17]. Available from: https://vniiplem.com/wp-content/uploads/2023/04/Ежегодник-свин.2022.pdf

20. Chernukha I, Abdelmanova A, Kotenkova E, Kharzinova V, Zinovieva NA. Assessing genetic diversity and searching for selection signatures by comparison between the indigenous Livni and Duroc breeds in local livestock of the central region of Russia. Diversity. 2022;14(10). https://doi.org/10.3390/d14100859

21. Redkin AP. Pig husbandry. Moscow: State Publishing House for Agricultural Literature; 1952. 488 p. (In Russ.).

22. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics. 2007;81(3):559-575. https://doi.org/10.1086/519795

23. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: Rising to the challenge of larger and richer datasets. GigaScience. 2015;4(1). https://doi.org/10.1186/s13742-015-0047-8

24. Keenan K, McGinnity P, Cross TF, Crozier WW, Prodöhl PA. diveRsity: An R package for the estimation of population genetics parameters and their associated errors. Methods in Ecology and Evolution. 2013;4(8):782-788. https://doi.org/10.1111/2041-210X.12067

25. Wickham H. ggplot2: Elegant graphics for data analysis. New York: Springer; 2009. 213 p. https://doi.org/10.1007/978-0-387-98141-3

26. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38(6):1358-1370. https://doi.org/10.2307/2408641

27. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution. 2006;23(2):254-267. https://doi.org/10.1093/molbev/msj030

28. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Research. 2009;19:1655-1664. https://doi.org/10.1101/gr.094052.109

29. Francis RM. pophelper: An R package and web app to analyse and visualise population structure. Molecular Ecology Resources. 2017;17(1):27-32. https://doi.org/10.1111/1755-0998.12509

30. Iso-Touru T, Tapio M, Vilkki J, Kiseleva T, Ammosov I, Ivanova Z, et al. Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe. Animal Genetics. 2016;47(6):647-657. https://doi.org/10.1111/age.12473

31. Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, et al. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology. 2012;10(2). https://doi.org/10.1371/journal.pbio.1001258

32. Zhao F, McParland S, Kearney F, Du L, Berry DP. Detection of selection signatures in dairy and beef cattle using high-density genomic information. Genetics Selection Evolution. 2015;47. https://doi.org/10.1186/s12711-015-0127-3

33. Biscarini F, Cozzi P, Gaspa G, Marras G. detectRUNS: Detect runs of homozygosity and runs of heterozygosity in diploid genomes [Internet]. [cited 2023 Aug 17]. Available from: https://cran.r-project.org/web/packages/detectRUNS/index.html

34. Ferenčaković M, Sölkner J, Curik I. Estimating autozygosity from high-throughput information: Effects of SNP density and genotyping errors. Genetics Selection Evolution. 2013;45. https://doi.org/10.1186/1297-9686-45-42

35. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, et al. Runs of homo-zygosity reveal highly penetrant recessive loci in schizophrenia. Proceedings of the National Academy of Sciences. 2007;104(50):19942-19947. https://doi.org/10.1073/pnas.0710021104

36. Purfield DC, Berry DP, McParland S, Bradley DG. Runs of homozygosity and population history in cattle. BMC Genetic. 2012;13. https://doi.org/10.1186/1471-2156-13-70

37. Peripolli E, Stafuzza NB, Munari DP, Lima ALF, Irgang R, Machado MA, et al. Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics. 2018;19. https://doi.org/10.1186/s12864-017-4365-3

38. Grilz-Seger G, Neuditschko M, Ricard A, Velie B, Lindgren G, Mesarič M, et al. Genome-wide homozygosity patterns and evidence for selection in a set of European and Near Eastern horse breeds. Genes. 2019;10(7). https://doi.org/10.3390/genes10070491

39. Fariello MI, Boitard S, Naya H, SanCristobal M, Servin B. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics. 2013;193(3):929-941. https://doi.org/10.1534/genetics.112.147231

40. Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. The American Journal of Human Genetics. 2006;78(4):629-644. https://doi.org/10.1086/502802

41. Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, et al. Ensembl BioMarts: A hub for data retrieval across taxonomic space. Database. 2011;2011. https://doi.org/10.1093/database/bar030

42. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols. 2009;4:44-57. https://doi.org/10.1038/nprot.2008.211

43. Richard AJ, Stephens JM. The role of JAK-STAT signaling in adipose tissue function. Biochimica et Biophysica Acta - Molecular Basis of Disease. 2014;1842(3):431-439. https://doi.org/10.1016/j.bbadis.2013.05.030

44. Sun WX, Wang HH, Jiang BC, Zhao YY, Xie ZR, Xiong K, et al. Global comparison of gene expression between subcutaneous and intramuscular adipose tissue of mature Erhualian pig. Genetics and Molecular Research. 2013;12(4):5085-5101. https://doi.org/10.4238/2013.October.29.3

45. Knights AJ, Liu S, Ma Y, Nudell VS, Perkey E, Sorensen MJ, et al. Acetyl-choline-synthesizing macrophages in subcutaneous fat are regulated by β2 -adrenergic signaling. The EMBO Journal. 2021;40(24). http://dx.doi.org/10.15252/embj.2020106061

46. Kim Y, Kang BE, Ryu D, Oh SW, Oh C-M. Comparative transcriptome profiling of young and old brown adipose tissue thermogenesis. International Journal of Molecular Sciences. 2021;22(23). https://doi.org/10.3390/ijms222313143

47. Zhao X, Wang C, Wang Y, Lin H, Wang H, Hu H, et al. Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork. BMC Genetics. 2019;20. https://doi.org/10.1186/s12863-019-0794-0

48. Kollara A, Brown TJ. Expression and function of nuclear receptor co-activator 4: Evidence of a potential role independent of co-activator activity. Cellular and Molecular Life Sciences. 2012;69:3895-3909. https://doi.org/10.1007/s00018-012-1000-y

49. Huang M, Zhang H, Wu ZP, Wang XP, Li DS, Liu SJ, et al. Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs. Animal. 2021;15(10). https://doi.org/10.1016/j.animal.2021.100354

50. Somekh J. A methodology for predicting tissue-specific metabolic roles of receptors applied to subcutaneous adipose. Scientific Reports. 2020;10. https://doi.org/10.1038/s41598-020-73214-w

51. Samad F, Bai H, Baik N, Haider P, Zhang Y, Rega-Kaun G, et al. The plasminogen receptor Plg-RKT regulates adipose function and metabolic homeostasis. Journal of Thrombosis and Haemostasis. 2022;20(3):742-754. https://doi.org/10.1111/jth.15622

