酉州乌羊五个组织的权重基因共表达网络分析

doi:10.3969/j.issn.1674-7968.2023.07.011

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Abstract Youzhou dark goat (Capra hircus) is the genetic resources of local characteristic goat. It is of great significance to study the forming mechanism of its characteristic traits. This study collected the transcriptome data of a total of 15 samples from the heart, liver, longissimus dorsi, anterior lip and skin of Youzhou dark goat (3 samples for each tissue) for analysis. The weighted gene co-expression network analysis (WGCNA) software package was used to construct the co-expression network, and the GO and KEGG enrichment analysis was performed on the genes in the specific modules. Results showed that one specific expression module was identified in the heart and liver respectively. The genes in the heart specific blue module were mainly enriched in the citric acid cycle signal pathway and various metabolic processes. The genes in the liver specific yellow module were mainly enriched in the functions of peroxidase, amino acid metabolic process and chemical carcinogenesis. Genes in the turquoise module are mainly enriched in protein binding and other functions, genes in the green module are mainly enriched in phosphatidylinositol binding and other functions, and genes in the brown module are mainly enriched in biological processes such as cell protein metabolism. Through the CytoHubba plug-in algorithm, the 10 genes with the highest connectivity in the turquoise, blue and brown modules were defined as core genes. The tissue expression level of 6 core genes in the 3 modules were verified by qRT-PCR, and the results showed that ADCY9 and ADCY6 genes had the highest expression in heart tissue, AKT2 and MAPK3 genes were highly expressed in the anterior lip tissue, and the CAMK2G and CAMK2B genes were highly expressed in the longissimus dorsi, which were consistent with the transcriptome sequencing results. The above results have reference value for further bioinformatics research on functional genes of Youzhou dark goat. This study provides basic data for the mining, development and utilization of characteristic traits of local goat genetic resources in China.

Key words： Youzhou dark goat Weighted gene co-expression network analysis (WGCNA) Enrichment analysis Core gene

Received: 12 July 2022

Corresponding Authors: *rhxe@163.com

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http://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2023.07.011 OR http://journal05.magtech.org.cn/Jwk_ny/EN/Y2023/V31/I7/1450

