|
|
Identify the Genes Related to Muscle Traits in Crossbred Sheep Populations (Ovis aries) by RNA-seq Technology |
SHI Jin-Ping1, MA Gui-Shan2, ZHANG Quan-Wei3, LIU Ting1, TONG Jian-Wei4, SUN Jian-Hong4, WEI Yu-Bing4, YANG Lei1, CHENG Shu-Ru1,* |
1 College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; 2 Gansu Province Tianzhu Tibetan Autonomous County Agriculture and Rural Bureau, Wuwei 733299, China; 3 College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; 4 Livestock Station of Pingshan Lake Mongolian Township, Ganzhou, Zhangye City, Zhangye 734000, China |
|
|
Abstract Meat quality is the main economic traits affecting the efficiency of sheep breeding. In order to select the high-efficiency commercial herds, transcriptome sequencing was applied for identifying the genes related to sheep growth performance and meat quality from the genetic level. The crossbred commercial generation herd (F1) of Small-tailed Han sheep ewe (STH)×Suffolk ram (SFK) and STH×Mongolian sheep ram (MG) was selected as the object. The slaughter performance and meat quality of these population were measured, meanwhile, transcriptome sequencing of longissimus dorsi muscle was also carried out for identifying the genes related to sheep growth performance and meat quality. The results showed that the production performance, slaughter performance and meat quality of STH (♀) × SFK (♂) generation was better than that of STH (♀) × MG (♂) generation. Transcriptomic results suggested that a total of 397 differentially expressed genes (DEGs) were identified in two generation. Most of these genes were mainly enrichmented in 46 Gene Ontology (GO) items such as growth and development and 26 pathways such as carbon metabolism, PI3K-Akt (phosphatidylinositide 3-kinases/protein kinase B), and amino acid synthesis. Finally, 3 genes of adiponectin (ADIPOQ), insulin-like growth factor binding protein 7 (IGFBP7) and actin α1 cardiac muscle(ACTC1) were taken as the candidate genes associated with meat quality traits according to results of function and pathway analysis. The results of qRT-PCR revealed that the relative expression of ADIPOQ and IGFBP7 in STH × SFK generation were significantly higher than that of STH (♀)×SFK (♂) generation (P<0.01), however the expression level of ACTC1 was significantly lower than that of STH (♀)×MG (♂) generation (P<0.01). These results indicated that the STH × SFK generation was superior to the STH×MG generation in slaughter performance and meat quality. The differentially expressed genes selected can be taken as candidate genes for improving the sheep meat quality.
|
Received: 18 May 2020
Published: 01 February 2021
|
|
|
|
|
[1] 陈晓勇, 孙洪新, 田树军, 等. 2015. 寒泊肉羊与小尾寒羊产肉性能及肉品质比较[J]. 畜牧与兽医, 47(09): 40-44. (Chen X Y, Sun H X, Tian S J, et.al.2017. Comparison of meat production performance and meat quality of Hanbo meat sheep and Small Tail Han sheep[J].Animal Husbandry & Veterinary Medicine, 47(09): 40-44.) [2] 戴丽荷. 2006. 猪脂联素基因内含子2的A/G突变检测及关联分析[C]//. 中国畜牧兽医学会, 361-365. (Dai L H.2006.The intron 2 of swine adiponectin gene is a chewing mutation detection and correlation analysis[C]//. Chinese Association of Animal Science and Veterinary Medicine, 361-365.) [3] 李娜, 王国栋, 王艺磊. 2012. IGFBP7基因的结构与功能的研究进展[J]. 生命科学, 24(10): 1189-1196. (Li N, Wang G D, Wang Y L.2012. Research progress on structure and function of insulin-like growth factor binding protein7[J]. Chinese Bulletin of Life Sciences, 24(10): 1189-1196.) [4] 刘重旭, 王凭青, 张宝云, 等. 2011. 贵州白山羊和古蔺马羊脂联素基因多态性及其与繁殖性能的关联研究[J]. 