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CT scanning technology to asses the genetic and phenotypic correlations, and selection potential of carcass traits in mutton sheep

  • Yuan Zhao (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Guoxing Jia (College of Animal Science and Technology, Gansu Agricultural University) ;
  • Xiaoxue Zhang (College of Animal Science and Technology, Gansu Agricultural University) ;
  • Huibin Tian (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Deyin Zhang (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Yukun Zhang (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Xiaolong Li (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Jiangbo Cheng (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Liming Zhao (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Quanzhong Xu (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Xiaobin Yang (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Zongwu Ma (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Dan Xu (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Fadi Li (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University) ;
  • Weimin Wang (State Key Laboratory of Herbage Improvement and Grassland AgroEcosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University)
  • Received : 2025.07.08
  • Accepted : 2025.11.25
  • Published : 2026.06.01

Abstract

Objective: This study aims to evaluate the variations in carcass fat percentage (CFP), carcass muscle percentage (CMP), carcass bone percentage (CBP), meat-to-bone ratio, carcass weight, loin eye area (REA), backfat thickness (BF), the total tissue depth of muscle and fat at the twelfth rib, 110 mm from the midline (GR), and dressing percentage in 574 mutton sheep using CT scanning technology. It also seeks to estimate the genetic and phenotypic correlations, as well as estimated genomic selection accuracy provides reference for breeding of mutton sheep carcasses. Methods: Phenotypic data from National Mutton Sheep Testing Station; uniform rearing for 155 days. CT scans were used to obtain body images of the sheep, and CT-Calc2012 software was employed to trait determination. Genomic data were sequenced using second-generation sequencing, and SNP calling was performed with GATK. A mixed linear model incorporating both genomic and pedigree data was used to estimate genetic parameters for various traits. Cross-validation through ten-fold was conducted to assess genomic selection accuracy, and both direct and correlated selection responses for carcass traits were analyzed. Results: The coefficient of variation for each trait ranging from 8.86% to 25.12%. All carcass composition traits demonstrated medium to high heritability (0.38-0.51). A strong genetic correlation was found between BF, REA, CFP, and CMP. The genomic selection accuracy for carcass traits ranged from 0.29 to 0.43, suggesting potential for genomic selection in mutton sheep breeding. The genetic progress of CMP and CFP after direct and indirect selection was tested, showing that indirect improvement of CMP and CFP was most significant when selecting for BF and REA. Conclusion: The study indicates that BF and REA are valuable traits for improving carcass composition in mutton sheep breeding, with genomic selection offering prospects for breeding carcass traits more effectively.

Keywords

Acknowledgement

This work was supported by the National Key Research and Development Program of China (2023YFF1001000), Gansu Provincial Department of Education: 2025 Graduate Innovation Star Project (2025CXZX-065), the Gansu Provincial Science and Technology Plan Project (24CXGH007), the Gansu Provincial Science and Technology Plan Project (25CXGH008), and the Gansu Provincial Science and Technology Plan Project (25YFNA017).

