基于转录组学和代谢组学研究调控驴背最长肌嫩度的分子机制

doi:10.11843/j.issn.0366-6964.2022.03.008

Abstract

Abstract: The study aimed to explore the molecular regulation mechanism of donkey meat tenderness based on the joint analysis of transcriptome and metabolome. In this study, 30 female Guangling donkeys with the same growth environment and feeding conditions, aged 33 to 36 months, were used as the research object. Shear force and intramuscular fat content were measured, and 8 donkeys were selected based on the shear force and intramuscular fat content. The donkeys were divided into high tenderness group (HT, n=4) and low tenderness group (LT, n=4). Differentially expressed genes and metabolites were screened by transcriptome and metabolome analysis, and then combined with KEGG pathway enrichment analysis to construct the relevant network interaction map. The results of transcriptome indicated that a total of 1 253 differetially expressed genes were found in HT group and LT group, of which 832 genes were up-regulated and 421 genes were down-regulated. The results of KEGG analysis indicated that the differetially expressed genes were mainly enriched in carbohydrate metabolism, lipid metabolism, endocrine system, signal transduction and cellular processes. The metabolome showed that 225 differential metabolites were identified in HT and LT group, of which 154 were up-regulated and 71 were down-regulated. KEGG pathway analysis showed that differential metabolites were mainly enriched in carbohydrate metabolism, lipid metabolism, amino acid metabolism, nucleotide metabolism and signal transduction. Joint analysis showed that differentially expressed genes and differential metabolites were significantly enriched in glycero-phospholipid metabolism, pentose phosphate pathway, alanine, aspartate and glutamate metabolism, arginine and proline metabolism and glucagon signaling pathway. Significant differentially expressed genes and metabolites played a key regulatory role in the above metabolic pathways, and can be used as potential candidate genes and metabolites for donkey meat tenderness, which lays a theoretical foundation for exploring the molecular regulation mechanism of meat tenderness and molecular breeding of donkey in the future.

Key words: Guangling donkey, tenderness, transcriptome, metabolome, combined analysis

CLC Number:

S822.2

LI Wufeng, GUAN Jiawei, QIU Lixia, SUN Yutong, DU Min. Study on the Molecular Mechanism of Regulating Tenderness of Longissimus Dorsi Muscle of Donkey Based on Transcriptomics and Metabolomics[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(3): 743-754.

