福清山羊与努比亚黑山羊背最长肌比较转录组分析
|
摘要
【目的】研究福清山羊与努比亚黑山羊背最长肌组织转录组差异表达水平,为地方山羊品种肉质、生长性状的遗传机制和遗传改良提供理论基础。【方法】分别测定周岁内羯羊育肥的福清山羊与努比亚黑山羊日增重(ADG)以及2个品种周岁背最长肌样品的肌内脂肪含量(inter-muscular fat,IMF);同时利用转录组测序方法对2个品种周岁背最长肌组织进行高通量测序,筛选品种间的差异表达基因(differentially expressed genes,DEGs),并对DEGs功能进行注释和测序结果的荧光定量PCR(quantitative real-time PCR,qRT-PCR)验证。【结果】在羯羊育肥条件下,福清山羊周岁内ADG为65.6g·d~(-1),极显著低于努比亚黑山羊的127.4g·d~(-1)(Sig.=0.000);而福清山羊周岁背最长肌IMF含量为3.69%,极显著高于努比亚黑山羊的1.83%(Sig.=0.003)。2个品种6个样品的背最长肌转录组测序共得到44.76Gb Clean Data,各样品的Clean reads与参考基因组(山羊)的比对效率在84.65%-86.17%之间。DESeq分析发现了努比亚黑山羊和福清山羊背最长肌的DEGs 608个,其中上调基因61个,下调基因547个。608个DEGs中的518个基因能够被GO(gene ontology)数据库注释,148个DEGs能够被COG(Cluster of Orthologous Groups of proteins)数据库注释,418个DEGs能够被KEGG(kyoto encyclopedia of genes and genomes)数据库注释。KEGG通路分析表明DEGs共富集到222条信号通路中,44条通路显著富集。经过文献检索和对筛选通路相关基因功能的分析,初步判断可能与羊肉质和生长性状相关的通路包括肌动蛋白细胞骨架调节(Regulation of actin cytoskeleton)、Jak-STAT信号转导通路{Janus kinase/signal transducer and activator of transcription(Jak-STAT)signaling pathway}、MAPK信号转导信号通路{mitogen-activated protein kinase(MAPK)signaling pathway}和Ⅰ型糖尿病通路(TypeⅠdiabetes mellitus);IGF1(Insulin-like growth factor 1,类胰岛素一号增长因子)、ACSL5(Long-chain fatty acyl-CoA synthetases 5,长链酯酰辅酶A合成酶5)、PCK2(phosphoenolpyruvate carboxykinase 2,磷酸烯醇丙酮酸羧激酶2)、PPARGC1A(Hepatic peroxisome proliferator-activated receptor gamma,coactivator 1 alpha,过氧化物酶体增殖激活受体γ共激活因子1α)、JAK2(Janus Kinase 2,Janus激酶2基因)、STAT4(signal transducer and activator of transcription 4,信号转导子和转录激活子4)、IRF8(interferon regulatory factor 8,干扰素调节因子8)、MAP4K1(mitogen-activated protein kinase kinase kinase kinase 1,有丝分裂原激活蛋白激激激激酶1)等DEGs可作为控制福清山羊肉质、生长性能的候选基因。进一步与参考基因组序列比对分析,共发掘707个新基因(转录本),其中15个基因(转录本)为2个品种的DEGs。经qRT-PCR验证,所选基因(转录本)表达变化模式与转录组测序结果一致,表明测序结果可靠。【结论】在转录组水平上筛选出了福清山羊和努比亚黑山羊周岁羯羊背最长肌组织的608个DEGs,发掘了707个新基因(转录本),初步认为肌动蛋白细胞骨架调节等4个信号通路在山羊肉质形成和生长发育过程中发挥了重要作用,为进一步探索山羊骨骼肌生长发育和IMF沉积的相关机理提供参考依据。
【Objective】The aim of this study was to analyze the transcriptome differentially genes expression of longissimus doris tissue in Fuqing goat and Nubian Black goat.【Method】Two goat breeds,including Fuqing goat and Nubian Black goat,were used as experimental animal,and fatten of castrated ram were used as experimental samples.We determined the samples’ADG in 12months,and IMF content in longissimus doris tissue at the age of 12 months.Transcriptome sequencing of longissimus doris tissue in Fuqing goat and Nubian Black goat were performed by using the Illumina HiSeq~(TM) 2500 platform with 3 biological replicates per goat breed,and verified by quantitative real-time PCR(qRT-PCR).Differentially expressed genes(DEGs)were selected and enriched based on GO and COG and KEGG database.【Result】By fatten of castrated ram,the ADG of Nubiya Black goats in 12 months was higher that of Fuqing goats(Sig.=0.000).But,the IMF content in longissimus doris tissue of Fuqing goats at age of 12 months was higher than that of Nubiya Black goat(Sig.