DOI QR코드

DOI QR Code

Genome-wide association research on the reproductive traits of Qianhua Mutton Merino sheep

  • Jiarong Li (College of Animal Science and Technology, Jilin Agricultural University) ;
  • Limin Sun (Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)) ;
  • Jiazhi Sun (Anhua Agricultural Insurance Co., Ltd. Changchun Central Branch) ;
  • Huaizhi Jiang (College of Animal Science and Technology, Jilin Agricultural University)
  • 투고 : 2023.09.14
  • 심사 : 2024.02.01
  • 발행 : 2024.09.01

초록

Objective: Qianhua Mutton Merino sheep is a new breed of meat wool sheep cultivated independently in China. In 2018, it was approved by the state and brought into the national list of livestock and poultry genetic resources. Qianhua Mutton Merino sheep have the common characteristics of typical meat livestock varieties with rapid growth and development in the early stage and high meat production performance. The objective of this research is to investigate the Genome-wide association of the reproductive traits of Qianhua Mutton Merino sheep. Methods: Qianhua Mutton Merino sheep from the breeding core group were selected as the research object, genome-wide association analysis was conducted on genes associated with the reproductive traits (singleton or twins, birth weight, age [in days] for sexual maturity, weaning weight, and daily gain from birth to weaning) of Qianhua mutton merino. Results: Our study findings showed that 151 loci of single-nucleotide polymorphisms (SNPs) were detected, among which 3 SNPs related to birth weight and weaning weight occupied a significant portion of the wide genome. The candidate genes preliminarily obtained were SYNE1, SLC12A4, BMP2K, CAMK2D, IMMP2L, DMD, and BCL2. Conclusion: We found 151 SNP loci for five traits related to reproduction (including singleton or twins, birth weight, age [in days] at sexual maturity, weaning weight, and daily weight gain from birth to weaning). The functions of these candidate genes were mainly enriched in nucleotide metabolism, metal ion binding, oxytocin signaling pathway, and neurotrophin signaling pathway.

키워드

과제정보

This work was supported by National Key Research and Development Project of China (2021YFF1000702).

