Analysis of Copy Number Variation of PPP3CA Gene and Its Association with Growth Traits in Goats (Capra hircus)
BAI Yang-Yang1, DU Shu-Zeng3, LI Xin1, ZHU Hai-Jing4, QU Lei4, GUO Zhen-Gang5, YANG Qing1,2,*, LAN Xian-Yong1,*
1 College of Animal Science and Technology, Northwest A&F University, Yangling 712000, China;
2 Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China;
3 Nanyang Agricultural Vocational College, Nanyang 473000, China;
4 Shaanxi Cashmere Goat Engineering Research Center, Yulin University, Yulin 719000, China;
5 Bijie Institute of Animal Science and Veterinary Science, Bijie 551700, China
Abstract Protein phosphatase 3 catalytic subunit alpha (PPP3CA) plays an important role in animal growth and development. This study aims to explore PPP3CA gene expression in different tissues and the genetic effects of copy number variation on the growth traits of different breeds of goats (Capra hircus). First, a total of 11 Shaanbei white cashmere goats were chosen to identify the expression levels of PPP3CA mRNA in the heart, liver, spleen, lung, kidney, muscle, brain, ovary, testis tissues. Then, copy number variation (CNV) of PPP3CA gene was detected in 306 Shaanbei white cashmere goats and 110 Guizhou Heima goats by qPCR. The associations between PPP3CA gene CNV loci and growth traits in goats were analyzed using ANOVA. In addition, the linkage disequilibrium block in these regions and the potential transcription factors that could bind to the 3 CNVs were analyzed by using bioinformatics. The results showed that PPP3CA mRNA was highly expressed in the lung, followed by the spleen, fallopian tube, testis, heart, liver, kidney, muscle and brain. Three CNVs were detected in PPP3CA gene. In the Shaanbei white cashmere goats population, CNV1 and CNV2 significantly correlated with goat chest circumference (P<0.05); CNV3 was significantly correlated with goat chest width, chest depth and chest circumference (P<0.05). In the Guizhou Heima goat population, there was no significant relationship between 3 CNVs and goat growth traits. The linkage disequilibrium (LD) haplotype block analysis showed that there was no LD block for PPP3CA gene, but these CNVs might bind to SPT23, SIP4, and YOX1 transcription factors. In summary, these findings indicated that the CNV1, CNV2, and CNV3 loci of the PPP3CA gene could be used as molecular markers for the selection of growth traits in Shaanbei white cashmere goats.
BAI Yang-Yang,DU Shu-Zeng,LI Xin, et al. Analysis of Copy Number Variation of PPP3CA Gene and Its Association with Growth Traits in Goats (Capra hircus)[J]. 农业生物技术学报, 2024, 32(5): 1071-1080.
[1] 黄冬维, 储明星. 2023. 两个品种山羊MTNR1A基因组织表达差异研究[J]. 中国草食动物科学, 43(06): 7-11.
(Huang D W, Chu M X.2023. Study on the differences of MTNR1A expression in two goat breeds[J]. China Herbivore Science, 43(06): 7-11.)
[2] 惠茂茂, 陈祥, 敖叶, 等. 2021. 黔北麻羊PPP3CA基因克隆、生物信息学分析及不同组织表达研究[J]. 中国畜牧杂志, 57(10): 84-88, 95.
(Hui M M, Chen X, Ao Y, et al.2021. Cloning, bioinformatics analysis and expression of PPP3CA gene in different tissues of Qianbei Ma goats[J]. Chinese Journal of Animal Science, 57(10): 84-88,95.
[3] 康雨欣, 毕谊, 罗弼豪, 等. 2022. 陕北白绒山羊产羔数与体尺性状的相关及回归分析[J]. 家畜生态学报, 43(01): 16-21.
(Kang Y X, Bi Y, Luo B H, et al.2022. Correlation and regression analysis between litter size and growth traits of shanbei white cashmere goat[J]. Acta Ecologae Animalis Domastici, 43(01):16-21).