=0.003).A total of 44.76 Gb clean data were obtained in six samples.We found 608 DEGs between Fuqing goat and Nubian Black goat,including 61 DEGs up-regulated genes and 547 DEGs down-regulated genes.Moreover518 DEGs and 148 DEGs and 418 DEGs were enriched by GO and COG and KEGG database,respectively.KEGG pathway analysis showed that DEGs annotated to 222 metabolic pathways,and 44 pathways were enriched significantly,such as regulation of actin cytoskeleton,and Jak-STAT signaling pathway,and MAPK signaling pathway and TypeⅠdiabetes mellitus associated with meat quality and growth traits in goat.The results showed that 8 DEGs(IGF1,ACSL5,PCK2,PPARGC1A,JAK2,STAT4,IRF8 and MAP4K1)might relate to meat quality and growth traits of goat were screened by GO functional enrichment and KEGG Pathway analysis.In addition,707 new genes or transcripts were found by BLAST,including 15 DEGs between two breeds.By qRT-PCR verification,the pattern of selected genes was consistent with the results of transcriptome sequencing,which showed the sequencing results were reliable.【Conclusion】Totally,608 DEGs and 707 new genes of longissimus doris tissue in Fuqing goat and Nubian Black goat were screened by transcriptional analysis,and revealed that four pathways might play an important role in goat meat quality and growth traits.
【Objective】The aim of this study was to analyze the transcriptome differentially genes expression of longissimus doris tissue in Fuqing goat and Nubian Black goat.【Method】Two goat breeds,including Fuqing goat and Nubian Black goat,were used as experimental animal,and fatten of castrated ram were used as experimental samples.We determined the samples’ADG in 12months,and IMF content in longissimus doris tissue at the age of 12 months.Transcriptome sequencing of longissimus doris tissue in Fuqing goat and Nubian Black goat were performed by using the Illumina HiSeq~(TM) 2500 platform with 3 biological replicates per goat breed,and verified by quantitative real-time PCR(qRT-PCR).Differentially expressed genes(DEGs)were selected and enriched based on GO and COG and KEGG database.【Result】By fatten of castrated ram,the ADG of Nubiya Black goats in 12 months was higher that of Fuqing goats(Sig.=0.000).But,the IMF content in longissimus doris tissue of Fuqing goats at age of 12 months was higher than that of Nubiya Black goat(Sig.=0.003).A total of 44.76 Gb clean data were obtained in six samples.We found 608 DEGs between Fuqing goat and Nubian Black goat,including 61 DEGs up-regulated genes and 547 DEGs down-regulated genes.Moreover518 DEGs and 148 DEGs and 418 DEGs were enriched by GO and COG and KEGG database,respectively.KEGG pathway analysis showed that DEGs annotated to 222 metabolic pathways,and 44 pathways were enriched significantly,such as regulation of actin cytoskeleton,and Jak-STAT signaling pathway,and MAPK signaling pathway and TypeⅠdiabetes mellitus associated with meat quality and growth traits in goat.The results showed that 8 DEGs(IGF1,ACSL5,PCK2,PPARGC1A,JAK2,STAT4,IRF8 and MAP4K1)might relate to meat quality and growth traits of goat were screened by GO functional enrichment and KEGG Pathway analysis.In addition,707 new genes or transcripts were found by BLAST,including 15 DEGs between two breeds.By qRT-PCR verification,the pattern of selected genes was consistent with the results of transcriptome sequencing,which showed the sequencing results were reliable.【Conclusion】Totally,608 DEGs and 707 new genes of longissimus doris tissue in Fuqing goat and Nubian Black goat were screened by transcriptional analysis,and revealed that four pathways might play an important role in goat meat quality and growth traits.