참고문헌

  1. Li Z, Wei S, Li H, et al. Genome-wide genetic structure and differentially selected regions among Landrace, Erhualian, and Meishan pigs using specific-locus amplified fragment sequencing. Sci Rep 2017;7:10063. https://doi.org/10.1038/s41598-017-09969-6
  2. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2007;23:2633-5. https://doi.org/10.1093/bioinformatics/btm308
  3. Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D. FaST linear mixed models for genome-wide association studies. Nat Methods 2011;8:833-5. https://doi.org/10.1038/nmeth.1681
  4. Sul JH, Eskin E. Mixed models can correct for population structure for genomic regions under selection. Nat Rev Genet 2013;14:300. https://doi.org/10.1038/nrg2813-c1
  5. 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
  6. Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25:2078-9. https://doi.org/10.1093/bioinformatics/btp352
  7. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006;38:904-9. https://doi.org/10.1038/ng1847
  8. Apel ED, Lewis RM, Grady RM, Sanes JR. Syne-1, a dystrophin- and Klarsicht-related protein associated with synaptic nuclei at the neuromuscular junction. J Biol Chem 2000;275:31986-95. https://doi.org/10.1074/jbc.M004775200
  9. Zhang J, Felder A, Liu Y, et al. Nesprin 1 is critical for nuclear positioning and anchorage. Hum Mol Genet 2010;19:329-41. https://doi.org/10.1093/hmg/ddp499
  10. Grady RM, Starr DA, Ackerman GL, Sanes JR, Han M. Syne proteins anchor muscle nuclei at the neuromuscular junction. Proc Natl Acad Sci USA 2005;102:4359-64. https://doi.org/10.1073/pnas.0500711102
  11. Morioka S, Perry JSA, Raymond MH, et al. Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release. Nature 2018;563:714-8. https://doi.org/10.1038/s41586-018-0735-5
  12. Hanzawa K, Lear TL, Piumi F, Bailey E. Mapping of equine potassium chloride co-transporter (SLC12A4) and amino acid transporter (SLC7A10) and preliminary studies on associations between SNPs from SLC12A4, SLC7A10 and SLC7A9 and osmotic fragility of erythrocytes. Anim Genet 2002;33:455-9. https://doi.org/10.1046/j.1365-2052.2002.00907.x
  13. Ducy P, Karsenty G. The family of bone morphogenetic proteins. Kidney Int 2000;57:2207-14. https://doi.org/10.1046/j.1523-1755.2000.00081.x
  14. Li Q. Association of BMP2 and PDGF-D gene polymorphisms with tail type and verification of cellular level function in sheep [master's dissertation]. Beijing, China: Chinese Academy of Agricultural Sciences; 2019.
  15. Ma Y, Zhang Z, Chen Z, et al. Suppression of inner mitochondrial membrane peptidase 2-like (IMMP2L) gene exacerbates hypoxia-induced neural death under high glucose condition. Neurochem Res 2017;42:1504-14. https://doi.org/10.1007/s11064-017-2207-y
  16. Han C, Zhao Q, Lu B. The role of nitric oxide signaling in food intake; insights from the inner mitochondrial membrane peptidase 2 mutant mice. Redox Biol 2013;1:498-507. https://doi.org/10.1016/j.redox.2013.10.003
  17. Yu X, Wang M, Han Q, et al. ZNF326 promotes a malignant phenotype of breast cancer by interacting with DBC1. Mol Carcinog 2018;57:1803-15. https://doi.org/10.1002/mc.22898
  18. Andersen OM, Reiche J, Schmidt V, et al. Neuronal sorting protein-related receptor sorLA/LR11 regulates processing of the amyloid precursor protein. Proc Natl Acad Sci USA 2005;102:13461-6. https://doi.org/10.1073/pnas.0503689102
  19. Lim AHL. Analysis of the subcellular localization of proteins implicated in Alzheimer's disease [Doctoral dissertation]. Adelaide SA, Australia: The University of Adelaide Australia; 2015.
  20. Jacobsen L, Madsen P, Moestrup SK, et al. Molecular characterization of a novel human hybrid-type receptor that binds the alpha2-macroglobulin receptor-associated protein. J Biol Chem 1996;271:31379-83. https://doi.org/10.1074/jbc.271.49.31379
  21. Henriquez-Rodriguez E, Bosch L, Tor M, Pena RN, Estany J. The effect of SCD and LEPR genetic polymorphisms on fat content and composition is maintained throughout fattening in Duroc pigs. Meat Sci 2016;121:33-9. https://doi.org/10.1016/j.meatsci.2016.05.012
  22. Piorkowska K, Malopolska M, Ropka-Molik K, et al. Evaluation of SCD, ACACA and FASN mutations: effects on pork quality and other production traits in pigs selected based on RNA-Seq results. Animals (Basel) 2020;10:123. https://doi.org/10.3390/ani10010123
  23. Corominas J, Ramayo-Caldas Y, Puig-Oliveras A, et al. Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition. BMC Genomics 2013;14:843. https://doi.org/10.1186/1471-2164-14-843
  24. Orth MF, Cazes A, Butt E, Grunewald TGP. An update on the LIM and SH3 domain protein 1 (LASP1): a versatile structural, signaling, and biomarker protein. Oncotarget 2015;6:26-42. https://doi.org/10.18632/oncotarget.3083
  25. Stolting M, Wiesner C, van Vliet V, et al. Lasp-1 regulates podosome function. PLoS One 2012;7:e35340. https://doi.org/10.1371/journal.pone.0035340
  26. Maj M, Wagner L, Tretter V. 20 years of secretagogin: exocytosis and beyond. Front Mol Neurosci 2019;12:29. https://doi.org/10.3389/fnmol.2019.00029
  27. Ferdaoussi M, Fu J, Dai X, et al. SUMOylation and calcium control syntaxin-1A and secretagogin sequestration by tomosyn to regulate insulin exocytosis in human ss cells. Sci Rep 2017;7:248. https://doi.org/10.1038/s41598-017-00344-z
  28. Yang SY, Lee JJ, Lee JH, et al. Secretagogin affects insulin secretion in pancreatic β-cells by regulating actin dynamics and focal adhesion. Biochem J 2016;473:1791-803. https://doi.org/10.1042/bcj20160137
  29. Karkkainen I, Rybnikova E, Pelto-Huikko M, Huovila AP. Metalloprotease-disintegrin (ADAM) genes are widely and differentially expressed in the adult CNS. Mol Cell Neurosci 2000;15:547-60. https://doi.org/10.1006/mcne.2000.0848
  30. Harris HA, Murrills RJ, Komm BS. Expression of meltrinalpha mRNA is not restricted to fusagenic cells. J Cell Biochem 1997;67:136-42. https://doi.org/10.1002/(sici)1097-4644(19971001)67:1<136::aid-jcb14>3.0.co;2-f
  31. Zhang L, Ma X, Xuan J, et al. Identification of MEF2B and TRHDE gene polymorphisms related to growth traits in a New Ujumqin sheep population. PLoS One 2016;11:e0159504. https://doi.org/10.1371/journal.pone.0159504
  32. Gholizadeh M, Rahimi-Mianji G, Nejati-Javaremi A. Genomewide association study of body weight traits in Baluchi sheep. J Genet 2015;94:143-6. https://doi.org/10.1007/s12041-015-0469-1
  33. Al-Mamun HA, Kwan P, Clark SA, Ferdosi MH, Tellam R, Gondro C. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genet Sel Evol 2015;47:66. https://doi.org/10.1186/s12711-015-0142-4
  34. Demars J, Fabre S, Sarry J, et al. Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyperprolificacy phenotype in sheep. PLoS Genet 2013;9:e1003482. https://doi.org/10.1371/journal.pgen.1003482
  35. Vage DI, Husdal M, Kent MP, Klemetsdal G, Boman IA. A missense mutation in growth differentiation factor 9 (GDF9) is strongly associated with litter size in sheep. BMC Genet 2013;14:1. https://doi.org/10.1186/1471-2156-14-1
  36. Gholizadeh M, Rahimi-Mianji G, Nejati-Javaremi A, De Koning DJ, Jonas E. Genomewide association study to detect QTL for twinning rate in Baluchi sheep. J Genet 2014;93:489-93. https://doi.org/10.1007/s12041-014-0372-1
  37. Wang S, Li X, Niu Z, Shi H. Whole genomic association analysis of polyembryonic gene in Duolang sheep. Acta Agric Jiangxi 2017;29:77-81. https://doi.org/10.19386/j.cnki.jxnyxb.2017.05.16
  38. Cai W, Luo C, Xiang Y, Zhang X, Xu N, Guo X. Genome-wide association study on reproductive traits in Jinhua pigs and Shengxian pigs based on 50K SNP chips technology. Chin J Anim Sci 2020;56:52-8. https://doi.org/10.19556/j.0258-7033.20190816-06
  39. Lu X, Zhou J, Yang C, et al. Functional annotation of candidate genes for milk production and reproductive traits in Xinjiang Brown cattle. Acta Agric Zhejiangensis 2019;31:1987-95. https://doi.org/10.3969/j.issn.1004-1524.2019.12.06