52. Fan B, Onteru SK, Mote BE, Serenius T, Stalder KJ, Rothschild MF. Large-scale association study for structural soundness and leg locomotion traits in the pig. Genetics Selection Evolution. 2009;41. https://doi.org/10.1186/1297-9686-41-14

53. Afonso MS, Verma N, van Solingen C, Cyr Y, Sharma M, Perie L, et al. MicroRNA-33 inhibits adaptive thermogenesis and adipose tissue beiging. Arteriosclerosis, Thrombosis, and Vascular Biology. 2021;41(4):1360-1373. https://doi.org/10.1161/ATVBAHA.120.315798

54. Piórkowska K, Żukowski K, Szmatoła T, Ropka-Molik K. Transcript variants of a region on SSC15 rich in QTLs associated with meat quality in pigs. Annals of Animal Science. 2017;17(3):703-715. https://doi.org/10.1515/aoas-2016-0095

55. Szántó M, Gupte R, Kraus WL, Pacher P, Bai P. PARPs in lipid metabolism and related diseases. Progress in Lipid Research. 2021;84. https://doi.org/10.1016/j.plipres.2021.101117

56. Fu Y, Li C, Tang Q, Tian S, Jin L, Chen J, et al. Genomic analysis reveals selection in Chinese native black pig. Scientific Reports. 2016;6. https://doi.org/10.1038/srep36354

57. Zhang W, Li X, Jiang Y, Zhou M, Liu L, Su S, et al. Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing. Frontiers in Genetics. 2022;13. https://doi.org/10.3389/fgene.2022.1022261

58. Xu J, Ruan Y, Sun J, Shi P, Huang J, Dai L, et al. Association analysis of PRKAA2 and MSMB polymorphisms and growth traits of Xiangsu hybrid pigs. Genes. 2023;14(1). https://doi.org/10.3390/genes14010113

59. Xing K, Zhu F, Zhai L, Liu H, Wang Z, Hou Z, et al. The liver transcriptome of two full-sibling Songliao black pigs with extreme differences in backfat thickness. Journal of Animal Science and Biotechnology. 2014;5. https://doi.org/10.1186/2049-1891-5-32

60. Dogan AE, Hamid SM, Yildirim AD, Yildirim Z, Sen G, Riera CE, et al. PACT establishes a post-transcriptional brake on mitochondrial biogenesis by promoting the maturation of miR-181c. Journal of Biological Chemistry. 2022;298(7). https://doi.org/10.1016/j.jbc.2022.102050

61. Waide EH, Tuggle CK, Serão NVL, Schroyen M, Hess A, Rowland RRR, et al. Genomewide association of piglet responses to infection with one of two porcine reproductive and respiratory syndrome virus isolates. Journal of Animal Science. 2017;95(1):16-38. https://doi.org/10.2527/jas.2016.0874

62. Pozhitkov AE, Neme R, Domazet-Lošo T, Leroux BG, Soni S, Tautz D, et al. Tracing the dynamics of gene transcripts after organismal death. Open Biology. 2017;7. https://doi.org/10.1098/rsob.160267

63. Guo F, Zhu Y, Han Y, Feng X, Pan Z, He Y, et al. DEPP deficiency contributes to browning of white adipose tissue. International Journal of Molecular Sciences. 2022;23(12). https://doi.org/10.3390/ijms23126563

64. Muñoz M, García-Casco JM, Caraballo C, Fernández-Barroso MÁ, Sánchez-Esquiliche F, Gómez F, et al. Identification of candidate genes and regulatory factors underlying intramuscular fat content through longissimus dorsi transcriptome analyses in heavy Iberian pigs. Frontiers in Genetics. 2018;9. https://doi.org/10.3389/fgene.2018.00608

65. Liu H, Nguyen YT, Nettleton D, Dekkers JCM, Tuggle CK. Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake. BMC Genomics. 2016;17. https://doi.org/10.1186/s12864-016-2395-x

66. Do DN, Strathe AB, Ostersen T, Pant SD, Kadarmideen HN. Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake. Frontiers in Genetics. 2014;5. https://doi.org/10.3389/fgene.2014.00307

67. Chalkias H. Genetic and clinical studies of teat traits in the pig. Doctoral Thesis. Uppsala: Swedish University of Agricultural Science; 2013. 64 p.

68. Fan S, Kong C, Chen Y, Zheng X, Zhou R, Zhang X, et al. Copy number variation analysis revealed the evolutionary difference between Chinese Indigenous pigs and Asian wild boars. Genes. 2023;14(2). https://doi.org/10.3390/genes14020472

69. Charlton CE, Reeves MA, Brandebourg TD. 140 relaxin regulates porcine adipose tissue development by inhibiting preadipocyte number, stimulating lipolysis, and upregulating mRNA expression of adipokine, fatty acid metabolism and extracellular matrix genes. Journal of Animal Science. 2020;98(Suppl.2):39-40. https://doi.org/10.1093/jas/skz397.090

70. Ghebrewold R. Genome-wide association study for the relationship between temperature and feed intake in beef cattle. M.S. Thesis. Lincoln: University of Nebraska; 2018.104 p.

71. Zhao YX, Gao GX, Zhou Y, Guo CX, Li B, El-Ashram S, et al. Genome-wide association studies uncover genes associated with litter traits in the pig. Animal. 2022;16(12). https://doi.org/10.1016/j.animal.2022.100672

72. Sun H, Wang Z, Zhang Z, Xiao Q, Mawed S, Xu Z, et al. Genomic signatures reveal selection of characteristics within and between Meishan pig populations. Animal Genetics. 2018;49(2):119-126. https://doi.org/10.1111/age.12642

73. Landua JD, Moraes R, Carpenter EM, Lewis MT. Hoxd10 is required systemically for secretory activation in lactation and interacts genetically with Hoxd9. Journal of Mammary Gland Biology and Neoplasia. 2020;25:145-62. https://doi.org/10.1007/s10911-020-09454-3

74. Clark DL, Boler DD, Kutzler LW, Jones KA, McKeith FK, Killefer J, et al. Muscle gene expression associated with increased marbling in beef cattle. Animal Biotechnology. 2011;22(2):51-63. https://doi.org/10.1080/10495398.2011.552031

75. Almeida OAC, Moreira GCM, Rezende FM, Boschiero C, de Oliveira Peixoto J, Ibelli AMG, et al. Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics. 2019;20. https://doi.org/10.1186/s12864-019-5811-1

76. Dubey NK, Mishra VK, Dubey R, Deng Y-H, Tsai F-C, Deng W-P. Revisiting the advances in isolation, characterization and secretome of adipose-derived stromal/stem cells. International Journal of Molecular Sciences. 2018;19(8). https://doi.org/10.3390/ijms19082200