References 44

[1]	张旭,乐宝玉,成志敏,等.广灵驴成纤维细胞系的建立及其相关生物学特性研究[J].中国畜牧兽医,2018,45(3):650-655.ZHANG X,LE B Y,CHENG Z M,et al.Establishment and biological characteristics analysis of fibroblast cell line of Guangling donkey[J].China Animal Husbandry&Veterinary Medicine,2018,45(3):650-655.(in Chinese)
[2]	闫俊峰.广灵驴特性和生长规律[J].农业技术与装备,2020(11):165-166.YAN J F.Characteristics and growth law of Guangling donkey[J].Agricultural Technology&Equipment,2020(11):165-166.(in Chinese)
[3]	BOUDON S,OUNAISSI D,VIALA D,et al.Label free shotgun proteomics for the identification of protein biomarkers for beef tenderness in muscle and plasma of heifers[J].J Proteomics,2020,217:103685.
[4]	侯旭,张一敏,毛衍伟,等.宰后盆骨吊挂方式及成熟时间对黄牛牛肉品质的影响[J].农业工程学报,2014,30(8):251-256.HOU X,ZHANG Y M,MAO Y W,et al.Effect of pelvic suspension and aging time on meat quality of Chinese yellow cattle[J].Transactions of the Chinese Society of Agricultural Engineering,2014,30(8):251-256.(in Chinese)
[5]	郝婉名,祝超智,赵改名,等.肌肉嫩度的影响因素及pH调节牛肉嫩化技术研究进展[J].食品工业科技,2019,40(24):349-354.HAO W M,ZHU C Z,ZHAO G M,et al.Research progress on the influence factors of the tenderness of the muscle and the technology of adjusting the tenderization of the beef[J].Science and Technology of Food Industry,2019,40(24):349-354.(in Chinese)
[6]	MARINO R,DELLA MALVA A,ALBENZIO M.Proteolytic changes of myofibrillar proteins in Podolian meat during aging:focusing on tenderness[J].J Anim Sci,2015,93(3):1376-1387.
[7]	MUNIZ M M M,FONSECA L F S,MAGALHÃES A F B,et al.Use of gene expression profile to identify potentially relevant transcripts to myofibrillar fragmentation index trait[J].Funct Integr Genomics,2020,20(4):609-619.
[8]	HE F Y,KIM H W,HWANG K E,et al.Effect of ginger extract and citric acid on the tenderness of duck breast muscles[J].Korean J Food Sci Anim Resour,2015,35(6):721-730.
[9]	JIANG H Z,YOON S C,ZHUANG H,et al.Tenderness classification of fresh broiler breast fillets using visible and near-infrared hyperspectral imaging[J].Meat Sci,2018,139:82-90.
[10]	FALKOVSKAYA A,GOWEN A.Literature review:spectral imaging applied to poultry products[J].Poult Sci,2020,99(7):3709-3722.
[11]	FERNANDEZ-BARROSO M A,CARABALLO C,SILIÓ L,et al.Differences in the loin tenderness of Iberian pigs explained through dissimilarities in their transcriptome expression profile[J].Animals (Basel),2020,10(9):1715.
[12]	MUNIZ M M M,FONSECA L F S,DOS SANTOS SILVA D B,et al.Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle[J].Meat Sci,2021,173:108378.
[13]	MUROYA S,UEDA S,KOMATSU T,et al.MEATabolomics:muscle and meat metabolomics in domestic animals[J]. Metabolites, 2020,10(5):188.
[14]	ZHU C L,PETRACCI M,LI C,et al.An untargeted metabolomics investigation of Jiulong yak (Bos grunniens) meat by 1H-NMR[J].Foods,2020,9(4):481.
[15]	MUROYA S,OE M,NAKAJIMA I,et al.CE-TOF MS-based metabolomic profiling revealed characteristic metabolic pathways in postmortem porcine fast and slow type muscles[J].Meat Sci,2014,98(4):726-735.
[16]	WANG Y,YANG Y,PAN D D,et al.Metabolite profile based on 1H NMR of broiler chicken breasts affected by wooden breast myodegeneration[J].Food Chem,2020,310:125852.
[17]	熊火,蔡欣,刘静波,等.高脂饲粮对生长育肥猪肉品质和骨骼肌蛋白质组的影响[J].畜牧兽医学报,2016,47(10):2052-2059.XIONG H,CAI X,LIU J B,et al.Effects of high-fat diet on meat quality traits and skeletal muscle proteome of growing-finishing pigs[J].Acta Veterinaria et Zootechnica Sinica,2016,47(10):2052-2059.(in Chinese)
[18]	JEONG J Y,KIM M,JI S Y,et al.Metabolomics analysis of the beef samples with different meat qualities and tastes[J].Food Sci Anim Resour,2020,40(6):924-937.
[19]	GONÇALVES T M,DE ALMEIDA REGITANO L C,KOLTES J E,et al.Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle[J].Front Genet,2018,9:441.
[20]	ARORA R,NAVEEN K S,SUDARSHAN S,et al.Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India[J].PLoS One,2019,14(6):e217461.
[21]	PIÓRKOWSKA K,UKOWSKI K,NOWAK J,et al.Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force[J].Anim Genet,2016,47(1):68-80.
[22]	LOVE M I,HUBER W,ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome Biol,2014,15(12):550.
[23]	XIE C,MAO X Z,HUANG J J,et al.KOBAS 2.0:a web server for annotation and identification of enriched pathways and diseases[J].Nucleic Acids Res,2011,39(S2):W316-W322.