引文
[1]张建,陈伟,张天阳,曾勇庆.猪肉质性状遗传改良研究进展.山东农业大学学报(自然科学版),2012,43(4):641-644.ZHANG J,CHEN W,ZHANG T Y,ZENG Y Q.Research progress on the improvement of meat quality traits in pigs.Journal of Shandong Agricultural University(Natural Science),2012,43(4):641-644.(in Chinese)
[2]国家畜禽遗传资源委员会.中国畜禽遗传资源志-羊志.北京:中国农业出版社,2011.The National Animal Genetic Resources Committee.Animal Genetic Resources in China Sheep and Goat.Beijing:China Agriculture Press,2011.(in Chinese)
[3]王位,付绍印,何小龙,王艳欣,王月星,王标,刘斌,刘永斌,张文广.基于RNA-Seq技术挖掘绵羊背最长肌肉质性状相关基因.中国畜牧兽医,2018,45(1):122-130.WANG W,FU S Y,HE X L,WANG Y X,WANG Y X,WANG B,LIU B,LIU Y B,ZHANG W G.Excavation of meat quality related genes in Longissmus Dorsi of Sheep by RNA-Seq.China Animal Husbandry and Veterinary Medicine,2018,45(1):122-130.(in Chinese)
[4]Valerio C,Claudia A,Italia D F,Alfredo C.Uncovering the complexity of transcriptomes with RNA-Seq.Journal of Biomedicine and Biotechnology,2010,2010:1-19.
[5]WANG Z,GERSTEIN M,SNYDER M.RNA-Seq:a revolutionary tool for transcriptomics.Nature Reviews Genetics,10(1):57-63.
[6]朱志明,陈红萍,林如龙,缪中伟,辛清武,李丽,张丹青,郑嫩珠.山麻鸭开产期和产蛋高峰期卵巢组织转录组分析.中国农业科学,2016,49(5):998-1007.ZHU Z M,CHEN H P,LIN R L,MIAO Z W,XIN Q W,LI L,ZHANG D Q,ZHENG N Z.Transcriptome analysis of ovary tissue in early laying period and egg laying peak period of Shanma ducks.Scientia Agricultura Sinica,2016,49(5):998-1007.(in Chinese)
[7]李丽,缪中伟,辛清武,朱志明,章琳俐,庄晓东,郑嫩珠.半番鸭与番鸭精巢组织差异表达转录组测序分析.中国农业科学,2017,50(18):3608-3619.LI L,MIAO Z W,XIN Q W,ZHU ZM,ZHANG L L,ZHUANG X D,ZHENG N Z.Transcriptome analysis of differentially gene expression associated with testis tissue in mule duck and Muscovy duck.Scientia Agricultura Sinica,2017,50(18):3608-3619.(in Chinese)
[8]字向东,罗斌,夏威,郑玉才,熊显荣,李键,钟金城,朱江江,张正帆.基于RNA-Seq技术的牦牛体外受精胚胎发育转录组分析.中国农业科学,2018,51(8):1577-1589.ZI X D,LUO B,XIA W,ZHENG Y C,XIONG X R,LI J,ZHONG JC,ZHU J J,ZHANG Z F.Transcriptomic analysis of IVF embryonic development in the YAK(Bos grunniens)Via RNA-Seq.Scientia Agricultura Sinica,2018,51(8):1577-1589.(in Chinese)
[9]孟宪然,杜琛,王静,付绍印,郑竹清,张文广,李金泉.基于RNA-Seq识别山羊肉品质候选基因.畜牧兽医学报,2015,46(8):1300-1307.MENG X R,DU C,WANG J,FU S Y,ZHENG Z Q,ZHANG W G,LI J Q.RNA-Seq Approach for identifying candidate genes of meat quality in goats.Acta Veterinaria et Zootechnica Sinica,2015,46(8):1300-1307.(in Chinese)
[10]张春兰.小尾寒羊和杜泊羊臂二头肌转录组及肌球蛋白轻链基因家族结构特征分析[D].泰安:山东农业大学,2014.ZHANG C L.Transcriptome analysis of small-tailed Han sheep and Dorper’s biceps brachii and structure characteristics of myosin light chain gene families[D].Taian:Shandong Agricultural University,2014.(in Chinese)
[11]赵珺.内蒙古绒山羊骨骼肌肌肉差异研究[D].呼和浩特:内蒙古农业大学,2015.ZHAO J.Differentially analysis of Inner Mongolian cashmere skeletal muscle[D].Hohhot:Inner Mongolian Agricultural University,2015.(in Chinese)
[12]陈其新,张建红,宋彦军,董济福.我国主要肉羊品种肉用性能的初步评价.中国草食动物科学,2012(s1):357-362.CHEN Q X,ZHANG J H,SONG Y J,DONG J F.Preliminary evaluation of meat performance of main mutton sheep and goats in China.China Herbivore Science,2012(s1):357-362.(in Chinese)
[13]KIM D,PERTEA G,TRAPNELL C,PIMENTEL H,KELLEY R,SALZBERG S L.TopHat2:accurate alignment of transcriptomes in the presence of insertions,deletions and gene fusions.Genome Biology,2013,14:R36.