77. Ahn J, Wu H, Lee K. Integrative analysis revealing human adipose-specific genes and consolidating obesity loci. Scientific Reports. 2019;9. https://doi.org/10.1038/s41598-019-39582-8

78. Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, et al. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3 Genes|Genomes|Genetics. 2022;12(2). https://doi.org/10.1093/g3journal/jkab424

79. Messad F, Louveau I, Koffi B, Gilbert H, Gondret F. Investigation of muscle transcriptomes using gradient boosting machine learning identifies molecular predictors of feed efficiency in growing pigs. BMC Genomics. 2019;20. https://doi.org/10.1186/s12864-019-6010-9

80. Messad F, Louveau I, Renaudeau D, Gilbert H, Gondret F. Analysis of merged whole blood transcriptomic datasets to identify circulating molecular biomarkers of feed efficiency in growing pigs. BMC Genomics. 2021;22. https://doi.org/10.1186/s12864-021-07843-4

81. Kumar V, Sekar M, Sarkar P, Acharya KK, Thirumurugan K. Dynamics of HOX gene expression and regulation in adipocyte development. Gene. 2021;768. https://doi.org/10.1016/j.gene.2020.145308

82. Lindholm-Perry AK, Rohrer GA, Kuehn LA, Keele JW, Holl JW, Shackelford SD, et al. Genomic regions associated with kyphosis in swine. BMC Genetics. 2010;11. https://doi.org/10.1186/1471-2156-11-112

83. Ferraz ALJ, Ojeda A, López-Béjar M, Fernandes LT, Castelló A, Folch JM, et al. Transcriptome architecture across tissues in the pig. BMC Genomics. 2008;9. https://doi.org/10.1186/1471-2164-9-173

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

85. Wu D-D, Yang C-P, Wang M-S, Dong K-Z, Yan D-W, Hao Z-Q, et al. Convergent genomic signatures of high-altitude adaptation among domestic mammals. National Science Review. 2020;7(6):952-963. https://doi.org/10.1093/nsr/nwz213

86. Kyle CJ, Nixon M, Homer NZM, Morgan RA, Andrew R, Stimson RH, et al. ABCC1 modulates negative feedback control of the hypothalamic-pituitary-adrenal axis in vivo in humans. Metabolism. 2022;128. https://doi.org/10.1016/j.metabol.2021.155118

87. Nixon M, Mackenzie SD, Taylor AI, Homer NZM, Livingstone DE, Mouras R, et al. ABCC1 confers tissue-specific sensitivity to cortisol versus corticosterone: A rationale for safer glucocorticoid replacement therapy. Science Translational Medicine. 2016;8(352). https://doi.org/10.1126/scitranslmed.aaf9074

88. Guo L, Sun H, Zhao Q, Xu Z, Zhang Z, Liu D, et al. Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data. Animal Genetics. 2021;52(2):143-154. https://doi.org/10.1111/age.13034

89. Zhang D, He X, Wang W, Liu D. Whole-genome sequencing reveals the genetic relationships and selection signatures of the Min pig. Pakistan Journal of Zoology. 2022;54(3):1187-1198. https://doi.org/10.17582/journal.pjz/20200709040722

90. Zhang Z, Wang Z, Yang Y, Zhao J, Chen Q, Liao R, et al. Identification of pleiotropic genes and gene sets underlying growth and immunity traits: A case study on Meishan pigs. Animal. 2016;10(4):550-557. https://doi.org/10.1017/S1751731115002761

91. Shi L, Wang L, Liu J, Deng T, Yan H, Zhang L, et al. Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population. Journal of Animal Science and Biotechnology. 2020;11. https://doi.org/10.1186/s40104-020-00447-0

92. Horodyska J, Hamill RM, Varley PF, Reyer H, Wimmers K. Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs. PLoS ONE. 2017;12(6). https://doi.org/10.1371/journal.pone.0173482

93. Mármol-Sánchez E, Quintanilla R, Cardoso TF, Vidal JJ, Amills M. Polymorphisms of the cryptochrome 2 and mitoguardin 2 genes are associated with the variation of lipid-related traits in Duroc pigs. Scientific Reports. 2019;9. https://doi.org/10.1038/s41598-019-45108-z

94. Cardoso TF, Quintanilla R, Tibau J, Gil M, Mármol-Sánchez E, González-Rodríguez O, et al. Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle. BMC Genomics. 2017;18. https://doi.org/10.1186/s12864-017-3986-x

95. Lee S-H, Kim J-M. Breeding potential for pork belly to the novel economic trait. Journal of Animal Science and Technology. 2023;65(1):1-15. https://doi.org/10.5187/jast.2022.e118

96. Baboota RK, Sarma SM, Boparai RK, Kondepudi KK, Mantri S, Bishnoi M. Microarray based gene expression analysis of murine brown and subcutaneous adipose tissue: Significance with human. PLoS ONE. 2015;10(5). https://doi.org/10.1371/journal.pone.0127701

97. Lee Y-S, Son S, Lee H-K, Lee RH, Shin D. Elucidating breed-specific variants of native pigs in Korea: Insights into pig breeds' genomic characteristics. Animal Cells and Systems. 2022;26(6):338-347. https://doi.org/10.1080/19768354.2022.2141316

98. Ran X, Hu F, Mao N, Ruan Y, Yi F, Niu X, et al. Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs. Porcine Health Management. 2021;7. https://doi.org/10.1186/s40813-021-00226-x

99. van Son M, Tremoen NH, Gaustad AH, Myromslien FD, Våge DI, Stenseth E-B, et al. RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars. BMC Veterinary Research. 2017;13. https://doi.org/10.1186/s12917-017-1279-x

100. Lee Y-S, Son S, Heo J, Shinm D. Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea. Animal Cells and Systems. 2021;25(6):416-423. https://doi.org/10.1080/19768354.2021.2006310

101. Serranito B, Cavalazzi M, Vidal P, Taurisson-Mouret D, Ciani E, Bal M, et al. Local adaptations of Mediterranean sheep and goats through an integrative approach. Scientific Reports. 2021;11. https://doi.org/10.1038/s41598-021-00682-z

102. Wang X, Ran X, Niu X, Huang S, Li S, Wang J. Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs. Scientific Reports. 2022;12. https://doi.org/10.1038/s41598-022-14686-w

103. Yonggang L. Differential display reveals a novel pig gene, PRPF3, which is differentially expressed in Large White versus Wujin skeletal muscle tissues. Molecular Biology Reports. 2010;37:2687-2692. https://doi.org/10.1007/s11033-009-9799-5

104. Puig-Oliveras A, Ballester M, Corominas J, Revilla M, Estellé J, Fernández AI, et al. A co-association network analysis of the genetic determination of pig conformation, growth and fatness. PLoS ONE. 2014;9(12). https://doi.org/10.1371/journal.pone.0114862