References

  1. Yu TY, Morton JD, Clerens S, Dyer JM. In-depth characterisation of the lamb meat proteome from longissimus lumborum. EuPA Open Proteom 2015;6:28-41. https://doi.org/10.1016/j.euprot.2015.01.001
  2. Luo Z, Ou H, McSweeney CS, Tan Z, Jiao J. Enhancing nutrient efficiency through optimizing protein levels in lambs: involvement of gastrointestinal microbiota. Anim Nutr 2025; 20:332-41. https://doi.org/10.1016/j.aninu.2024.09.006
  3. Daza A, Rey AI, Lopez-Carrasco C, Lopez-Bote CJ. Influence of feeding system on growth performance, carcass characteristics and meat and fat quality of Avileña-Negra Ibérica calves' breed. Spanh J Agric Res 2014;12:409-18. https://doi.org/10.5424/sjar/2014122-4096
  4. Tian Y, Zhao Y, Yao Y, et al. Genetic and functional validation of CTSS in regulating intramuscular fat content of Duroc–Landrace–Yorkshire pigs. Anim Genet 2025;56:e70010. https://doi.org/10.1111/age.70010
  5. Arikawa LM, Mota LFM, Schmidt PI, et al. Genome-wide scans identify biological and metabolic pathways regulating carcass and meat quality traits in beef cattle. Meat Sci 2024; 209:109402. https://doi.org/10.1016/j.meatsci.2023.109402
  6. Lopez BIM, Song C, Seo K. Genetic parameters and trends for production traits and their relationship with litter traits in Landrace and Yorkshire pigs. Anim Sci J 2018;89:1381-8. https://doi.org/10.1111/asj.13090
  7. Gozalo-Marcilla M, Buntjer J, Johnsson M, et al. Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds. Genet Sel Evol 2021;53:76. https://doi.org/10.1186/s12711-021-00671-w
  8. Lee SH, Kim S, Kim JM. Genetic correlation between biopsied and post-mortem muscle fibre characteristics and meat quality traits in swine. Meat Sci 2022;186:108735. https://doi.org/10.1016/j.meatsci.2022.108735
  9. Mortimer SI, Fogarty NM, van der Werf JHJ, et al. Genetic correlations between meat quality traits and growth and carcass traits in Merino sheep. J Anim Sci 2018;96:3582-98. https://doi.org/10.1093/jas/sky232
  10. Mortimer SI, Hatcher S, Fogarty NM, et al. Genetic correlations between wool traits and carcass traits in Merino sheep. J Anim Sci 2017;95:2385-98. https://doi.org/10.2527/jas.2017.1385
  11. Ding R, Zhuang Z, Qiu Y, et al. Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis. J Anim Sci 2022;100:skac012. https://doi.org/10.1093/jas/skac012
  12. Kodama Y, Shumway M, Leinonen R. The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res 2012;40:D54-6. https://doi.org/10.1093/nar/gkr854
  13. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30: 2114-20. https://doi.org/10.1093/bioinformatics/btu170
  14. Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 2009;25:1754-60. https://doi.org/10.1093/bioinformatics/btp324
  15. 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
  16. 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
  17. Cingolani P, Platts A, Wang LL, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012;6:80-92. https://doi.org/10.4161/fly.19695
  18. Yin L, Zhang H, Tang Z, et al. HIBLUP: an integration of statistical models on the BLUP framework for efficient genetic evaluation using big genomic data. Nucleic Acids Res 2023; 51:3501-12. https://doi.org/10.1093/nar/gkad074
  19. Johnson DL, Thompson R. Restricted maximum likelihood estimation of variance components for univariate animal models using sparse matrix techniques and average information. J Dairy Sci 1995;78:449-56. https://doi.org/10.3168/jds.S0022-0302(95)76654-1
  20. Falconer DS. Introduction to quantitative genetics. Pearson Education India; 1996.
  21. Moraes GF, Abreu LRA, Toral FLB, et al. Selection for feed efficiency does not change the selection for growth and carcass traits in Nellore cattle. J Anim Breed Genet 2019;136:464-73. https://doi.org/10.1111/jbg.12423
  22. Kava R, Peripolli E, Brunes LC, et al. Estimates of genetic and phenotypic parameters for feeding behaviour and feed efficiency-related traits in Nelore cattle. J Anim Breed Genet 2023;140:264-75. https://doi.org/10.1111/jbg.12756
  23. Cavanagh CR, Jonas E, Hobbs M, Thomson PC, Tammen I, Raadsma HW. Mapping quantitative trait loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL. Genet Sel Evol 2010;42:36. https://doi.org/10.1186/1297-9686-42-36
  24. Davoli R, Catillo G, Serra A, et al. Genetic parameters of backfat fatty acids and carcass traits in large white pigs. Animal 2019;13:924-32. https://doi.org/10.1017/S1751731118002082
  25. Zhang F, Wang Y, Mukiibi R, et al. Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits. BMC Genomics 2020;21:36. https://doi.org/10.1186/s12864-019-6362-1