[4] 金美林, 卢曾奎, 李青, 等. 2019. 畜禽拷贝数变异研究进展[J]. 农业生物技术学报, 27(10): 1840-1848.
(Jin M L, Lu Z K, Li Q, et al.2019. Research progress on copy number variation of livestock and poultry[J]. Journal of Agricultural Biotechnology, 27(10): 1840-1848.
[5] 经珍珠, 秦盼盼, 陈冰洁, 等. 2021. 拷贝数变异在畜禽中的研究进展[J]. 中国畜牧兽医, 48(07): 2512-2522.
(Jing Z Z, Qin P P, Chen B J, et al.2021. Research progress of copy number variation in livestock and poultry[J]. China Animal Husbandry & Veterinary Medicine, 48(07): 2512-2522.
[6] 单艳菊, 宋迟, 束婧婷, 等. 2015. 钙调磷酸酶催化亚基A基因(PPP3CA)在不同品种鸭发育早期肌肉中的表达及其与肌纤维特性的相关性[J]. 农业生物技术学报, 23(02): 236-243.
(Shan Y J, Song C, Shu J T, et al.2015. Expression profile of protein phosphatase 3 catalytic a gene (PPP3CA) mRNA in muscles of two duck breeds (Anas platyrhynchos domestica) and its relationship with myofiber traits during early development[J]. Journal of Agricutural Biotechnology, 23(02): 236-243.
[7] 王今越, 王小虹, 陈民盛. 2009. 核转录因子κB与肌细胞的生长和运动[J]. 中国组织工程研究与临床康复, 13(50): 9954-9957.
(Wang J Y, Wang X H, Chen M S, et al.2009. Growth and movement of nuclear factor kappa B and muscle cells[J]. Journal of Clinical Rehabilitative Tissue Engineering Research, 13(50): 9954-9957.
[8] Akhatayeva Z, Cao C, Huang Y, et al.2022. Newly reported 90-bp deletion within the ovine BMPRIB gene: Does it widely distribute, link to the famous FecB (p. Q249R) mutation, and affect litter size[J]. Theriogenology, 189: 222-229.
[9] Auld K L, Silver P A.2006. Transcriptional regulation by the proteasome as a mechanism for cellular protein[J]. Cell Cycle, 5(14): 1503-1505.
[10] Bai Y, Li J, Zhu H, et al.2021.Deletion mutation within the goat PPP3CA gene identified by GWAS significantly affects litter size[J]. Reproduction, Fertility and Development, 33(7): 476-483.
[11] Bai Y, Zhang T, Liu N, et al.2022. Investigation of copy number variations (CNVs) of the goat PPP3CA gene and their effect on litter size and semen quality[J]. Animals, 12(4): 445.
[12] Bär L, Großmann C, Gekle M, et al.2017. Calcineurin inhibitors regulate fibroblast growth factor 23 (FGF23) synthesis[J]. Naunyn-Schmiedeberg's Archives of Pharmacology, 390: 1117-1123.
[13] Bi Y, Wang Z, Wang Q, et al.2022. Are copy number variations within the FecB gene significantly associated with morphometric traits in goats[J]. Animals, 12(12): 1547.
[14] Conti M M, Ghizzoni J M, Gil-Bona A, et al.2022. Repression of essential cell cycle genes increases cellular fitness[J]. PLOS Genetics, 18(8): e1010349.
[15] Fan T, Huang Y.2021. Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis[J]. Scientific Reports, 11(1): 7896.
[16] Feng Z, Li X, Cheng J, et al.2020. Copy number variation of the PIGY gene in sheep and its association analysis with growth traits[J]. Animals, 10(4): 688.
[17] Hoppe T, Matuschewski K, Rape M, et al.2000. Activation of a membrane-bound transcription factor by regulated ubiquitin/proteasome-dependent processing[J]. Cell, 102(5): 577-586.
[18] Hou M.2018. Force-length relation of skeletal muscles: from sarcomeres to myofibril[J]. Biomechanics and Modeling In Mechanobiology, 17(6): 1797-1810.