105. Jensen KS, Binderup T, Jensen KT, Therkelsen I, Borup R, Nilsson E, et al. FoxO3A promotes metabolic adaptation to hypoxia by antagonizing Myc function. The EMBO Journal. 2011;30(22):4554-4570. https://doi.org/10.1038/emboj.2011.323

106. Yu J, Zhou Q-Y, Zhu M-J, Li C-C, Liu B, Fan B, et al. The Porcine FoxO1, FoxO3a and FoxO4 genes: cloning, mapping, expression and association analysis with meat production traits. Asian-Australasian Journal of Animal Sciences. 2007;20(5):627-632. https://doi.org/10.5713/ajas.2007.627

107. García-Contreras C, Madsen O, Groenen MAM, López-García A, Vázquez-Gómez M, Astiz S, et al. Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs. PLoS ONE. 2020;15(1). https://doi.org/10.1371/journal.pone.0227861

108. Zhang X, Liu Q, Zhang X, Guo K, Zhang X, Zhou Z. FOXO3a regulates lipid accumulation and adipocyte inflammation in adipocytes through autophagy. Inflammation Research. 2021;70:591-603. https://doi.org/10.1007/s00011-021-01463-0

109. Zhang B, Qiangba Y, Shang P, Wang Z, Ma J, Wang L, et al. A comprehensive microRNA expression profile related to hypoxia adaptation in the Tibetan pig. PLoS ONE. 2015;10(11). https://doi.org/10.1371/journal.pone.0143260

110. Yang Y, Yuan H, Yang T, Li Y, Gao C, Jiao T, et al. The expression regulatory network in the lung tissue of Tibetan pigs provides insight into hypoxia-sensitive pathways in high-altitude hypoxia. Frontiers in Genetics. 2021;12. https://doi.org/10.3389/fgene.2021.691592

111. Xing K, Zhao X, Liu Y, Zhang F, Tan Z, Qi X, et al. Identification of differentially expressed microRNAs and their potential target genes in adipose tissue from pigs with highly divergent backfat thickness. Animals. 2020;10(4). https://doi.org/10.3390/ani10040624

112. He D, Zou T, Gai X, Ma J, Li M, Huang Z, et al. MicroRNA expression profiles differ between primary myofiber of lean and obese pig breeds. PLoS ONE. 2017;12(7). https://doi.org/10.1371/journal.pone.0181897

113. Liu X, Gong J, Wang L, Hou X, Gao H, Yan H, et al. Genome-wide profiling of the microrna transcriptome regulatory network to identify putative candidate genes associated with backfat deposition in pigs. Animals. 2019;9(6). https://doi.org/10.3390/ani9060313

114. Gurgul A, Jasielczuk I, Ropka-Molik K, Semik-Gurgul E, Pawlina-Tyszko K, Szmatoła T, et al. A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland. BMC Genetics. 2018;19. https://doi.org/10.1186/s12863-018-0681-0

115. Xu Y, Han Q, Ma C, Wang Y, Zhang P, Li C, et al. Comparative proteomics and phosphoproteomics analysis reveal the possible breed difference in Yorkshire and Duroc boar spermatozoa. Frontiers in Cell and Developmental Biology. 2021;9. https://doi.org/10.3389/fcell.2021.652809

116. Mancini C, Gohlke S, Garcia-Carrizo F, Zagoriy V, Stephanowitz H, Schulz TJ. Identification of biomarkers of brown adipose tissue aging highlights the role of dysfunctional energy and nucleotide metabolism pathways. Scientific Reports. 2021;11. https://doi.org/10.1038/s41598-021-99362-1

117. Jung SM, Doxsey WG, Le J, Haley JA, Mazuecos L, Luciano AK, et al. In vivo isotope tracing reveals the versatility of glucose as a brown adipose tissue substrate. Cell Reports. 2021;36(4). https://doi.org/10.1016/j.celrep.2021.109459

118. Zekri Y, Guyot R, Suñer IG, Canaple L, Stein AG, Petit JV, et al. Brown adipocytes local response to thyroid hormone is required for adaptive thermogenesis in adult male mice. eLife. 2022;11. https://doi.org/10.7554/eLife.81996

119. Ponsuksili S, Reyer H, Trakooljul N, Murani E, Wimmers K. Single- and Bayesian multi-marker genome-wide association for haematological parameters in pigs. PLoS ONE. 2016;11(7). https://doi.org/10.1371/journal.pone.0159212

120. Paul E, Cronan R, Weston PJ, Boekelheide K, Sedivy JM, Lee S-Y, et al. Disruption of Supv3L1 damages the skin and causes sarcopenia, loss of fat, and death. Mammalian Genome. 2009;20:92-108. https://doi.org/10.1007/s00335-008-9168-z

121. Ropka-Molik K, Bereta A, Żukowski K, Tyra M, Piórkowska K, Żak G, et al. Screening for candidate genes related with histological microstructure, meat quality and carcass characteristic in pig based on RNA-seq data. Asian-Australasian Journal of Animal Sciences. 2018;31(10):1565-1574. https://doi.org/10.5713/ajas.17.0714

122. Hong J-K, Lee J-B, Ramayo-Caldas Y, Kim S-D, Cho E-S, Kim Y-S, et al. Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs. Scientific Reports. 2020;10. https://doi.org/10.1038/s41598-020-71647-x

123. Zhang Y, O'Keefe RJ, Jonason JH. BMP-TAK1 (MAP3K7) induces adipocyte differentiation through PPARγ signaling. Journal of Cellular Biochemistry. 2017;118(1):204-210. https://doi.org/10.1002/jcb.25626

124. Long F, Bhatti MR, Kellenberger A, Sun W, Modica S, Höring M, et al. A low-carbohydrate diet induces hepatic insulin resistance and metabolic associated fatty liver disease in mice. Molecular Metabolism. 2023;69. https://doi.org/10.1016/j.molmet.2023.101675

125. Zhou S, Ding R, Meng F, Wang X, Zhuang Z, Quan J, et al. A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations. BMC Genomics. 2021;22. https://doi.org/10.1186/s12864-020-07288-1

126. Xu Z, Sun H, Zhang Z, Zhao Q, Olasege BS, Li Q, et al. Assessment of autozygosity derived from runs of homozygosity in Jinhua pigs disclosed by sequencing data. Frontiers in Genetics. 2019;10. https://doi.org/10.3389/fgene.2019.00274

127. Pamenter ME, Hall JE, Tanabe Y, Simonson TS. Cross-species insights into genomic adaptations to hypoxia. Frontiers in Genetics. 2020;11. https://doi.org/10.3389/fgene.2020.00743