[14]DONG Y,XIE M,JIANG Y,XIAO N Q,DU X Y,ZHANG W G,TOSSER-KLOPP G,WANG J H,YANG S,LIANG J,CHEN W B,CHEN J,ZENG P,HOU Y,BIAN C,PAN S K,LI Y X,LIU X,WANG W L,SERVIN B,SAYRE B,ZHU B,SWEENEY D,MOORE R,NIE W H,SHEN Y Y,ZHAO R P,ZHANG G J,LI J Q,FARAUT T,WOMACK J,ZHANG Y P,KIJAS J,COCKETT N,XUX,ZHAO S H,WANG J,WANG W.Sequencing and automated whole-genome optical mapping of the genome of a domestic goat(Capra hircus).Nature Biotechnology,2013,31(2):135-141.
[15]JIANG H,WONG W H.Statistical inferences for isoform expression in RNA-Seq.Bioinformatics,2009,25(8):1026-1032.
[16]FLOREA L,SONG L,SALZBERG S L.Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.F1000 Research,2013,2:188.
[17]WANG L,FENG Z,WANG X,WANG X,ZHANG X.DEGseq:an Rpackage for identifying differentiallyly expressed genes from RNA-seq data.Bioinformatics,2010,26,136-138.
[18]ALEXA A,RAHNENFUHRER J.TopGO:enrichment analysis for gene ontology.R package version 2.8,2010.
[19]TATUSOV R L,GALPERIN M Y,NATALE D A.The COG database:a tool for genome scale analysis of protein functions and evolution.Nucleic Acids Research,2000,28(1):33-36.
[20]KANEHISA M,GOTO S,KAWASHIMA S,OKUNO Y,HATTORIM.The KEGG resource for deciphering the genome.Nucleic Acids Research,2004,32:D277-D280.
[21]张静.巴美肉羊和苏尼特羊Fox01、My HC基因表达规律及对肉质的影响[D].呼和浩特:内蒙古农业大学,2015.ZHANG J.The expression of FoxO1、My HC gene family and its effect on meat quality in Bamei and Sunit Sheep[D].Hohhot:Inner Mongolian Agricultural University,2015.(in Chinese)
[22]沈林園,张顺华,吴泽辉,郑梦月,李学伟,朱砺.骨骼肌卫星细胞对肉品质的影响及其分化调控.遗传,2013,35(9):1081-1086.SHEN L Y,ZHANG S H,WU Z H,ZHENG M Y,LI X W,ZHU L.The influence of satellite cells on meat quality and its differential regulation.Hereditas(Beijing),2013,35(9):1081-1086.(in Chinese)
[23]尹靖东,李德发.猪肉质形成的分子机制与营养调控.动物营养学报,2014,26(10):2979-2985.YIN J D,LI D F.Molecular mechanism underlying meat quality formation and its nutritional regulation in pigs.Chinese Journal of Animal Nutrition,2014,26(10):2979-2985.(in Chinese)
[24]安静.IGF1在绵羊成肌细胞增殖与分化中的作用[D].乌鲁木齐:新疆农业大学,2013.AN J.The role of IGF1 in proliferation and differentiation of sheep myoblast[D].Urumchi:Xinjiang Agricultural University,2013.(in Chinese)
[25]向浩.安徽白山羊卵巢组织差异表达基因的筛选及分析[D].合肥:安徽农业大学,2014.XIANG H.Screening and analysis of differentially expressed genes in ovary of Anhui white goat[D].Hefei:Anhui Agricultural University,2014.(in Chinese)
[26]梁素芸,周正奎,侯水生.基于测序技术的畜禽基因组学研究进展.遗传,2017,39(4):276-292.LIANG S Y,ZHOU Z K,HOU S S.The research progress of farm animal genomics based on sequencing technologies.Hereditas(Beijing),2017,39(4):276-292.(in Chinese)
[27]冯小婷.梅山-大白猪肌肉组织差异表达基因的筛选、鉴定及功能研究[D].武汉:华中农业大学,2011.FENG X T.Screening,identification and function analysis of genes differentially expressed in porcine skeletal muscle between Meishan and Yorkshire pigs[D].Wuhan:Huazhong Agricultural University,2011.(in Chinese)
[28]GAO Y,ZHANG Y H,JIANG H,Xiao S Q,WANG S,MA Q,SUN GJ,LI F J,DENG Q,DAI L S,ZHANG Z H,CUI X S,ZHANG S M,LIU D F,ZHANG J B.Detection of differentially expressed genes in the longissimus dorsi of Northeastern Indigenous and Large White pigs.Genetics and Molecular Research,2011,10(2):779-791.