[24]	马会芳.基于质谱技术的甘油磷脂和甘油三酯高效分析方法及其应用研究[D].北京:中国农业科学院,2018.MA H F.High performance analysis of phospholipids and triglycerides based on mass spectrometry and its application[D]. Beijing:Chinese Academy of Agricultural Sciences,2018.(in Chinese)
[25]	YE J J,BIAN X,LIM J,et al.Adiponectin and related C1q/TNF-related proteins bind selectively to anionic phospholipids and sphingolipids[J].Proc Natl Acad Sci U S A,2020,117(29):17381-17388.
[26]	PUIG-OLIVERAS A,REVILLA M,CASTELLÓ A,et al.Expression-based GWAS identifies variants,gene interactions and key regulators affecting intramuscular fatty acid content and composition in porcine meat[J].Sci Rep,2016,6:31803.
[27]	MANNERÅS-HOLM L,KIRCHNER H,BJÖRNHOLM M,et al.mRNA expression of diacylglycerol kinase isoforms in insulin-sensitive tissues:effects of obesity and insulin resistance[J].Physiol Rep,2015,3(4):e12372.
[28]	MANNERÅS-HOLM L,SCHÖNKE M,BROZINICK J T,et al.Diacylglycerol kinase ε deficiency preserves glucose tolerance and modulates lipid metabolism in obese mice[J].J Lipid Res,2017,58(5):907-915.
[29]	YU H B,ZHAO Z H,YU X Z,et al.Bovine lipid metabolism related gene GPAM:Molecular characterization,function identification,and association analysis with fat deposition traits[J].Gene,2017,609:9-18.
[30]	HAMILL R M,MCBRYAN J,MCGEE C,et al.Functional analysis of muscle gene expression profiles associated with tenderness and intramuscular fat content in pork[J].Meat Sci,2012,92(4):440-450.
[31]	蔡洪容.肿瘤细胞中磷酸戊糖途径概述[J].临床医药文献电子杂志,2020,7(13):183,185.CAI H R.Overview of the pentose phosphate pathway in tumor cells[J].Journal of Clinical Medical Literature,2020,7(13):183,185.(in Chinese)
[32]	王坤,豆腾飞,徐志强,等.大围山微型鸡和艾维茵肉鸡PFKM基因表达量与pH值及肌糖原含量相关性研究[J].中国家禽, 2018,40(14):10-13.WANG K,DOU T F,XU Z Q,et al.Correlation analysis on PFKM gene expression,pH value,muscle glycogen content in Daweishan mini chicken and Avian broiler[J].China Poultry,2018,40(14):10-13.(in Chinese)
[33]	JIANG S W,LIU Y S,SHEN Z L,et al.Acetylome profiling reveals extensive involvement of lysine acetylation in the conversion of muscle to meat[J].J Proteomics,2019,205:103412.
[34]	SILVA L H P,RODRIGUES R T S,ASSIS D E F,et al.Explaining meat quality of bulls and steers by differential proteome and phosphoproteome analysis of skeletal muscle[J].J Proteomics,2019,199:51-66.
[35]	KWAK S E,SHIN H E,ZHANG D D,et al.Potential role of exercise-induced glucose-6-phosphate isomerase in skeletal muscle function[J].J Exerc Nutrition Biochem,2019,23(2):28-33.
[36]	李清平,张秀飞,梁明,等.果糖1,6-二磷酸酯酶研究进展[J].聊城大学学报:自然科学版,2021,34(2):73-80.LI Q P,ZHANG X F,LIANG M,et al.Research progress of fructose-1,6-bisphosphatase[J].Journal of Liaocheng University:Natural Science Edition,2021,34(2):73-80.(in Chinese)
[37]	巨晓军,束婧婷,章明,等.不同品种、饲养周期肉鸡肉品质和风味的比较分析[J].动物营养学报,2018,30(6):2421-2430.JU X J,SHU J T,ZHANG M,et al.Comparison analysis of meat quality and flavor of different breeds and feeding periods of broilers[J].Chinese Journal of Animal Nutrition,2018,30(6):2421-2430.(in Chinese)
[38]	KAMEI Y,HATAZAWA Y,UCHITOMI R,et al.Regulation of skeletal muscle function by amino acids[J].Nutrients, 2020, 12(1):261.
[39]	KATANE M,MATSUDA S,SAITOH Y,et al.Glyoxylate reductase/hydroxypyruvate reductase regulates the free D-aspartate level in mammalian cells[J].J Cell Biochem,2021,122(11):1639-1652.
[40]	KAZAK L,COHEN P.Creatine metabolism:energy homeostasis,immunity and cancer biology[J].Nat Rev Endocrinol,2020, 16(8):421-436.
[41]	ROSA A F,MONCAU C T,POLETI M D,et al.Proteome changes of beef in Nellore cattle with different genotypes for tenderness[J].Meat Sci,2018,138:1-9.
[42]	KIM J,YANG G,KIM Y,et al.AMPK activators:mechanisms of action and physiological activities[J].Exp Mol Med,2016, 48(4):e224.
[43]	HERZIG S,SHAW R J.AMPK:guardian of metabolism and mitochondrial homeostasis[J].Nat Rev Mol Cell Biol,2018,19(2):121-135.
[44]	梁鹏,邵顺成,张稳,等.PRKAG3基因与畜禽肉质性状相关性的研究进展[J].黑龙江畜牧兽医,2021(3):45-49,53.LIANG P,SHAO S C,ZHANG W,et al.Research progress on the correlation between PRKAG3 gene and meat quality of livestock and poultry[J].Heilongjiang Animal Science and Veterinary Medicine,2021(3):45-49,53.(in Chinese)