128. Ramayo-Caldas Y, Ballester M, Fortes MRS, Esteve-Codina A, Castelló A, Noguera JL, et al. From SNP co-association to RNA co-expression: Novel insights into gene networks for intramuscular fatty acid composition in porcine. BMC Genomics. 2014;15. https://doi.org/10.1186/1471-2164-15-232

129. Ding Y, Hou Y, Ling Z, Chen Q, Xu T, Liu L, et al. Identification of candidate genes and regulatory competitive endogenous RNA (ceRNA) networks underlying intramuscular fat content in Yorkshire pigs with extreme fat deposition phenotypes. International Journal of Molecular Sciences. 2022;23(20). https://doi.org/10.3390/ijms232012596

130. Li W, Yang Y, Liu Y, Liu S, Li X, Wang Y, et al. Integrated analysis of mRNA and miRNA expression profiles in livers of Yimeng black pigs with extreme phenotypes for backfat thickness. Oncotarget. 2017;8:114787-114800. https://doi.org/10.18632/oncotarget.21918

131. Diao S, Xu Z, Ye S, Huang S, Teng J, Yuan X, et al. Exploring the genetic features and signatures of selection in South China indigenous pigs. Journal of Integrative Agriculture. 2021;20(5):1359-1371. https://doi.org/10.1016/S2095-3119(20)63260-9

132. Falker-Gieske C, Blaj I, Preuß S, Bennewitz J, Thaller G, Tetens J. GWAS for meat and carcass traits using imputed sequence level genotypes in pooled F2-designs in pigs. G3 Genes|Genomes|Genetics. 2019;9(9):2823-2834. https://doi.org/10.1534/g3.119.400452

133. Liu X, Wang L, Liang J, Yan H, Zhao K, Li N, et al. Genome-wide association study for certain carcass traits and organ weights in a Large White×Minzhu intercross porcine population. Journal of Integrative Agriculture. 2014;13(12):2721-2730. https://doi.org/10.1016/S2095-3119(14)60787-5

134. Sidibeh CO, Pereira MJ, Abalo XM, Boersma GJ, Skrtic S, Lundkvist P, et al. FKBP5 expression in human adipose tissue: Potential role in glucose and lipid metabolism, adipogenesis and type 2 diabetes. Endocrine. 2018;62:116-128. https://doi.org/10.1007/s12020-018-1674-5

135. Wang Z, Shang P, Li Q, Wang L, Chamba Y, Zhang B, et al. iTRAQ-based proteomic analysis reveals key proteins affecting muscle growth and lipid deposition in pigs. Scientific Reports. 2017;7. https://doi.org/10.1038/srep46717

136. Li L, Xu X, Xiao M, Huang C, Cao J, Zhan S, et al. The profiles and functions of RNA editing sites associated with high-altitude adaptation in goats. International Journal of Molecular Sciences. 2023;24(4). https://doi.org/10.3390/ijms24043115

137. Shimada K, Park S, Miyata H, Yu Z, Morohoshi A, Oura S, et al. ARMC12 regulates spatiotemporal mitochondrial dynamics during spermiogenesis and is required for male fertility. Proceedings of the National Academy of Sciences. 2021;118(6). https://doi.org/10.1073/pnas.2018355118

138. Liu Q, Yue J, Niu N, Liu X, Yan H, Zhao F, et al. Genome-wide association analysis identified BMPR1A as a novel candidate gene affecting the number of thoracic vertebrae in a Large White × Minzhu intercross pig population. Animals. 2020;10(11). https://doi.org/10.3390/ani10112186

139. Ding R, Quan J, Yang M, Wang X, Zheng E, Yang H, et al. Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars. PLoS ONE. 2017;12(8). https://doi.org/10.1371/journal.pone.0183244

140. Whittle A, Vidal-Puig A. When BAT is lacking, WAT steps up. Cell Research. 2013;23:868-869. https://doi.org/10.1038/cr.2013.58

141. Qian S, Tang Y, Tang Q-Q. Adipose tissue plasticity and the pleiotropic roles of BMP signaling. Journal of Biological Chemistry. 2021;296. https://doi.org/10.1016/j.jbc.2021.100678

142. Ou C-Y, Chen T-C, Lee JV, Wang J-C, Stallcup MR. Coregulator cell cycle and apoptosis regulator 1 (CCAR1) positively regulates adipocyte differentiation through the glucocorticoid signaling pathway. Journal of Biological Chemistry. 2014;289:17078-17086. https://doi.org/10.1074/jbc.M114.548081

143. Xu Z, Sun H, Zhang Z, Zhang C-Y, Zhao Q, Xiao Q, et al. Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs. Asian-Australasian Journal of Animal Sciences. 2020;33(2):187-196. https://doi.org/10.5713/ajas.18.0658

144. Jankowiak H. Effect of colipase Gene (CLPS) polymorphism on carcass and meat quality in pigs. Folia Biologica. 2005;53(Suppl.1):91-93. https://doi.org/10.3409/173491605775789461

145. Kapelański W, Wilkanowska A, Cebulska A, Biegniewska M. The effect of CLPS and RYR1 gene polymorphism on meat quality of Złotnicka spotted pigs. Journal of Central European Agriculture. 2010;11(1):93-98. https://doi.org/10.5513/JCEA01/11.1.817

146. Kim H-Y, Caetano-Anolles K, Seo M, Kwon Y, Cho S, Seo K, et al. Prediction of genes related to positive selection using whole-genome resequencing in three commercial pig breeds. Genomics and Informatics. 2015;13(4):137-145. https://doi.org/10.5808/GI.2015.13.4.137

147. Liu X, Bai Y, Cui R, He S, Ling Y, Wu C, et al. Integrated analysis of the ceRNA network and M-7474 function in testosterone-mediated fat deposition in pigs. Genes. 2022;13(4). https://doi.org/10.3390/genes13040668

148. Dou Y, Qi K, Liu Y, Li C, Song C, Wei Y, et al. Identification and functional prediction of long non-coding RNA in longissimus dorsi muscle of Queshan Black and Large White pigs. Genes. 2023;14(1). https://doi.org/10.3390/genes14010197

149. Yudin NS, Larkin DM. Whole genome studies of origin, selection and adaptation of the Russian cattle breeds. Vavilov Journal of Genetics and Breeding. 2019;23(5):559-568. (In Russ.). https://doi.org/10.18699/VJ19.525

150. Weldenegodguad M, Popov R, Pokharel K, Ammosov I, Ming Y, Ivanova Z, et al. Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions. Frontiers in Genetics. 2019;9. https://doi.org/10.3389/fgene.2018.00728

151. Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner J-B. Genomics of adaptations in ungulates. Animals. 2021;11(6). https://doi.org/10.3390/ani11061617

