不同养殖密度虹鳟幼鱼生长和肌肉转录组比较分析

doi:10.16378/j.cnki.1003-1111.21234

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Abstract In order to study the effect of culture density on growth of rainbow trout Oncorhynchus mykiss, the growth performance and muscle transcriptome of rainbow trout under high density (6.99 kg/m³), med-density (4.66 kg/m³) and low density (2.33 kg/m³) culture conditions were compared and analyzed, respectively. The results showed that after 32 days of breeding, the final quality and other growth-related indices were higher in low density group than those in med-density group and high density group. For each sample, the effective data of transcriptome all reached 5.99 Gb, and the comparison efficiency ranged from 91.67 to 92.77%. A total of 5501 new genes were discovered, of which 4121 were annotated and 1380 were not annotated. 2760, 654 and 2316 differentially expressed genes (DEGs) were obtained in low density group vs high density group, low density group vs med-density group, and med-density group vs high density group, respectively. Their biological processes and cell components were enriched in DNA integration, DNA-mediated translocation and folding. The molecular functions were mainly enriched in the structural composition of cytoskeleton (for the DEGs of low density group vs high density group, med-density group vs high density group and DNA binding and oxidoreductase activity acting on paired donor binding or recombination (for the DEGs in low density. group vs medium density group). 920, 196 and 743 DEGs are located in 212, 112 and 189 specific metabolic pathways respectively. Furthermore, 19 gene sequences related to growth and stress were obtained by artificial screening. The results showed that the culture density had a significant effect on the growth of rainbow trout and the expression of related genes.

Key words： Oncorhynchus mykiss culture density growth transcriptome comparative analysis

Received: 11 November 2021

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	Articles by authors
	ZHU Minjie
	ZENG Qi
	CHENG Chao
	XIAO Min
	LI Aiping
	JIAN Shaoqing
	ZHAO Daxian

Cite this article:

ZHU Minjie,ZENG Qi,CHENG Chao, et al. Comparative Analysis of Growth and Muscle Transcriptome of Juvenile Rainbow Trout Oncorhynchus mykiss under Different Culture Densities[J]. Fisheries Science, 2023, 42(5): 747-759.

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https://www.shchkx.com/EN/10.16378/j.cnki.1003-1111.21234 OR https://www.shchkx.com/EN/Y2023/V42/I5/747