Study on the Molecular Mechanism of Regulating Tenderness of Longissimus Dorsi Muscle of Donkey Based on Transcriptomics and Metabolomics

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 44

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	CHEN Zhe, QU Xiaolu, GUO Binbin, SUN Xuefeng, YAN Leyan. Study on Candidate Genes for Green Light Affecting Early Development of Goose Embryo Heart Based on Transcriptome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1978-1988.
[2]	XU Junjie, ZHANG Lutong, WANG Jinjie, CHEN Xiaochen, HE Weixian, CAI Chuanjiang, CHU Guiyan, YANG Gongshe. Exploring the Effect of Epimedium on Estrus of Gilts Based on Multiomics and Network Pharmacology [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1615-1628.
[3]	WANG Xin, NIE Tong, LI Aqun, MA Jun. Hesperidin Alleviates High-fat-diet Induced Hepatic Oxidative Stress in Mice via Oxidative Phosphorylation Pathway [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 1302-1313.
[4]	GAO Yawei, PENG Di, SUN Zhaoyang, YAN Ziyue, CUI Kai, MA Zefang. Mining the Molecular Mechanism of Exogenous Melatonin Affecting the Development of Mink Ovary Based on Transcriptome Data [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(2): 607-618.
[5]	LIU Yili, TANG Jiao, MIN Qi, YANG Lu, WANG Zening, HU Lian, ZHAO Di, JIANG Mingfeng. Mining Key Candidate Genes of Development and Metabolism in Yak Abomasum Based on Transcriptome Data [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 153-168.
[6]	HU Ting, ZHANG Yonghong, HOU Xiaolin, YAO Hua, CUI Defeng, PAN Zaozao, ZHANG Lingyu, ZHANG Jiaxi, WU Qiong. The Effects of Bisphenol A on Inflammation and Amino Acid Metabolism Pathways in Porcine Testis Sertoli Cells Based on Transcriptome Analysis [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2858-2871.
[7]	LIU Hang, WANG Huanhuan, GE Ying, ZHANG Lei, ZHANG Weiwu, WEI Yinghui, LI Qinghai, FAN Jinghui, ZHANG Xuedong. Screening of Candidate Genes of Skin Color of Black-Bone Chicken Based on Transcriptome and Proteome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2320-2329.
[8]	BAI Lu, WANG Mengjie, MA Xiaochun, HE Zhengxiao, KONG Fuli, LIU Dawei, YING Fan, ZHU Dan, ZHAO Guiping, WEN Jie, LIU Ranran. Study of the Alteration of Wooden Breast Histological and Molecular Regulatory Pathways in Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1915-1926.
[9]	WANG Meihui, ZHONG Zhenyu, BAI Jiade, SHAN Yunfang, CHENG Zhibin, ZHANG Qingxun, MENG Yuping, DONG Yulan, GUO Qingyun. Transcriptomic Analysis of Key Genes and Pathways in Deer Gut Infected by Clostridium perfringens Type C [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 2147-2157.
[10]	SUN Meijie, CAO Liwen, ZHENG Wenjin, SHEN Junshi, ZHU Weiyun. Effect of Dietary Urea Supplementation on Liver Ammonia Metabolism in Fattening Hu Lambs Based on Transcriptome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1148-1159.
[11]	LIU Yuanyi, LI Xinyu, Bayinnamula, CUI Fang, MANG Lai, DU Ming. Single-Cell Transcriptome Sequencing Technology and its Application in Animal Reproduction [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 421-433.
[12]	YU Zuhua, JIA Yanyan, HE Lei, LIAO Chengshui, LI Jing, WEI Ying, CHEN Jian, CHEN Songbiao, SHANG Ke, DING Ke. Effects of gga-miR-155 on MDCC-MSB1 Cell Transcriptomes [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 663-672.
[13]	HAN Haoyuan, LI Shikai, YANG Ruiqiao, LI Manman, LI Jun, HA Si, ZHAO Jinyan, WEI Hongfang, QUAN Kai. Mining Key Candidate Genes for High Reproduction Performance of Huai Goats Based on Transcriptome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5077-5090.
[14]	WANG Wenxiang, DU Lili, HU Junwei, ZHANG Yanxiang, MA Minghao, DUAN Rui, QIAN Cong, WANG Xinyue, LI Sanlu, ZHANG Changqing, ZHANG Lupei, GAO Xue, XU Lingyang, LI Junya, GAO Huijiang. Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4589-4604.
[15]	ZHANG Qian, CUI Yan, YU Sijiu, HE Junfeng, PAN Yangyang, WANG Meng. Transcriptome Analysis of the Cerebral Cortex in Newborn and Adult Yaks (Bos grunniens) [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4605-4614.