[29]王颖萍.猪脂肪沉积相关miRNA初步筛选[D].泰安:山东农业大学,2015.WANG Y P.Identification of microRNA related to porcine fat deposition[D].Taian:Shandong Agricultural University,2015.(in Chinese)
[30]XUE Q,ZHANG G,LI T,LING J,ZHANG X,WANG J.Transcriptomic profile of leg muscle during early growth in chicken.PLoS One,2017,12(3):e0173824.
[31]LIU J,FU R Q,LIU R R,ZHAO G P,ZHENG M Q,CUI H X,LI QH,SONG J,WANG J,WEN J.Protein profiles for muscle development and intramuscular fat accumulation at different post-hatching ages in chickens.PLoS One,2016,11(8):e0159722.
[32]ZHANG C,WANG G Z,WANG J M,JI Z B,LIU Z H,PI X S,CHEN C X.Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.PLoS One,2013,8(8):e72686.
[33]PEARSON G,ROBINSON F,BEERS G T,XU B E,KARANDIKARM,BERMAN K,COBB M H.Mitogen-activated protein(MAP)kinase pathways:regulation and physiological functions.Endocrine Reviews,2001,22(2):153-183.
[34]PERDIGUERO E,RUIZ-BONILLA V,GRESH L,HUI L,BALLESTAR E,SOUSA-VICTOR P,BAEZA-RAJA B,JARDI M,BOSCH-COMAS A,ESTELLER M,CAELLES C,SERRANO A L,WAGNER E F,MUNOZ-CANOVES P.Genetic analysis of p38 MAPkinases in myogenesis:fundamental role of p38alpha in abrogating myoblast proliferation.EMBO Journal,2007,26(5):1245-1256.
[35]STRLE K,BROUSSARD S R,MCCUSKER R H,SHEN W H,LECLEIR J M,JOHNSON R W,FREUND G G,DANTZER R,KELLEY K W.C-jun N-terminal kinase mediates tumor necrosis factor-alpha suppression of differentiation in myoblasts.Endocrinology,2006,147(9):4363-4373.
[36]HUANG Z,CHEN D,ZHANG K,YU B,CHEN X,MENG J.Regulation of myostatin signaling by c-Jun N-terminal kinase in C2C12 cells.Cell Signaling Technology,2007,19(11):2286-2295.
[37]YANG W,CHEN Y,ZHANG Y,WANG X,YANG N,ZHU D.Extracellular signal-regulated kinase 1/2 mitogen-activated protein kinase pathway is involved in myostatin-regulated differentiation repression.Cancer Research,2006,66(3):1320-1326.
[38]HOU X,TANG Z,LIU H,WANG N,JU H,LI K.Discovery of MicroRNAs associated with myogenesis by deep sequencing of serial developmental skeletal muscles in pigs.PLoS One,2012,7(12):e52123.
[39]LUO W,LIN S M,LI G H,NIE Q H,ZHANG X Q.Integrative analyses of miRNA-mRNA interactions reveal let-7b,miR-128 and MAPK Pathway Involvement in muscle mass loss in sex-linked dwarf chickens.International Journal of Molecular Sciences,2016,17:276.
