Association analysis of the sorting nexin 29 (SNX29) gene copy number variations with growth traits in Diannan small-ear (DSE) pigs

References

• McGlone JJ. The future of pork production in the world: towards sustainable, welfare-positive systems. Animals (Basel). 2013;3(2):1–8.
   PubMedGoogle Scholar
• Ai H, Ren J, Zhang Z, et al. Detection of quantitative trait loci for growth- and fatness-related traits in a large-scale White Duroc × Erhualian intercross pig population. Anim Genet. 2012;43(4):383–391.
   PubMed Web of Science ®Google Scholar
• Mohammadabadi M, Bordbar F, Jensen J, et al. Key genes regulating skeletal muscle development and growth in farm animals. Animals (Basel). 2021;11(3):835.
   PubMedGoogle Scholar
• McOrist S, Khampee K, Guo A. Modern pig farming in the People’s Republic of China: growth and veterinary challenges. Rev Sci Tech. 2011;30(3):961–968.
   PubMed Web of Science ®Google Scholar
• Wang Z, Li Q, Chamba Y, et al. Identification of genes related to growth and lipid deposition from transcriptome profiles of pig muscle tissue. PLoS One. 2015;10(10):e0141138.
   PubMed Web of Science ®Google Scholar
• Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science. 2004;305(5683):525–528.
   PubMed Web of Science ®Google Scholar
• Li C, Basarab J, Snelling WM, et al. Assessment of positional candidate genes myf5 and igf1 for growth on bovine chromosome 5 in commercial lines of Bos taurus. J Anim Sci. 2004;82(1):1–7.
   PubMed Web of Science ®Google Scholar
• Wang A, Zhang Y, Li M, et al. SNP identification in FBXO32 gene and their associations with growth traits in cattle. Gene. 2013;515(1):181–186.
   PubMed Web of Science ®Google Scholar
• Yang AQ, et al. The application of genomic selection in pig cross breeding. Yi Chuan. 2020;42(2):145–152.
   PubMedGoogle Scholar
• Revilla M, Puig-Oliveras A, Castelló A, et al. A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits. PLoS One. 2017;12(5):e0177014.
   PubMed Web of Science ®Google Scholar
• Dong Q, Liu H, Li X, Wei W, Zhao S, Cao J. A genome-wide association study of five meat quality traits in Yorkshire pigs. Front Agr Sci Eng. 2014;1(2):137–143.
   Google Scholar
• Müllenbach R, Lagoda PJ, Welter C. An efficient salt-chloroform extraction of DNA from blood and tissues. Trends Genet. 1989;5(12):391.
   PubMed Web of Science ®Google Scholar
• Chen Y, Yang L, Lin X, et al. Effects of genetic variation of the Sorting Nexin 29 (SNX29) gene on growth traits of Xiangdong black goat. Animals (Basel). 2022;12(24):3461.
   PubMedGoogle Scholar
• Wang X, Zheng Z, Cai Y, et al. CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations. Gigascience. 2017;6(12):1–12.
   Web of Science ®Google Scholar
• Lye ZN, Purugganan MD. Copy number variation in domestication. Trends Plant Sci. 2019;24(4):352–365.
   PubMed Web of Science ®Google Scholar
• Knol EF, van der Spek D, Zak LJ. Genetic aspects of piglet survival and related traits: a review. J Anim Sci. 2022;100(6):190.
   Web of Science ®Google Scholar
• Zhang B, Shang P, Tao Z, et al. Effect of a single nucleotide polymorphism in the growth hormone secretagogue receptor (GHSR) gene on growth rate in pigs. Gene. 2017;634:68–73.
   PubMed Web of Science ®Google Scholar
• Zhou T, Wei H, Li D, et al. A novel missense mutation within the domain of lysine demethylase 4D (KDM4D) gene is strongly associated with testis morphology traits in pigs. Anim Biotechnol. 2020;31(1):52–58.
   PubMed Web of Science ®Google Scholar
• Henrichsen CN, Vinckenbosch N, Zöllner S, et al. Segmental copy number variation shapes tissue transcriptomes. Nat Genet. 2009;41(4):424–429.
   PubMed Web of Science ®Google Scholar
• He X, Tian M, Wang W, et al. Identification of candidate genes for min pig villi hair traits by genome-wide association of copy number variation. Vet Sci. 2023;10(5):307.
   PubMedGoogle Scholar
• Elbert K, Matthews N, Wassmuth R, et al. Effects of sire line, birth weight and sex on growth performance and carcass traits of crossbred pigs under standardized environmental conditions. Arch Anim Breed. 2020;63(2):367–376.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Peng M, Wen Y, et al. Copy number variation of EIF4A2 loci related to phenotypic traits in Chinese cattle. Vet Med Sci. 2022;8(5):2147–2156.
   PubMed Web of Science ®Google Scholar
• Hu L, Yu J, Huang R, et al. Copy number variation of the CCDC39 gene is associated with growth traits in Chinese cattle. Vet Med Sci. 2022;8(2):917–924.
   PubMed Web of Science ®Google Scholar
• Liu M, Woodward-Greene J, Kang X, et al. Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats. Genomics. 2020;112(2):1477–1480.
   PubMed Web of Science ®Google Scholar
• Tummaruk P, Tantasuparuk W, Techakumphu M, et al. The association between growth rate, body weight, backfat thickness and age at first observed oestrus in crossbred Landrace x Yorkshire gilts. Anim Reprod Sci. 2009;110(1-2):108–122.
   PubMed Web of Science ®Google Scholar
• Harewood L, Chaignat E, Reymond A. Structural variation and its effect on expression. Methods Mol Biol. 2012;838:173–186.
   PubMedGoogle Scholar
• Peng S, Song C, Li H, et al. Circular RNA SNX29 sponges miR-744 to regulate proliferation and differentiation of myoblasts by activating the Wnt5a/Ca(2+) signaling pathway. Mol Ther Nucleic Acids. 2019;16:481–493.
   PubMedGoogle Scholar
• Liu M, Lan Q, Yang L, et al. Genome-wide association analysis identifies genomic regions and candidate genes for growth and fatness traits in Diannan small-ear (DSE) pigs. Animals (Basel). 2023;13(9):1571.
   PubMedGoogle Scholar
• Tummaruk P, Tantasuparuk W, Techakumphu M, et al. Age, body weight and backfat thickness at first observed oestrus in crossbred Landrace x Yorkshire gilts, seasonal variations and their influence on subsequence reproductive performance. Anim Reprod Sci. 2007;99(1-2):167–181.
   PubMed Web of Science ®Google Scholar
• Amaral Filha WS, Bernardi ML, Wentz I, et al. Reproductive performance of gilts according to growth rate and backfat thickness at mating. Anim Reprod Sci. 2010;121(1-2):139–144.
   PubMed Web of Science ®Google Scholar
• Tarrés J, Tibau J, Piedrafita J, et al. Factors affecting longevity in maternal Duroc swine lines. Livestock Science. 2006;100(2-3):121–131.
   Web of Science ®Google Scholar
• Hasan N, Choudhary S, Naaz N, et al. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol. 2021;19(1):128.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Fan G, Liu X, et al. The genome of the naturally evolved obesity-prone Ossabaw miniature pig. iScience. 2021;24(9):103081.
   PubMed Web of Science ®Google Scholar
• Wei C, Hou D, Feng Y, et al. Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens. Gene. 2020;761:145046.
   PubMed Web of Science ®Google Scholar
• Pös O, Radvanszky J, Buglyó G, et al. DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects. Biomed J. 2021;44(5):548–559.
   PubMed Web of Science ®Google Scholar