[1] 农业农村部渔业渔政管理局、全国水产技术推广总站、中国水产学会.2021中国渔业统计年鉴[M].北京:中国农业出版社,2021:24-25.
[2] REBL A,VERLEIH M,KÖBIS J M,et al.Transcriptome profiling of gill tissue in regionally bred and globally farmed rainbow trout strains reveals different strategies for coping with thermal stress[J].Marine Biotechnology,2013,15(4):445-460.
[3] ARAGÃO C,COSTAS B,VARGAS-CHACOFF L,et al.Changes in plasma amino acid levels in a euryhaline fish exposed to different environmental salinities[J].Amino Acids,2010,38(1):311-317.
[4] JIANG G Z,LIU W B,LI G F,et al.Effects of different dietary glycyrrhetinic acid (GA) levels on growth,body composition and plasma biochemical index of juvenile channel catfish,Ictalurus punctatus[J].Aquaculture,2012,338/339/340/341:167-171.
[5] TAN E K,WONGWARANGKANA C,KINOSHITA S,et al.Global gene expression analysis of gill tissues from normal and thermally selected strains of rainbow trout[J].Fisheries Science,2012,78(5):1041-1049.
[6] HASENBEIN M,FANGUE N A,GEIST J P,et al.Physiological stress biomarkers reveal stocking density effects in late larval delta smelt (Hypomesus transpacificus)[J].Aquaculture,2016,450:108-115.
[7] CAIPANG C M A,BRINCHMANN M F,BERG I,et al.Changes in selected stress and immune-related genes in Atlantic cod,Gadus morhua,following overcrowding[J].Aquaculture Research,2008,39(14):1533-1540.
[8] VESTERLUND L,JIAO H,UNNEBERG P,et al.The zebrafish transcriptome during early development[J].BMC Developmental Biology,2011,11:30.
[9] SUN F Y,PEATMAN E,LI C,et al.Transcriptomic signatures of attachment,NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection[J].Developmental & Comparative Immunology,2012,38(1):169-180.
[10] LIU S X,GAO G T,PALTI Y,et al.RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout[J].PLoS One,2014,9(2):e88492.
[11] YU E M,XIE J,WANG G J,et al.Gene expression profiling of grass carp (Ctenopharyngodon idellus) and crisp grass carp[J].International Journal of Genomics,2014,2014:639687.
[12] HE L B,PEI Y Y,JIANG Y,et al.Global gene expression patterns of grass carp following compensatory growth[J].BMC Genomics,2015,16(1):184.
[13] QIAN X,BA Y,ZHUANG Q F,et al.RNA-Seq technology and its application in fish transcriptomics[J].Omics:a Journal of Integrative Biology,2014,18(2):98-110.
[14] MARTIN S A M,KRÓL E.Nutrigenomics and immune function in fish:new insights from omics technologies[J].Developmental & Comparative Immunology,2017,75:86-98.
[15] DE WIT P,PESPENI M H,LADNER J T,et al.The simple fool's guide to population genomics via RNA-Seq:an introduction to high-throughput sequencing data analysis[J].Molecular Ecology Resources,2012,12(6):1058-1067.
[16] 母尹楠.大黄鱼脾脏转录组和表达谱分析以及过氧化物酶4结构与功能研究[D].厦门:国家海洋局第三海洋研究所,2011.
[17] SCHUNTER C,VOLLMER S V,MACPHERSON E,et al.Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics[J].BMC Genomics,2014,15:167.
[18] KURE E H,SÆBØ M,STANGELAND A M,et al.Molecular responses to toxicological stressors:profiling microRNAs in wild Atlantic salmon (Salmo salar) exposed to acidic aluminum-rich water[J].Aquatic Toxicology,2013,138/139:98-104.
[19] 邵邻相,谢炜,叶菲菲.养殖密度对地图鱼幼鱼生长发育的影响[J].水产科学,2005,24(4):7-9.
[20] REFAEY M M,LI D P,TIAN X,et al.High stocking density alters growth performance,blood biochemistry,intestinal histology,and muscle quality of channel catfish Ictalurus punctatus[J].Aquaculture,2018,492:73-81.
[21] 庄平,李大鹏,王明学,等.养殖密度对史氏鲟稚鱼生长的影响[J].应用生态学报,2002,13(6):735-738.
[22] MILLÁN-CUBILLO A F,MARTOS-SITCHA J A,RUIZ-JARABO I,et al.Low stocking density negatively affects growth,metabolism and stress pathways in juvenile specimens of meagre (Argyrosomus regius,Asso 1801)[J].Aquaculture,2016,451:87-92.
[23] RAFATNEZHAD S,FALAHATKAR B,TOLOUEI GILANI M H.Effects of stocking density on haematological parameters,growth and fin erosion of great sturgeon (Huso huso) juveniles[J].Aquaculture Research,2008,39(14):1506-1513.
[24] WONG J M,BENZIE J A H.The effects of temperature,Artemia enrichment,stocking density and light on the growth of juvenile seahorses,Hippocampus whitei (Ble-eker,1855),from Australia[J].Aquaculture,2003,228(1/2/3/4):107-121.