[40]DURONIO V,SCHEID M P,ETTINGER S.Downstream signalling events regulated by phosphatidylinositol 3-kinase activity.Cell Signaling Technology,1998,10(4):233-239.
[2]国家畜禽遗传资源委员会.中国畜禽遗传资源志-羊志.北京:中国农业出版社,2011.The National Animal Genetic Resources Committee.Animal Genetic Resources in China Sheep and Goat.Beijing:China Agriculture Press,2011.(in Chinese)
[3]王位,付绍印,何小龙,王艳欣,王月星,王标,刘斌,刘永斌,张文广.基于RNA-Seq技术挖掘绵羊背最长肌肉质性状相关基因.中国畜牧兽医,2018,45(1):122-130.WANG W,FU S Y,HE X L,WANG Y X,WANG Y X,WANG B,LIU B,LIU Y B,ZHANG W G.Excavation of meat quality related genes in Longissmus Dorsi of Sheep by RNA-Seq.China Animal Husbandry and Veterinary Medicine,2018,45(1):122-130.(in Chinese)
[4]Valerio C,Claudia A,Italia D F,Alfredo C.Uncovering the complexity of transcriptomes with RNA-Seq.Journal of Biomedicine and Biotechnology,2010,2010:1-19.
[5]WANG Z,GERSTEIN M,SNYDER M.RNA-Seq:a revolutionary tool for transcriptomics.Nature Reviews Genetics,10(1):57-63.
[6]朱志明,陈红萍,林如龙,缪中伟,辛清武,李丽,张丹青,郑嫩珠.山麻鸭开产期和产蛋高峰期卵巢组织转录组分析.中国农业科学,2016,49(5):998-1007.ZHU Z M,CHEN H P,LIN R L,MIAO Z W,XIN Q W,LI L,ZHANG D Q,ZHENG N Z.Transcriptome analysis of ovary tissue in early laying period and egg laying peak period of Shanma ducks.Scientia Agricultura Sinica,2016,49(5):998-1007.(in Chinese)
[7]李丽,缪中伟,辛清武,朱志明,章琳俐,庄晓东,郑嫩珠.半番鸭与番鸭精巢组织差异表达转录组测序分析.中国农业科学,2017,50(18):3608-3619.LI L,MIAO Z W,XIN Q W,ZHU ZM,ZHANG L L,ZHUANG X D,ZHENG N Z.Transcriptome analysis of differentially gene expression associated with testis tissue in mule duck and Muscovy duck.Scientia Agricultura Sinica,2017,50(18):3608-3619.(in Chinese)
[8]字向东,罗斌,夏威,郑玉才,熊显荣,李键,钟金城,朱江江,张正帆.基于RNA-Seq技术的牦牛体外受精胚胎发育转录组分析.中国农业科学,2018,51(8):1577-1589.ZI X D,LUO B,XIA W,ZHENG Y C,XIONG X R,LI J,ZHONG JC,ZHU J J,ZHANG Z F.Transcriptomic analysis of IVF embryonic development in the YAK(Bos grunniens)Via RNA-Seq.Scientia Agricultura Sinica,2018,51(8):1577-1589.(in Chinese)
[9]孟宪然,杜琛,王静,付绍印,郑竹清,张文广,李金泉.基于RNA-Seq识别山羊肉品质候选基因.畜牧兽医学报,2015,46(8):1300-1307.MENG X R,DU C,WANG J,FU S Y,ZHENG Z Q,ZHANG W G,LI J Q.RNA-Seq Approach for identifying candidate genes of meat quality in goats.Acta Veterinaria et Zootechnica Sinica,2015,46(8):1300-1307.(in Chinese)
[10]张春兰.小尾寒羊和杜泊羊臂二头肌转录组及肌球蛋白轻链基因家族结构特征分析[D].泰安:山东农业大学,2014.ZHANG C L.Transcriptome analysis of small-tailed Han sheep and Dorper’s biceps brachii and structure characteristics of myosin light chain gene families[D].Taian:Shandong Agricultural University,2014.(in Chinese)
[11]赵珺.内蒙古绒山羊骨骼肌肌肉差异研究[D].呼和浩特:内蒙古农业大学,2015.ZHAO J.Differentially analysis of Inner Mongolian cashmere skeletal muscle[D].Hohhot:Inner Mongolian Agricultural University,2015.(in Chinese)
[12]陈其新,张建红,宋彦军,董济福.我国主要肉羊品种肉用性能的初步评价.中国草食动物科学,2012(s1):357-362.CHEN Q X,ZHANG J H,SONG Y J,DONG J F.Preliminary evaluation of meat performance of main mutton sheep and goats in China.China Herbivore Science,2012(s1):357-362.(in Chinese)
[13]KIM D,PERTEA G,TRAPNELL C,PIMENTEL H,KELLEY R,SALZBERG S L.TopHat2:accurate alignment of transcriptomes in the presence of insertions,deletions and gene fusions.Genome Biology,2013,14:R36.