152. Zhu Y, Li W, Yang B, Zhang Z, Ai H, Ren J, et al. Signatures of selection and interspecies introgression in the genome of Chinese domestic pigs. Genome Biology and Evolution. 2017;9(10):2592-2603. https://doi.org/10.1093/gbe/evx186

153. Wang C, Wang H, Zhang Y, Tang Z, Li K, Liu B. Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs. Molecular Ecology Resources. 2015;15(2):414-424. https://doi.org/10.1111/1755-0998.12311

154. Groenen MAM. A decade of pig genome sequencing: a window on pig domestication and evolution. Genetics Selection Evolution. 2016;48. https://doi.org/10.1186/s12711-016-0204-2

155. Dong K, Yao N, Pu Y, He X, Zhao Q, Luan Y, et al. Genomic scan reveals loci under altitude adaptation in Tibetan and Dahe pigs. PLoS ONE. 2014;9(10). https://doi.org/10.1371/journal.pone.0110520

156. Bovo S, Mazzoni G, Bertolini F, Schiavo G, Galimberti G, Gallo M, et al. Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. Scientific Reports. 2019;9. https://doi.org/10.1038/s41598-019-43297-1

157. Buerger F, Müller S, Ney N, Weiner J, Heiker JT, Kallendrusch S, et al. Depletion of Jmjd1c impairs adipogenesis in murine 3T3-L1 cells. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2017;1863(7):1709-1717. https://doi.org/10.1016/j.bbadis.2017.05.011

158. Rabiee A, Plucińska K, Isidor MS, Brown EL, Tozzi M, Sidoli S, et al. White adipose remodeling during browning in mice involves YBX1 to drive thermogenic commitment. Molecular Metabolism. 2021;44. https://doi.org/10.1016/j.molmet.2020.101137

159. Wang Z, Zhao Q, Li X, Yin Z, Chen S, Wu S, et al. MYOD1 inhibits avian adipocyte differentiation via miRNA-206/KLF4 axis. Journal of Animal Science and Biotechnology. 2021;12. https://doi.org/10.1186/s40104-021-00579-x

160. Stupka R, Citek J, Sprysl M, Okrouhla M, Brzobohaty L. The impact of MYOG, MYF6 and MYOD1 genes on meat quality traits in crossbred pigs. African Journal of Biotechnology. 2012;11(88):15405-15409. https://doi.org/10.5897/AJB12.1820

161. Lee EA, Kim JM, Lim KS, Ryu YC, Jeon WM, Hong KC. Effects of variation in porcine MYOD1 gene on muscle fiber characteristics, lean meat production, and meat quality traits. Meat Science. 2012;92(1):36-43. https://doi.org/10.1016/j.meatsci.2012.03.018

162. Guiatti D, Stefanon B, Sgorlon S. Association analysis between single nucleotide polymorphisms in the promoter region of LEP, MYF6, MYOD1, OPN, SCD genes and carcass traits in heavy pigs. Italian Journal of Animal Science. 2013;12(1). https://doi.org/10.4081/ijas.2013.e13

163. Cao R, Feng J, Xu Y, Fang Y, Zhao W, Zhang Z, et al. Genomic signatures reveal breeding effects of Lulai pigs. Genes. 2022;13(11). https://doi.org/10.3390/genes13111969

164. Braglia S, Davoli R, Zappavigna A, Zambonelli P, Buttazzoni L, Gallo M, et al. SNPs of MYPN and TTN genes are associated to meat and carcass traits in Italian Large White and Italian Duroc pigs. Molecular Biology Reports. 2013;40:6927-6933. https://doi.org/10.1007/s11033-013-2812-z

165. Zhai LW, Wang LX, Zhou WL, Wang CD. Association of the MYPN gene polymorphisms with meat quality in commercial pigs. Journal of Animal and Veterinary Advances. 2010;9(4):705-709. https://doi.org/10.3923/javaa.2010.705.709

166. Lents CA, Barb CR, Hausman GJ, Nonneman D, Heidorn NL, Cisse RS, et al. Effects of nesfatin-1 on food intake and LH secretion in prepubertal gilts and genomic association of the porcine NUCB2 gene with growth traits. Domestic Animal Endocrinology. 2013;45(2):89-97. https://doi.org/10.1016/j.domaniend.2013.06.002

167. Shimizu H, Tanaka M, Osaki A. Transgenic mice overexpressing nesfatin/nucleobindin-2 are susceptible to high-fat diet-induced obesity. Nutrition and Diabetes. 2016;6. https://doi.org/10.1038/nutd.2015.42

168. Wang Y, Li Z, Zhang X, Xiang X, Li Y, Mulholland MW, et al. Nesfatin-1 promotes brown adipocyte phenotype. Scientific Reports. 2016;6. https://doi.org/10.1038/srep34747

169. Fan S, Liu H, Li L. The REEP family of proteins: Molecular targets and role in pathophysiology. Pharmacological Research. 2022;185. https://doi.org/10.1016/j.phrs.2022.106477

170. Favero G, Krajčíková K, Bonomini F, Rodella LF, Tomečková V, Rezzani R. Browning of adipose tissue and sirtuin involvement. In: Szablewski L, editor. Adipose tissue. IntechOpen; 2018. https://doi.org/10.5772/intechopen.74760

171. Majeed Y, Halabi N, Madani AY, Engelke R, Bhagwat AM, Abdesselem H, et al. SIRT1 promotes lipid metabolism and mitochondrial biogenesis in adipocytes and coordinates adipogenesis by targeting key enzymatic pathways. Scientific Reports. 2021;11. https://doi.org/10.1038/s41598-021-87759-x

172. Ran H, He Q, Han Y, Wang J, Wang H, Yue B, et al. Functional study and epigenetic targets analyses of SIRT1 in intramuscular preadipocytes via ChIP-seq and mRNA-seq. Epigenetics. 2023;18(1). https://doi.org/10.1080/15592294.2022.2135194

173. Cao Y, Zhang M, Li Y, Lu J, Zhou W, Li X, et al. O-GlcNAcylation of sirt1 protects against cold stress-induced skeletal muscle damage via amelioration of mitochondrial homeostasis. International Journal of Molecular Sciences. 2022;23(23). https://doi.org/10.3390/ijms232314520

174. Rodríguez-Barrueco R, Latorre J, Devis-Jáuregui L, Lluch A, Bonifaci N, Llobet FJ, et al. A microRNA cluster controls fat cell differentiation and adipose tissue expansion by regulating SNCG. Advanced Science. 2022;9(4). https://doi.org/10.1002/advs.202104759