[25] ANDRADE T,AFONSO A,PÉREZ-JIMÉNEZ A,et al.Evaluation of different stocking densities in a Senegalese sole (Solea senegalensis) farm:implications for growth,humoral immune parameters and oxidative status[J].Aquaculture,2015,438:6-11.
[26] 杨天燕,蒋艳琳,韩志强,等.基于RNA-seq技术的江鳕不同组织转录组比较分析[J].农业生物技术学报,2020,28(2):291-301.
[27] 张燕萍,章海鑫,崔璀,等.基于RNA-seq的黄尾鲴肝脏转录组测序与分析[J].水生态学杂志,2018,39(6):87-94.
[28] 赵文,高峰英,石振广.达氏鳇肌肉组织转录组测序和功能分析[J].水产学报,2014,38(9):1255-1262.
[29] 赵永丽,夏明哲,吴蓉蓉,等.基于高通量测序的花斑裸鲤转录组及功能分析[J].青海大学学报(自然科学版),2018,36(1):1-8.
[30] 刘凯,谢楠,冯晓宇,等.基于RNA-seq技术对乌鳢和斑鳢肝脏的转录组分析[J].经济动物学报,2015,19(4):213-219.
[31] OHAMA M,WASHIO Y,KISHIMOTO K,et al.Growth performance of myostatin knockout red sea bream Pagrus major juveniles produced by genome editing with CRISPR/Cas9[J].Aquaculture,2020,529:735672.
[32] WU L M,LI Y J,XU Y F,et al.The roles of two myostatins and immune effects after inhibition in Qi river crucian carp (Carassius auratus)[J].Fish & Shellfish Immunology,2020,98:710-719.
[33] KIM J H,KIM J H,SUTIKNO L A,et al.Identification of the minimum region of flatfish myostatin propeptide (Pep45-65) for myostatin inhibition and its potential to enhance muscle growth and performance in animals[J].PLoS One,2019,14(4):e0215298.
[34] WU L M,LI Y J,XU Y F,et al.Cloning and characterization of wnt4a gene in a natural triploid teleost,Qi river crucian carp (Carassius auratus)[J].General and Comparative Endocrinology,2019,277:104-111.
[35] SU J Z,MEI L Y,XI L W,et al.Responses of glycolysis,glycogen accumulation and glucose-induced lipogenesis in grass carp and Chinese longsnout catfish fed high-carbohydrate diet[J].Aquaculture,2021,533:736146.
[36] CARUSO M A,SHERIDAN M A.Differential regulation of the multiple insulin and insulin receptor mRNAs by somatostatin[J].Molecular and Cellular Endocrinology,2014,384(1/2):126-133.
[37] CAMARATA T,VASILYEV A,HADJIARGYROU M.Cloning of zebrafish Mustn1 orthologs and their expression during early development[J].Gene,2016,593(1):235-241.
[38] GUSTAFSON B,HAMMARSTEDT A,HEDJAZIFAR S,et al.BMP4 and BMP antagonists regulate human white and beige adipogenesis[J].Diabetes,2015,64(5):1670-1681.
[39] ZHANG W Z,LAN T,NIE C H,et al.Characterization and spatiotemporal expression analysis of nine bone morphogenetic protein family genes during intermuscular bone development in blunt snout bream[J].Gene,2018,642:116-124.
[40] ALEXANDER K A,CHANG M K,MAYLIN E R,et al.Osteal macrophages promote in vivo intramembranous bone healing in a mouse tibial injury model[J].Journal of Bone and Mineral Research,2011,26(7):1517-1532.
[41] KNOWLES H J,MOSKOVSKY L,THOMPSON M S,et al.Chondroclasts are mature osteoclasts which are capable of cartilage matrix resorption[J].Virchows Archiv,2012,461(2):205-210.
[42] OTA N,TAKAISHI H,KOSAKI N,et al.Accelerated cartilage resorption by chondroclasts during bone fracture healing in osteoprotegerin-deficient mice[J].Endocrinology,2009,150(11):4823-4834.
[43] TAKEYAMA K,CHATANI M,INOHAYA K,et al.TGFβ-2 signaling is essential for osteoblast migration and differentiation during fracture healing in medaka fish[J].Bone,2016,86:68-78.
[44] NAM B H,PARK E M,KIM Y O,et al.Identification of two differentially expressed forms of progranulin mRNA in the teleost fish Paralichthys olivaceus[J].Fish & Shellfish Immunology,2009,26(1):177-182.
[45] ABLOOGLU A J,TKACHENKO E,KANG J,et al.Integrin alpha V is necessary for gastrulation movements that regulate vertebrate body asymmetry[J].Development (Cambridge,England),2010,137(20):3449-3458.
[46] CHEN L,SUN L.Cathepsin B of Cynoglossus semilaevis:identification,expression,and activity analysis[J].Comparative Biochemistry and Physiology Part B:Biochemistry and Molecular Biology,2012,161(1):54-59.
[47] OHASHI K,BURKART V,FLOHÉ S,et al.Cutting edge:heat shock protein 60 is a putative endogenous ligand of the toll-like receptor-4 complex[J].Journal of Immunology,2000,164(2):558-561.
[48] BARANOV M,TER BEEST M,REINIEREN-BEEREN I,et al.Podosomes of dendritic cells facilitate antigen sampling[J].Journal of Cell Science,2014,127(Pt 5):1052-1064.