[1] 付琳, 蒋婧, 周鹏, 等 . 2018. 成年酉州乌羊与本地白山羊母羊肌肉营养成分对嫩度及风味的影响比较研究[J]. 黑龙江畜牧兽医 , 8: 32-35.
(Fu L, Jiang J, Zhou P, et al.2018. The effect of muscle nutritional components on its tenderness and flavor in adult female Youzhou Black goat[J]. Heilongjiang Animal Science and Veterinary Medicine, 8: 32-35.)
[2] 蒋婧, 黄勇富, 周鹏, 等 . 2014. 6 月龄酉州乌羊公羔的屠宰性能及肉质理化特性研究[J]. 中国草食动物科学, S1: 306-308.
(Jiang J, Huang Y F, Zhou P, et al.2014. Study on slaughter performance and meat quality physico‐ chemical properties of 6 month Youzhou dark goat male lambs[J]. China Herbivore Science, S1: 306-308.)
[3] 蒋婧, 周鹏, 张丽, 等 . 2018. 酉州乌羊与本地其他山羊肉品质特性比较[J]. 黑龙江畜牧兽医 , 6: 47-50.
(Jiang J, Zhou P, Zhang L, et al.2018. Comparative study on meat quality characteristics between Youzhou Black goat and other local goat breeds[J]. Heilongjiang Ani‐ mal Science and Veterinary Medicine, 6: 47-50.)
[4] 刘桂琼, 黄勇富, 何春波, 等 . 2012. 湖北乌羊和酉州乌羊血液生化指标比较分析[J]. 中国草食动物 , 03: 34-37.
(Liu G Q, Huang Y F, He C B, et al.Comparison on se‐ rum biochemical parameters of Hubei Black-boned goats and Youzhou Black goats[J]. China Herbivore Sci‐ ence, 03: 34-37.)
[5] 任航行, 王高富, 陆健, 等 . 2015. 不同肤色山羊皮肤组织形态学及黑色素生成相关基因的表达分析[J]. 畜牧兽医学报, 46(09): 1525-1531.
(Ren H X, Wang G F, Lu J, et al.2015. The characteristic histomorphology of various skin colors and expression of genes involved in melano‐ genesis in goats[J]. Acta Veterinaria et Zootechnica Sini‐ ca, 46(09): 1525-1531.)
[6] 王高富, 黄勇富, 周鹏, 等 . 2012. 酉州乌羊生理生化指标测定[J]. 中国草食动物科学 , S1: 384-386.
(Wang G F, Huang Y F, Zhou P, et al.2012. Determination of physi‐ ological and biochemical index of Youzhou dark goat[J]. China Herbivore Science, S1: 384-386.)
[7] 周鹏, 蒋婧, 黄勇富, 等 . 2017. 酉州乌羊, 白山羊和波杂羊的屠宰性能及肉品质研究[J]. 西南大学学报, 39(01): 9-15.
(Zhou P, Jiang J, Huang Y F, et al.2017. Study on carcass quality and meat traits of Youzhou Black goats, local white goats and upgrading offspring of Boer goat population[J]. Journal of Southwest University, 39(01): 9-15.)
[8] Agolini E, Cherchi C, Bellacchio E, et al.2020. Expanding the clinical and molecular spectrum of lethal congenital contracture syndrome 8 associated with biallelic vari‐ ants of ADCY6[J]. Clinical Genetics, 97(4): 649-654.
[9] Chen Y, Fan Z M, Wang X X, et al.2020. PI3K/Akt signaling pathway is essential for de novo hair follicle regenera‐ tion[J]. Stem Cell Research Therapy, 11: 144.
[10] Dai W, Choubey M, Patel S, et al.2021. Adipocyte CAMK2 deficiency improves obesity-associated glucose intoler‐ance[J]. Molecular Metabolism, 53: 101300.
[11] Fedorova E S, Dementieva N V, Shcherbakov Y S, et al.2022. Identification of key candidate genes in runs of homozy‐ gosity of the genome of two chicken breeds, associated with cold adaptation[J]. Biology, 11(4): 547.
[12] Fernández-Pérez M P, Montenegro M F, Sáez-Ayala M, et al.2013. Suppression of antifolate resistance by targeting the myosin Ⅴ a trafficking pathway in melanoma[J]. Neoplasia, 15(7): 826-839.
[13] Fukuda M.2021. Rab GTPases: Key players in melanosome biogenesis, transport, and transfer[J]. Pigment Cell Mel‐ anoma Research, 34(2): 222-235.
[14] Fuller T F, Ghazalpour A, Aten J E, et al.2007. Weighted gene co-expression network analysis strategies applied to mouse weight[J]. Mammalian Genome, 18: 463-472.
[15] Hu S, Li C, Wu D B L, et al.2022. The dynamic change of gene-regulated networks in cashmere goat skin with sea‐ sonal variation[J]. Biochemical Genetics, 60(2): 527-542.
[16] Jing R X, Gu L T, Li J Q, et al.2018. A transcriptomic com‐ parison of theca and granulosa cells in chicken and cat‐ tle follicles reveals ESR2 as a potential regulator of CYP19A1 expression in the theca cells of chicken folli‐ cles[J]. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, 27:40-53.
[17] Kingo K, Aunin E, Karelson M, et al.2008. Expressional changes in the intracellular melanogenesis pathways and their possible role in the pathogenesis of vitiligo[J]. Journal of Dermatological Science, 52(1): 39-46.
[18] Kong D D, Xu J Q, Wang L, et al.2022. Combined RNA-seq and phenotype analysis reveals a potential molecular mechanism of the difference in grain size of naked bar‐ ley from the Qinghai-Tibetan plateau[J]. Frontiers in Plant Science, 13: 822607.