[14]DONG Y,XIE M,JIANG Y,XIAO N Q,DU X Y,ZHANG W G,TOSSER-KLOPP G,WANG J H,YANG S,LIANG J,CHEN W B,CHEN J,ZENG P,HOU Y,BIAN C,PAN S K,LI Y X,LIU X,WANG W L,SERVIN B,SAYRE B,ZHU B,SWEENEY D,MOORE R,NIE W H,SHEN Y Y,ZHAO R P,ZHANG G J,LI J Q,FARAUT T,WOMACK J,ZHANG Y P,KIJAS J,COCKETT N,XUX,ZHAO S H,WANG J,WANG W.Sequencing and automated whole-genome optical mapping of the genome of a domestic goat(Capra hircus).Nature Biotechnology,2013,31(2):135-141.
[15]JIANG H,WONG W H.Statistical inferences for isoform expression in RNA-Seq.Bioinformatics,2009,25(8):1026-1032.
[16]FLOREA L,SONG L,SALZBERG S L.Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.F1000 Research,2013,2:188.
[17]WANG L,FENG Z,WANG X,WANG X,ZHANG X.DEGseq:an Rpackage for identifying differentiallyly expressed genes from RNA-seq data.Bioinformatics,2010,26,136-138.
[18]ALEXA A,RAHNENFUHRER J.TopGO:enrichment analysis for gene ontology.R package version 2.8,2010.
[19]TATUSOV R L,GALPERIN M Y,NATALE D A.The COG database:a tool for genome scale analysis of protein functions and evolution.Nucleic Acids Research,2000,28(1):33-36.
[20]KANEHISA M,GOTO S,KAWASHIMA S,OKUNO Y,HATTORIM.The KEGG resource for deciphering the genome.Nucleic Acids Research,2004,32:D277-D280.
[21]张静.巴美肉羊和苏尼特羊Fox01、My HC基因表达规律及对肉质的影响[D].呼和浩特:内蒙古农业大学,2015.ZHANG J.The expression of FoxO1、My HC gene family and its effect on meat quality in Bamei and Sunit Sheep[D].Hohhot:Inner Mongolian Agricultural University,2015.(in Chinese)
[22]沈林園,张顺华,吴泽辉,郑梦月,李学伟,朱砺.骨骼肌卫星细胞对肉品质的影响及其分化调控.遗传,2013,35(9):1081-1086.SHEN L Y,ZHANG S H,WU Z H,ZHENG M Y,LI X W,ZHU L.The influence of satellite cells on meat quality and its differential regulation.Hereditas(Beijing),2013,35(9):1081-1086.(in Chinese)
[23]尹靖东,李德发.猪肉质形成的分子机制与营养调控.动物营养学报,2014,26(10):2979-2985.YIN J D,LI D F.Molecular mechanism underlying meat quality formation and its nutritional regulation in pigs.Chinese Journal of Animal Nutrition,2014,26(10):2979-2985.(in Chinese)
[24]安静.IGF1在绵羊成肌细胞增殖与分化中的作用[D].乌鲁木齐:新疆农业大学,2013.AN J.The role of IGF1 in proliferation and differentiation of sheep myoblast[D].Urumchi:Xinjiang Agricultural University,2013.(in Chinese)
[25]向浩.安徽白山羊卵巢组织差异表达基因的筛选及分析[D].合肥:安徽农业大学,2014.XIANG H.Screening and analysis of differentially expressed genes in ovary of Anhui white goat[D].Hefei:Anhui Agricultural University,2014.(in Chinese)
[26]梁素芸,周正奎,侯水生.基于测序技术的畜禽基因组学研究进展.遗传,2017,39(4):276-292.LIANG S Y,ZHOU Z K,HOU S S.The research progress of farm animal genomics based on sequencing technologies.Hereditas(Beijing),2017,39(4):276-292.(in Chinese)
[27]冯小婷.梅山-大白猪肌肉组织差异表达基因的筛选、鉴定及功能研究[D].武汉:华中农业大学,2011.FENG X T.Screening,identification and function analysis of genes differentially expressed in porcine skeletal muscle between Meishan and Yorkshire pigs[D].Wuhan:Huazhong Agricultural University,2011.(in Chinese)
[28]GAO Y,ZHANG Y H,JIANG H,Xiao S Q,WANG S,MA Q,SUN GJ,LI F J,DENG Q,DAI L S,ZHANG Z H,CUI X S,ZHANG S M,LIU D F,ZHANG J B.Detection of differentially expressed genes in the longissimus dorsi of Northeastern Indigenous and Large White pigs.Genetics and Molecular Research,2011,10(2):779-791.