[19] Hudson M B, Price S R.2013. Calcineurin: A poorly understood regulator of muscle mass[J]. The International Journal of Biochemistry & Cell Biology, 45(10): 2173-2178.
[20] Islam R, Liu X, Gebreselassie G, et al.2020. Genome-wide association analysis reveals the genetic locus for high reproduction trait in Chinese Arbas Cashmere goat[J]. Genes & Genomics, 42: 893-899.
[21] Kang Y, Zhu Q, Meng F, et al.2022. Rapid detection of InDel within the KDM3B gene in five sheep breeds using the mathematical expectation (ME) method[J]. Gene, 834: 146598.
[22] Kang Z, Jiang E, Wang K, et al.2019. Goat membrane associated ring-CH-type finger 1 (MARCH1) mRNA expression and association with litter size[J]. Theriogenology, 128: 8-16.
[23] Kim S A, Brossard M, Roshandel D, et al.2019. Gpart: Human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks[J]. Bioinformatics, 35(21): 4419-4421.
[24] Li L J, Yang P, Shi S Y, et al.2020. Association analysis to copy number variation (CNV) of Opn4 gene with growth traits of goats[J]. Animals, 10(3): 441.
[25] Liu M, Li B, Shi T, et al.2019. Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle[J]. Journal of Applied Genetics, 60: 199-207.
[26] Liu X, Yang P, Sun H, et al.2022. CNV analysis of VAMP7 gene reveals variation associated with growth traits in Chinese cattle[J]. Animal Biotechnology, 34(4): 1095-1101.
[27] Mallinson J, Meissner J, Chang K C.2009. Calcineurin signaling and the slow oxidative skeletal muscle fiber type[J]. International Review of Cell and Molecular Biology, 277: 67-101.
[28] Masaki T, Habara M, Sato Y, et al.2021. Calcineurin regulates the stability and activity of estrogen receptor α[J]. Proceedings of the National Academy of Sciences, 118(44): e2114258118.
[29] Parsons S A, Wilkins B J, Bueno O F, et al.2003. Altered skeletal muscle phenotypes in calcineurin Aalpha and Abeta gene-targeted mice[J].Molecular and Cellular Biology, 23(12): 4331-4343.
[30] Redgrove K A, Bernstein I R, Pye V J, et al.2016. Dynamin 2 is essential for mammalian spermatogenesis[J]. Scientific Reports, 6(1): 1-14.
[31] Rusnak F, Mertz P.2000. Calcineurin: Form and function[J]. Physiological Reviews, 80(4): 1483-1521.
[32] Selvakumar P, Lakshmikuttyamma A, Anderson D H, et al.2005. Molecular cloning, expression, purification and characterization of calcineurin from bovine cardiac muscle[J]. Biochimie, 87(11): 975-983.
[33] Vincent O, Carlson M.1998. Sip4, a Snf1 kinase-dependent transcriptional activator, binds to the carbon source-responsive element of gluconeogenic genes[J]. The EMBO Journal, 17(23): 7002-7008.
[34] Wan L, Ma J, Xu G, et al.2014. Molecular cloning, structural analysis and tissue expression of protein phosphatase 3 catalytic subunit alpha isoform (PPP3CA) gene in Tianfu goat muscle[J]. International Journal of Molecular Sciences, 15(2): 2346-2358.
[35] Wang X, Zheng Z, Cai Y, et al.2017. CNVcaller: Highly efficient and widely applicable software for detecting copy number variations in large populations[J]. Gigascience, 6(12): gix115.
[36] Wang Z, Wang R, Pan C, et al.2022. Genetic variations and mRNA expression of goat DNAH1 and their associations with litter size[J]. Cells, 11(8): 1371.
[37] Xu Z, Wang X, Zhang Z, et al.2020. Copy number variation of CADM2 gene revealed its association with growth traits across Chinese Capra hircus (goat) populations[J]. Gene, 741: 144519.
[38] Zhang B, Li H, Hu Z, et al.2021. Generation of mouse-human chimeric embryos[J]. Nature Protocols, 16(8): 3954-3980.