[19] Langfelder P, Horvath S.2008. WGCNA: An R package for weighted correlation network analysis[J]. BMC Bioin‐ formatics, 9: 559.
[20] Li N, Hwangbo C, Jaba I M, et al.2016. miR-182 modulates myocardial hypertrophic response induced by angiogen‐ esis in heart[J]. Scientific Reports, 6: 21228.
[21] Li Y F, Yuan P T, Fan S X, et al.2022a. Weighted gene co-ex‐ pression network indicates that the DYNLL2 is an im‐ portant regulator of chicken breast muscle development and is regulated by miR-148a-3p[J]. BMC Genomics, 23(1): 258.
[22] Li Z, Du X S, Wen L T, et al.2022b. Transcriptome analysis reveals the involvement of ubiquitin-proteasome path‐ way in the regulation of muscle growth of rice flower carp[J]. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, 41: 100948.
[23] Liu B T, Zhan Y, Chen X N, et al.2020. Weighted gene co‐ex‐ pression network analysis can sort cancer ‐ associated fi‐ broblast‐specific markers promoting bladder cancer pro‐ gression[J]. Journal of Cellular Physiology, 236(2): 1321-1331.
[24] Loite U, Raam L, Reimann E, Reemann P, et al.2021. The ex‐ pression pattern of genes related to melanogenesis and endogenous opioids in psoriasis[J]. International Journal of Molecular Sciences, 22: 13056.
[25] Luo Y P, Coskun V, Liang A B, et al.2015. Single-cell tran‐ scriptome analyses reveal signals to activate dormant neural stem cells[J]. Cell, 161(5): 1175-1186.
[26] Luo Z H, Wang W X, Li F, et al.2019. Pan-cancer analysis identifies telomerase-associated signatures and cancer subtypes[J]. Molecular Cancer, 18(1): 106.
[27] Lv J P, Fu Y, Gao R Y, et al.2019. Diazepam enhances mela‐ nogenesis, melanocyte dendricity and melanosome transport via the PBR/cAMP/PKA pathway[J]. Interna‐ tional Journal of Biochemistry & Cell Biology, 116: 105620.
[28] Ma J, Zhang T L, Wang W X, et al.2021. Comparative tran‐ scriptome analysis of gayal (Bos frontalis), yak (Bos grunniens), and cattle (Bos taurus) reveal the high-alti‐tude adaptation[J]. Frontiers in Genetics, 12: 778788.
[29] Mishra D C, Arora D, Budhlakoti N, et al.2021. Identification of potential cytokinin responsive key genes in rice treat‐ ed with trans-zeatin through systems biology approach[J]. Frontiers in Genetics, 12: 780599.
[30] Mukhopadhyay A, Krishnaswami S R, Yu B D Y.2011. Acti‐ vated Kras alters epidermal homeostasis of mouse skin, resulting in redundant skin and defective hair cycling[J]. The Journal of Investigative Dermatology, 131(2): 311-319.
[31] Palencia-Campos A, Aoto P C, Machal E M F, et al.2020. Germline and mosaic variants in PRKACA and PRKACB cause a multiple congenital malformation syndrome[J]. American Journal of Human Genetics, 107(5): 977-988.
[32] Qian J, Yang J, Liu X X, et al.2020. Analysis of lncRNA- mRNA networks after MEK1/2 inhibition based on WGCNA in pancreatic ductal adenocarcinoma[J]. Jour‐ nal of Cellular Physiology, 235(4): 3657-3668.
[33] Ren H X, Wang G F, Chen L, et al.2016. Genome-wide analy‐sis of long non-coding RNAs at early stage of skin pig‐mentation in goats (Capra hircus)[J]. BMC Genomics,17: 67.
[34] Ren H X, Wang G F, Jiang J, et al.2017. Comparative tran‐scriptome and histological analyses provide insights into the prenatal skin pigmentation in goat (Capra hircus)[J]. Physiological Genomics, 49(12): 703-711.
[35] Wu C Lung, Dicks A, Steward N, et al.2021. Single cell tran‐ scriptomic analysis of human pluripotent stem cell chon‐ drogenesis[J]. Nature Communications, 12(1): 362.
[36] Wu Y H, Wang T F, Qiao L, et al.2022. Upregulated microR‐ NA-210-3p improves sevoflurane-induced protective ef‐ fect on ventricular remodeling in rats with myocardial infarction by inhibiting ADCY9[J]. Functional & Integra‐tive Genomics, 22(3): 279-289.
[37] Yang C Y, Zhu Y, Ding Y L, et al.2022. Identifying the key genes and functional enrichment pathways associated with feed efficiency in cattle[J]. Gene, 807: 145934.
[38] Zeng Z C, Zhang S C, Li W Y, et al.2022. Gene-coexpression network analysis identifies specific modules and hub genes related to cold stress in rice[J]. BMC Genomics, 23(1): 251.
[39] Zhang X L, Bao P J, Ye N, et al.2022. Identification of the key genes associated with the yak hair follicle cycle[J]. Genes, 13(1): 32.