[29]王颖萍.猪脂肪沉积相关miRNA初步筛选[D].泰安:山东农业大学,2015.WANG Y P.Identification of microRNA related to porcine fat deposition[D].Taian:Shandong Agricultural University,2015.(in Chinese)
[30]XUE Q,ZHANG G,LI T,LING J,ZHANG X,WANG J.Transcriptomic profile of leg muscle during early growth in chicken.PLoS One,2017,12(3):e0173824.
[31]LIU J,FU R Q,LIU R R,ZHAO G P,ZHENG M Q,CUI H X,LI QH,SONG J,WANG J,WEN J.Protein profiles for muscle development and intramuscular fat accumulation at different post-hatching ages in chickens.PLoS One,2016,11(8):e0159722.
[32]ZHANG C,WANG G Z,WANG J M,JI Z B,LIU Z H,PI X S,CHEN C X.Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.PLoS One,2013,8(8):e72686.
[33]PEARSON G,ROBINSON F,BEERS G T,XU B E,KARANDIKARM,BERMAN K,COBB M H.Mitogen-activated protein(MAP)kinase pathways:regulation and physiological functions.Endocrine Reviews,2001,22(2):153-183.
[34]PERDIGUERO E,RUIZ-BONILLA V,GRESH L,HUI L,BALLESTAR E,SOUSA-VICTOR P,BAEZA-RAJA B,JARDI M,BOSCH-COMAS A,ESTELLER M,CAELLES C,SERRANO A L,WAGNER E F,MUNOZ-CANOVES P.Genetic analysis of p38 MAPkinases in myogenesis:fundamental role of p38alpha in abrogating myoblast proliferation.EMBO Journal,2007,26(5):1245-1256.
[35]STRLE K,BROUSSARD S R,MCCUSKER R H,SHEN W H,LECLEIR J M,JOHNSON R W,FREUND G G,DANTZER R,KELLEY K W.C-jun N-terminal kinase mediates tumor necrosis factor-alpha suppression of differentiation in myoblasts.Endocrinology,2006,147(9):4363-4373.
[36]HUANG Z,CHEN D,ZHANG K,YU B,CHEN X,MENG J.Regulation of myostatin signaling by c-Jun N-terminal kinase in C2C12 cells.Cell Signaling Technology,2007,19(11):2286-2295.
[37]YANG W,CHEN Y,ZHANG Y,WANG X,YANG N,ZHU D.Extracellular signal-regulated kinase 1/2 mitogen-activated protein kinase pathway is involved in myostatin-regulated differentiation repression.Cancer Research,2006,66(3):1320-1326.
[38]HOU X,TANG Z,LIU H,WANG N,JU H,LI K.Discovery of MicroRNAs associated with myogenesis by deep sequencing of serial developmental skeletal muscles in pigs.PLoS One,2012,7(12):e52123.
[39]LUO W,LIN S M,LI G H,NIE Q H,ZHANG X Q.Integrative analyses of miRNA-mRNA interactions reveal let-7b,miR-128 and MAPK Pathway Involvement in muscle mass loss in sex-linked dwarf chickens.International Journal of Molecular Sciences,2016,17:276.
[40]DURONIO V,SCHEID M P,ETTINGER S.Downstream signalling events regulated by phosphatidylinositol 3-kinase activity.Cell Signaling Technology,1998,10(4):233-239.