中国农业科学, 44(09): 1916-1922. (Liu C X, Wang P Q, Zhang B Y, et al.2011. Polymorphism of adiponectin gene and its relationship with reproductive ability in guizhou white and gulin ma goats[J]. Scientia Agricultura Sinica, 44(09): 1916-1922.) [5] 刘冠卿. 2015. 小尾寒羊CSRP2、CSRP3和FSTL1基因克隆、结构特征及组织表达分析[D]. 硕士学位论文, 山东农业大学, 导师: 王建民. (Liu G Q.2015. Molecular cloning characterization and tissue expression analysis of the ovine CSRP2、CSRP3 and FSTL1 genes from Small-tail Han sheep[D]. Thesis for M. S., Shandong Agricultural University, Supervisor: Wang J M.) [6] 罗娜. 2010. 利用斑马鱼模型研究心脏和肌肉高水平表达基因POP3在心脏发育中的生物学功能[D]. 博士学位论文, 湖南师范大学, 导师: 袁婺洲, pp. 79-86. (Luo N.2010. Studies on the function of heart and skeletal muscle high-expression gene POP3 in zebrafish heart development[D]. Thesis for Ph.D., Hunan Normal University, Supervisor: Yuan W Z, pp. 79-86.) [7] 罗宗刚, 李祥, 李明洲. 2011. 脂联素(AdipoQ)及其受体基因(AdipoR1 and AdipoR2)在猪背最长肌和腰大肌中的表达差异[J]. 农业生物技术学报, 19(03): 507-512. (Luo Z G, Li X, Li M Z.2011. Expression changes of adiponection (AdipoQ) and its receptor genes (AdipoR1 and AdipoR2) in porcine longissimus dorsi and psoas major muscles[J]. Journal of Agricultural Biotechnology, 19(03): 507-512.) [8] 孟祥忍, 张成龙, 樊永亮, 等. 2017. 基于RNA-Seq转录组测序技术揭示南方黄牛肉质嫩度调控相关的分子机制[J]. 中国畜牧杂志, 53(09): 26-32, 68. (Meng X R,Zhang C L,Fan Y L, et al.2017. Molecular mechanism analysis of meat tenderness in chinese south cattle based on rna-seq transcriptome sequencing technology[J]. Chinese Journal of Animal Science , 53(09): 26-32, 68.) [9] 齐昱. 2017. 基于转录组学的蒙古牛抗寒机制的研究[D]. 博士学位论文, 内蒙古农业大学, 导师: 周欢敏, pp.7-11 (Qi Y.2017. Study on could resistance mechanism of Mongolian cattle based on transcriptome[D]. Thesis for M.S, Inner Mongolia Agricultural University, Supervisor: Zhou H M, pp.7-11 ) [10] 史关燕, 赵雄伟, 韩渊怀. 2020. 基于多组学解析作物杂种优势机制及其利用展望[J]. 山西农业大学学报(自然科学版), 40(04):1-9. (Shi G Y, Zhao X W, Han Y H.2020. Recent research progress on the crop heterosis mechanism based on mutil-omics and prospects of heterotic utilization[J]. Journal of Shanxi Agricultural University, 40(04): 1-9.) [11] 孙丽敏, 李佳蓉, 贾超, 等. 2017. 小尾寒羊为母本二元及三元肉羊杂交模式杂种优势比较分析[J]. 中国畜牧杂志, 53(03): 45-48. (Sun L M, Li J R, Jia C, et al.2017. Small-tailed Han sheep is an excellent crossbreed for female binary and ternary mutton sheep Potential comparative analysis[J]. Chinese Journal of Animal Science, 53(03): 45-48.) [12] 谭向荣, 张立岗, 朱冠虹, 等. 2019. 杜泊、萨福克与小尾寒羊杂交效果对比试验[J].畜牧兽医杂志, 38(01):11-13+16. (Tan X R, Zhang L G, Zhu G Het al.2019. Comparative test of the effect of crossing Dorper and Suffolk with Small-Tail Han sheep[J]. Journal of Animal Science and Veterinary Medicine, 38(01): 11-13, 16.) [13] 汤继顺. 2019. 利用转录组测序和蛋白质组学分析筛选绵羊多羔候选基因的研究[D]. 博士学位论文, 中国农业科学院, 导师: 储明星, pp.1-2. (Tang J S.2019. Study on screening polytocous candidate genes in sheep based transcriptome sequencing and proteomics[D]. Thesis for Ph.D. Chinese Academy of Agricultural Sciences, Supervisor: Chu M X, pp.1-2) [14] 王敏贤, 李守诚, 杨茂虎. 1982. 兰州大尾羊的屠宰试验[J]. 甘肃畜牧兽医, (4): 23-25. (Wang M X, Li S C, Yang M H. 1982. The slaughter test of Lanzhou fat-tailed sheep[J]. Gansu Animal Husbandry and Veterinary, (4): 23-25.) [15] 王位, 付绍印, 何小龙, 等. 2018. 基于RNA-Seq技术挖掘绵羊背最长肌肉质性状相关基因[J]. 中国畜牧兽医, 45(01): 122-130. (Wang W, Fu S Y, He X L.2018. Excavation of meat quality related genes in longissimus dorsi of sheep by RNA-Seq[J]. China Animal Husbandry & Veterinary Medicine, 45(01): 122-130.) [16] 谢珊珊. 2019. 利用整合组学开展MSTN编辑梅山猪的表型遗传分析[D]. 博士学位论文, 中国农业科学院, 导师: 崔文涛, pp. 65-68. (Xie S S.2019. Phenotypic genetic analysis of MSTN-edited Meishan pigs by integrated omics[D]. Thesis for M.S, Chinese Academy of Agricultural Sciences, Supervisor: Cui W T, pp. 65-68.) [17] 邢红文, 张德安, 肉孜·纳衣甫. 2012. 