175. Du K, Chen G-H, Bai X, Chen L, Hu S-Q, Li Y-H, et al. Dynamics of transcriptome and chromatin accessibility revealed sequential regulation of potential transcription factors during the brown adipose tissue whitening in rabbits. Frontiers in Cell and Developmental Biology. 2022;10. https://doi.org/10.3389/fcell.2022.981661

176. Kuehn LA, Rohrer GA, Nonneman DJ, Thallman RM, Leymaster KA. Detection of single nucleotide polymorphisms associated with ultrasonic backfat depth in a segregating Meishan × White Composite population. Journal of Animal Science. 2007;85(5):1111-1119. https://doi.org/10.2527/jas.2006-704

177. Sarkar P, Thirumurugan K. New insights into TNFα/PTP1B and PPARγ pathway through RNF213-a link between inflammation, obesity, insulin resistance, and Moyamoya disease. Gene. 2021;771. https://doi.org/10.1016/j.gene.2020.145340

178. Pollaci G, Gorla G, Potenza A, Carrozzini T, Canavero I, Bersano A, et al. Novel multifaceted roles for RNF213 protein. International Journal of Molecular Sciences. 2022;23(9). https://doi.org/10.3390/ijms23094492

179. Zappaterra M, Gioiosa S, Chillemi G, Zambonelli P, Davoli R. Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs. PLoS ONE. 2020;15(5). https://doi.org/10.1371/journal.pone.0233372

180. Zeng H, Zhong Z, Xu Z, Teng J, Wei C, Chen Z, et al. Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait. BMC Genomics. 2022;23. https://doi.org/10.1186/s12864-022-09036-z

181. Verardo LL, Silva FF, Lopes MS, Madsen O, Bastiaansen JWM, Knol EF, et al. Revealing new candidate genes for reproductive traits in pigs: Combining Bayesian GWAS and functional pathways. Genetics Selection Evolution. 2016;48. https://doi.org/10.1186/s12711-016-0189-x

182. Li D, Huang M, Zhuang Z, Ding R, Gu T, Hong L, et al. Genomic analyses revealed the genetic difference and potential selection genes of growth traits in two Duroc lines. Frontiers in Veterinary Science. 2021;8. https://doi.org/10.3389/fvets.2021.725367

183. Ma J, Yang J, Zhou L, Zhang Z, Ma H, Xie X, et al. Genome-wide association study of meat quality traits in a White Duroc×Erhualian F2 intercross and Chinese Sutai pigs. PLoS ONE. 2013;8(5). https://doi.org/10.1371/journal.pone.0064047

184. Wang BB, Hou LM, Zhou WD, Liu H, Tao W, Wu WJ, et al. Genome-wide association study reveals a quantitative trait locus and two candidate genes on Sus scrofa chromosome 5 affecting intramuscular fat content in Suhuai pigs. Animal. 2021;15(9). https://doi.org/10.1016/j.animal.2021.100341

185. Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nature Genetics. 2013;45:1431-1438. https://doi.org/10.1038/ng.2811

186. Im D-S. Discovery of new G protein-coupled receptors for lipid mediators. Journal of Lipid Research. 2004;45(3):410-418. https://doi.org/10.1194/jlr.R300006-JLR200

187. Hlongwane NL, Hadebe K, Soma P, Dzomba EF, Muchadeyi FC. Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa. Frontiers in Genetics. 2020;11. https://doi.org/10.3389/fgene.2020.00344

188. Hamza MS, Pott S, Vega VB, Thomsen JS, Kandhadayar GS, Ng PWP, et al. De-novo identification of PPARγ/RXR binding sites and direct targets during adipogenesis. PLoS ONE. 2009;4(3). https://doi.org/10.1371/journal.pone.0004907

189. Honda T, Ishii A, Inui M. Regulation of adipocyte differentiation of 3T3-L1 cells by PDZRN3. American Journal of Physiology-Cell Physiology. 2013;304(11):C1091-С1097. https://doi.org/10.1152/ajpcell.00343.2012

190. Fontanesi L, Schiavo G, Galimberti G, Calò DG, Russo V. A genomewide association study for average daily gain in Italian Large White pigs. Journal of Animal Science. 2014;92(4):1385-1394. https://doi.org/10.2527/jas.2013-7059

191. Oqani RK, So S, Lee Y, Ko JJ, Kang E. Artificial oocyte: Development and potential application. Cells. 2022;11(7). https://doi.org/10.3390/cells11071135

192. Böttcher Y, Unbehauen H, Klöting N, Ruschke K, Körner A, Schleinitz D, et al. Adipose tissue expression and genetic variants of the bone morphogenetic protein receptor 1A gene (BMPR1A) are associated with human obesity. Diabetes. 2009;58(9):2119-2128. https://doi.org/10.2337/db08-1458

193. Keipert S, Kutschke M, Ost M, Schwarzmayr T, van Schothorst EM, Lamp D, et al. Long-term cold adaptation does not require FGF21 or UCP1. Cell Metabolism. 2017;26(2):437-446. https://doi.org/10.1016/j.cmet.2017.07.016

194. Schulz TJ, Huang P, Huang TL, Xue R, McDougall LE, Townsend KL, et al. Brown-fat paucity due to impaired BMP signalling induces compensatory browning of white fat. Nature. 2013;495:379-383. https://doi.org/10.1038/nature11943

195. Qiao R, Zhang M, Zhang B, Li X, Han X, Wang K, et al. Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs. Frontiers in Genetics. 2022;13. https://doi.org/10.3389/fgene.2022.1039838

196. Burl RB, Rondini EA, Wei H, Pique-Regi R, Granneman JG. Deconstructing cold-induced brown adipocyte neogenesis in mice. eLife. 2022;11. https://doi.org/10.7554/eLife.80167

197. Poklukar K, Čandek-Potokar M, Vrecl M, Batorek-Lukač N, Fazarinc G, Kress K, et al. Adipose tissue gene expression of entire male, immunocastrated and surgically castrated pigs. International Journal of Molecular Sciences. 2021;22(4). https://doi.org/10.3390/ijms22041768

198. Blasetti Fantauzzi C, Iacobini C, Menini S, Vitale M, Sorice GP, Mezza T, et al. Galectin-3 gene deletion results in defective adipose tissue maturation and impaired insulin sensitivity and glucose homeostasis. Scientific Reports. 2020;10. https://doi.org/10.1038/s41598-020-76952-z

199. Wang GX, Meyer JG, Cai W, Softic S, Li ME, Verdin E, et al. Regulation of UCP1 and mitochondrial metabolism in brown adipose tissue by reversible succinylation. Molecular Cell. 2019;74(4):844-857. https://doi.org/10.1016/j.molcel.2019.03.021