  26. Zuin RG, Buzanskas ME, Caetano SL, et al. Genetic analysis on growth and carcass traits in Nelore cattle. Meat Sci 2012; 91:352-7. https://doi.org/10.1016/j.meatsci.2012.02.018
  27. McGilchrist P, Alston CL, Gardner GE, Thomson KL, Pethick DW. Beef carcasses with larger eye muscle areas, lower ossification scores and improved nutrition have a lower incidence of dark cutting. Meat Sci 2012;92:474-80. https://doi.org/10.1016/j.meatsci.2012.05.014
  28. van Heelsum AM, Lewis RM, Davies MH, Haresign W. Genetic relationships among objectively and subjectively assessed traits measured on crossbred (mule) lambs. Anim Sci 2006;82:141-9. https://doi.org/10.1079/ASC200523
  29. Matika O, Riggio V, Anselme-Moizan M, et al. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish blackface lambs. Genet Sel Evol 2016;48:1-15. https://doi.org/10.1186/s12711-016-0191-3
  30. Conington J, Bishop SC, Waterhouse A, Simm G. A comparison of growth and carcass traits in Scottish blackface lambs sired by genetically lean or fat rams. Anim Sci 1998;67:299-309. https://doi.org/10.1017/S1357729800010067
  31. Johnson PL, Lopez-Villalobos N, Bryant JR, Blair HT. Genetic parameters for carcass cuts using data from a progeny test of Romney rams. In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production; 2006 Aug 13-18; Belo Horizonte, Brazil. CABI; 2006.
  32. Lorentzen TK, Vangen O. Genetic and phenotypic analysis of meat quality traits in lamb and correlations to carcass composition. Livest Sci 2012;143:201-9. https://doi.org/10.1016/j.livsci.2011.09.016
  33. Jones HE, Lewis RM, Young MJ, Simm G. Genetic parameters for carcass composition and muscularity in sheep measured by X-ray computer tomography, ultrasound and dissection. Livest Prod Sci 2004;90:167-79. https://doi.org/10.1016/j.livprodsci.2004.04.004
  34. Karamichou E, Richardson RI, Nute GR, McLean KA, Bishop SC. Genetic analyses of carcass composition, as assessed by X-ray computer tomography, and meat quality traits in Scottish blackface sheep. Anim Sci 2006;82:151-62. https://doi.org/10.1079/ASC200518
  35. Kvame T, Vangen O. Selection for lean weight based on ultrasound and CT in a meat line of sheep. Livest Sci 2007;106: 232-42. https://doi.org/10.1016/j.livsci.2006.08.007
  36. Lambe NR, Conington J, Bishop SC, et al. Relationships between lamb carcass quality traits measured by X-ray computed tomography and current UK hill sheep breeding goals. Animal 2008;2:36-43. https://doi.org/10.1017/S1751731107001061
  37. Barro AG, Marestone BS, dos SER, et al. Genetic parameters for frame size and carcass traits in Nellore cattle. Trop Anim Health Prod 2023;55:71. https://doi.org/10.1007/s11250-023-03464-z
  38. Keele JW, Foraker BA, Boldt R, Kemp C, Kuehn LA, Woerner DR. Genetic parameters for carcass traits of progeny of beef bulls mated to dairy cows. J Anim Sci 2024;102:skae075. https://doi.org/10.1093/jas/skae075
  39. Arikawa LM, Mota LFM, Schmidt PI, et al. Genetic parameter estimates for carcass and meat quality traits and their genetic associations with sexual precocity indicator traits in Nellore cattle. J Anim Breed Genet 2025;142:581-93. https://doi.org/10.1111/jbg.12927
  40. Pauling RC, Speidel SE, Thomas MG, Holt TN, Enns RM. Genetic parameters for pulmonary arterial pressure, yearling performance, and carcass ultrasound traits in Angus cattle. J Anim Sci 2023;101:skad288. https://doi.org/10.1093/jas/skad288
  41. Xie L, Qin J, Rao L, et al. Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig. J Anim Sci Biotechnol 2023;14:116. https://doi.org/10.1186/s40104-023-00914-4
  42. Walsh JB. Genomic selection signatures and animal breeding. J Anim Breed Genet 2021;138:1-3. https://doi.org/10.1111/jbg.12527
  43. Iqbal A, Choi TJ, Kim YS, et al. Comparison of genomic predictions for carcass and reproduction traits in Berkshire, Duroc and Yorkshire populations in Korea. Asian-Australas J Anim Sci 2019;32:1657-63. https://doi.org/10.5713/ajas.18.0672
  44. Lopes FB, Baldi F, Brunes LC, et al. Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm. J Anim Breed Genet 2023;140:1-12. https://doi.org/10.1111/jbg.12740
  45. Misztal I, Aguilar I, Lourenco D, Ma L, Steibel JP, Toro M. Emerging issues in genomic selection. J Anim Sci 2021;99: skab092. https://doi.org/10.1093/jas/skab092
  46. Brito LF, Clarke SM, McEwan JC, et al. Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip. BMC Genetics 2017;18:7. https://doi.org/10.1186/s12863-017-0476-8