良种肉羊杜泊、萨福克羊引进及利用效果研究[J]. 新疆畜牧业, (07): 24-26. (Xing H W, Zhang D A, Ruzy N. 2012. Study on the introduction and utilization of improved breeds of sheep Dorper and Suffolk[J]. Xinjiang Animal Husbandry, (07): 24-26.) [18] 杨建敏. 2016. 杜洛克猪与槐猪背最长肌转录组分析[D]. 硕士学位论文, 福建农林大学, 导师: 肖天放. (Transcriptomic analysis of longissimus muscle of Duroc pig and Huai pig[D]. Thesis for M.S., Fujian Agriculture and Forestry University, Supervisor: Xiao T F.) [19] 袁茂, 江明锋, 徐亚欧, 等. 2019. 藏鸡不同发育阶段腿部肌肉组织转录组及microRNA联合分析[J]. 畜牧兽医学报, 50(12): 2400-2412. (Yuan M, Jiang M F, Xu Y O, 等. 2019. Analysis of transcriptome and microRNA in leg muscle of Tibetan chicken at different developmental stages[J]. Chinese Journal of Animal and Veterinary Sciences, 50(12): 2400-2412.) [20] 訾宝兵. 2018. 基于转录组学分析的日粮蛋白质对略阳乌鸡生长发育调控的分子机制[D].博士学位论文, 西北农林科技大学, 导师: 刘福柱, pp.7-9 (Zi B B.2018. Molecular mechanism of growth and development in lveyang black-bone chcken regulating of dietary protein based on the transcriptional analysis[D]. Thesis for M.S, Northwest A&F University, Supervisor: Liu F Z, pp.7-9). [21] 赵有璋. 2002. 羊生产学[M]. 北京: 中国农业出版社. (ZHAO Y Z.2002. Sheep Production[M]. China Agriculture Press, Beijing, China.) [22] Amemiya Y, Yang W, Benatar T, et al.2011. Insulin like growthfactor binding protein-7 reduces growth of human breastcancer cells and xenografted tumors[J]. Breast Cancer ResTreat, 126(2) : 373-84. [23] Ben L, Steven L S.2012.Fast gapped-read alignment with Bowtie 2[J]. Nature methods, 9(4): 357-359. [24] Cao Y, Jin H G, Ma H H, et al.2017. Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep[J]. Asian-Australasian Journal of Animal Sciences,(30)11: 1529-1539. [25] Kim D, Pertea G, Trapnell C, et al.2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions[J]. Genome Biology, 14(4): 3-13. [26] Li B, Dewey C N.2011. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome[J]. BMC Bioinformatics, 12(1): 323-323. [27] Miao X Y, Luo Q M, Qin X Y, et al.2015. Genome-wide mRNA-seq profiling reveals predominant down-regulation of lipid metabolic processes in adipose tissues of Small Tail Han than Dorset sheep[J]. Biochemical & Biophysical Research Communications. 467(2): 413-420. [28] Moss J B, Olson E N, Schwartz R J.1996. The myogenic regulatory factor MRF4 represses the cardiac alpha-actin promoter through a negative-acting N-terminal protein domain[J]. The Journal of Biological Chemistry, 271(49): 31688-31694. [29] Pereira R C, Blanquaert F, Canalis E.1999. Cortisol enhances the expression of mac25/insulin-like growth factor-binding protein-related protein-1 in cultured osteoblasts[J]. Endocrinology, 140(140): 228-232. [30] Peter G, Geraldine O, Edna H.2008. Tropomyosin-based regulation of the actin cytoskeleton in time and space[J]. Physiological Reviews, 88(1): 1-35. [31] Rudnicki M A, Jaenisch R.1995. The MyoD family of transcription factors and skeletal myogenesis[J]. BioEssays, 17(3): 203-209. [32] Sun L, Bai M, Xiang L, et al.2016. Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep[J]. Scientific Reports, 6: 33586. [33] Trapnell C, Roberts A, Goff L, et al.2014. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks[J]. Nature Protocols, 7(3): 562. [34] Wang Z, Gerstein M, Snyder M.2010. RNA-Seq: A revolutionary tool for transcriptomics[J]. Nature Reviews Genetics, 10(1): 57-63. [35] Zhang C L, Wang G Z, Wang J M, et al.2013. Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique[J]. PLOS ONE, 8(8): e72686. |
|
|
|