200. Okamatsu-Ogura Y, Kuroda M, Tsutsumi R, Tsubota A, Saito M, Kimura K, et al. UCP1-dependent and UCP1-independent metabolic changes induced by acute cold exposure in brown adipose tissue of mice. Metabolism. 2020;113. https://doi.org/10.1016/j.metabol.2020.154396

201. Wen X, Zhang B, Wu B, Xiao H, Li Z, Li R, et al. Signaling pathways in obesity: Mechanisms and therapeutic interventions. Signal Transduction and Targeted Therapy. 2022;7. https://doi.org/10.1038/s41392-022-01149-x

202. Tang Q, Liu Q, Li J, Yan J, Jing X, Zhang J, et al. MANF in POMC neurons promotes brown adipose tissue thermogenesis and protects against diet-induced obesity. Diabetes. 2022;71(11):2344-2359. https://doi.org/10.2337/db21-1128

203. Yang S, Yang H, Chang R, Yin P, Yang Y, Yang W, et al. MANF regulates hypothalamic control of food intake and body weight. Nature Communications. 2017;8. https://doi.org/10.1038/s41467-017-00750-x

204. Sell-Kubiak E, Dobrzanski J, Derks MFL, Lopes MS, Szwaczkowski T. Meta-analysis of SNPs determining litter traits in pigs. Genes. 2022;13(10). https://doi.org/10.3390/genes13101730

205. Li R, Meng S, Ji M, Rong X, You Z, Cai C, et al. HMG20A inhibit adipogenesis by transcriptional and epigenetic regulation of MEF2C expression. International Journal of Molecular Sciences. 2022;23(18). https://doi.org/10.3390/ijms231810559

206. Ren H, Xiao W, Qin X, Cai G, Chen H, Hua Z, et al. Myostatin regulates fatty acid desaturation and fat deposition through MEF2C/miR222/SCD5 cascade in pigs. Communications Biology. 2020;3. https://doi.org/10.1038/s42003-020-01348-8

207. Onteru SK, Fan B, Du Z-Q, Garrick DJ, Stalder KJ, Rothschild MF. A whole-genome association study for pig reproductive traits. Animal Genetics. 2012;43(1):18-26. https://doi.org/10.1111/j.1365-2052.2011.02213.x

208. Gautier M, Moazami-Goudarzi K, Levéziel H, Parinello H, Grohs C, Rialle S, et al. Deciphering the wisent demographic and adaptive histories from individual whole-genome sequences. Molecular Biology and Evolution. 2016;33(11):2801-2814. https://doi.org/10.1093/molbev/msw144

209. Liu H, Song H, Jiang Y, Jiang Y, Zhang F, Liu Y, et al. A Single-Step Genome wide association study on body size traits using imputation-based whole-genome sequence data in Yorkshire pigs. Frontiers in Genetics. 2021;12. https://doi.org/10.3389/fgene.2021.629049

210. Chen D, Wu P, Yang Q, Wang K, Zhou J, Yang X, et al. Genome-wide association study for backfat thickness at 100 kg and loin muscle thickness in domestic pigs based on genotyping by sequencing. Physiological Genomics. 2019;51(7):261-266. https://doi.org/10.1152/physiolgenomics.00008.2019

211. Martínez-Montes ÁM, Fernández A, Muñoz M, Noguera JL, Folch JM, Fernández AI. Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed. PLoS ONE. 2018;13(3). https://doi.org/10.1371/journal.pone.0190184

212. Yang W, Wu J, Yu J, Zheng X, Kang H, Wang Z, et al. A genome-wide association study reveals additive and dominance effects on growth and fatness traits in large white pigs. Animal Genetics. 2021;52(5):749-753. https://doi.org/10.1111/age.13131

213. Bal NC, Maurya SK, Singh S, Wehrens XHT, Periasamy M. Increased reliance on muscle-based thermogenesis upon acute minimization of brown adipose tissue function. Journal of Biological Chemistry. 2016;291(33):17247-17257. https://doi.org/10.1074/jbc.M116.728188

214. Lu Y, Fujioka H, Joshi D, Li Q, Sangwung P, Hsieh P, et al. Mitophagy is required for brown adipose tissue mitochondrial homeostasis during cold challenge. Scientific Reports. 2018;8. https://doi.org/10.1038/s41598-018-26394-5

215. Tabuchi C, Sul HS. Signaling pathways regulating thermogenesis. Frontiers in Endocrinology. 2021;12. https://doi.org/10.3389/fendo.2021.595020

216. Kunej T, Wu X-L, Michal JJ, Berlic TM, Jiang Z, Dovc P. The porcine mitochondrial transcription factor a gene: Molecular characterization, radiation hybrid mapping and genetic diversity among 12 pig breeds. American Journal of Animal and Veterinary Sciences. 2009;4(4):129-135.

217. Song Q, Zhang W, Wu F, Xu N, Zhang J, Xu M, et al. Cloning and expression levels of TFAM and TFB2M gene and their correlation with meat and carcass quality traits in Jiaxing Black Pig. Annals of Animal Science. 2019;19(2):327-341. https://doi.org/10.2478/aoas-2018-0056

218. Palombo V, D’Andrea M, Licastro D, Dal Monego S, Sgorlon S, Sandri M, et al. Single-step genome wide association study identifies QTL signals for untrimmed and trimmed thigh weight in Italian crossbred pigs for dry-cured ham production. Animals. 2021;11(6). https://doi.org/10.3390/ani11061612

219. Li M, Xia Y, Gu Y, Zhang K, Lang Q, Chen L, et al. MicroRNAome of porcine pre- and postnatal development. PLoS ONE. 2010;5(7). https://doi.org/10.1371/journal.pone.0011541

220. Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, et al. Structured RNAs and synteny regions in the pig genome. BMC Genomics. 2014;15. https://doi.org/10.1186/1471-2164-15-459

221. Fyda TJ, Spencer C, Jastroch M, Gaudry MJ. Disruption of thermogenic UCP1 predated the divergence of pigs and peccaries. Journal of Experimental Biology. 2020;223(15). https://doi.org/10.1242/jeb.223974

222. Jastroch M, Andersson L. When pigs fly, UCP1 makes heat. Molecular Metabolism. 2015;4(5):359-362. https://doi.org/10.1016/j.molmet.2015.02.005

223. Zhao J, Tao C, Chen C, Wang Y, Liu T. Formation of thermogenic adipocytes: What we have learned from pigs. Fundamental Research. 2021;1(4):495-502. https://doi.org/10.1016/j.fmre.2021.05.004

224. Lin J, Cao C, Tao C, Ye R, Dong M, Zheng Q, et al. Cold adaptation in pigs depends on UCP3 in beige adipocytes. Journal of Molecular Cell Biology. 2017;9(5):364-375. https://doi.org/10.1093/jmcb/mjx018