3种白鲫杂交子代的转录组学分析
|
摘要
【目的】研究3种白鲫杂交子代转录组学特征,为揭示鲫鲤杂交优势的分子机理提供理论依据,同时为在生产上培育出生长速度快、肉质好、适应能力强的杂交品种提供技术参考。【方法】以白鲫(♀)×黑龙江野鲤(♂)杂交子代(简称HB)、白鲫(♀)×散鳞镜鲤(♂)杂交子代(简称SB)和白鲫(♀)×兴国红鲤(♂)杂交子代(简称XB)为研究对象,利用RNA-seq高通量测序技术构建3种白鲫杂交子代转录组文库,以HiSeq PE150进行测序分析,原始序列经Trinity组装后进行功能注释(E-value<1e-5);以DESeq2 R鉴定差异表达基因,利用GOseq R和KOBAS分别对差异表达的基因进行GO和KEGG富集分析;并采用MicroSAtellite对转录本中的SSR位点进行挖掘。【结果】共组装得225858条unigenes,平均长度为668 bp,N50为938 bp,有171461条unigenes可注释到蛋白质数据库(Nr)、非冗余核苷酸数据库(Nt)、蛋白质序列数据库(SwissPort)、基因本体论(GO)、直系同源基因簇(COG/KOG)和京都基因与基因组百科全书(KEGG)数据库中,注释比例为75.92%。其中,52630条unigenes注释到NR数据库,43659条unigenes注释到SwissPort数据库,35756条unigenes注释到COG/KOG数据库,包括生化代谢、信号转导机制、防御系统和细胞结构等。差异表达基因KEGG分析结果显示,较多的差异表达基因注释到内吞作用、Jak-STAT信号通路、溶酶体、吞噬体和Wnt信号通路等免疫相关及与生长发育相关的MAPK信号通路、Hippo信号通路和背腹轴形成等通路中。此外,从获得的转录组序列中共鉴定出20272个SSR位点,大多数为二核苷酸重复基元(占62.15%)。【结论】不同白鲫杂交子代间存在较多的差异表达基因,从中获得参与抗氧化、免疫和生长发育相关的通路和基因序列,且挖掘出20272个SSR位点,有助于选择性育种、分子标记开发及开展遗传多样性、遗传图谱构建和QTL定位等研究。
【Objective】Transcriptomics characteristics of three Carassius auratus cuvieri hybrids were studied to provide reference for molecular mechanism of hybrid heterosis of the hybrids,and also to offer technical support for breeding hybrids with rapid growth,quality meat and strong adaptability.【Method】Three white crucian carp hybrids i.e. C. auratus cuvier(i♀)×Cyprinus carpio haermatopterus(♂)(abbreviated as HB),C. auratus cuvier(i♀)×C. carpio L(.♂)(abbreviated as SB)and C. auratus cuvier(i♀)×C. carpio var. singuonensis(♂)(abbreviated as XB)were used as research objectives.RNA-seq high-throughput sequencing was used to construct C. auratus cuvieri hybrids transcriptome library. HiSeq PE150 was used to conduct sequencing analysis,and the function annotation on original sequence after Trinity assembling was carried out(E-value<1 e-5). Differentially expressed genes was identified by DESeq2 R,then GO and KEGG enrichment analysis of differentially expressed genes were conducted by GOseq R and KOBAS respectively. MicroSAtellite was used to dig SSR loci in transcript.【Result】A total of 225858 unigenes,with average length of 668 bp and N50 of 938 bp were generated. Of these,a total of 171461 unigenes could be annotated in protein sequence database(Nr),non-redundant nucleotide database(Nt),protein sequence database(SwissProt),Gene Ontology database(GO),Clusters of Orthologous Groups(COG/KOG)and Kyoto Encyclopedia of Genes and Genomes(KEGG)database. The annotation ratio was75.92%. There were 52630 unigenes annotated in NR database,43659 unigenes annotated in SwissPort database,35756 unigenes annotated in COG/KOG database,including biochemical metabolism,signal transduction mechanism,defensive system and cell structure. KEGG analysis of differentially expressed genes showed that more differentially expressed genes were involved in immune-related pathways such as endocytosis,Jak-STAT signaling pathway,lysosome,phagosome and Wnt signaling pathways,and growth and development related pathways such as MAPK signaling pathway,Hip-po signaling pathway and dorso-ventral axis formation. In addition,20272 SSR loci were identified from transcriptome sequence and majority of which were dinucleotide repeats units(accounted for 62.15%).【Conclusion】There are many differentially expressed genes in different hybrids. Some pathways and gene sequences involved in antioxidation,immunity,growth and development are preliminarily obtained. A total of 20272 SSR loci are dug. This result is helpful for selective breeding,molecular markers development,researches in genetic diversity,genetic map construction and QTL mapping.
【Objective】Transcriptomics characteristics of three Carassius auratus cuvieri hybrids were studied to provide reference for molecular mechanism of hybrid heterosis of the hybrids,and also to offer technical support for breeding hybrids with rapid growth,quality meat and strong adaptability.【Method】Three white crucian carp hybrids i.e. C. auratus cuvier(i♀)×Cyprinus carpio haermatopterus(♂)(abbreviated as HB),C. auratus cuvier(i♀)×C. carpio L(.♂)(abbreviated as SB)and C. auratus cuvier(i♀)×C. carpio var. singuonensis(♂)(abbreviated as XB)were used as research objectives.RNA-seq high-throughput sequencing was used to construct C. auratus cuvieri hybrids transcriptome library. HiSeq PE150 was used to conduct sequencing analysis,and the function annotation on original sequence after Trinity assembling was carried out(E-value<1 e-5). Differentially expressed genes was identified by DESeq2 R,then GO and KEGG enrichment analysis of differentially expressed genes were conducted by GOseq R and KOBAS respectively. MicroSAtellite was used to dig SSR loci in transcript.【Result】A total of 225858 unigenes,with average length of 668 bp and N50 of 938 bp were generated. Of these,a total of 171461 unigenes could be annotated in protein sequence database(Nr),non-redundant nucleotide database(Nt),protein sequence database(SwissProt),Gene Ontology database(GO),Clusters of Orthologous Groups(COG/KOG)and Kyoto Encyclopedia of Genes and Genomes(KEGG)database. The annotation ratio was75.92%. There were 52630 unigenes annotated in NR database,43659 unigenes annotated in SwissPort database,35756 unigenes annotated in COG/KOG database,including biochemical metabolism,signal transduction mechanism,defensive system and cell structure. KEGG analysis of differentially expressed genes showed that more differentially expressed genes were involved in immune-related pathways such as endocytosis,Jak-STAT signaling pathway,lysosome,phagosome and Wnt signaling pathways,and growth and development related pathways such as MAPK signaling pathway,Hip-po signaling pathway and dorso-ventral axis formation. In addition,20272 SSR loci were identified from transcriptome sequence and majority of which were dinucleotide repeats units(accounted for 62.15%).【Conclusion】There are many differentially expressed genes in different hybrids. Some pathways and gene sequences involved in antioxidation,immunity,growth and development are preliminarily obtained. A total of 20272 SSR loci are dug. This result is helpful for selective breeding,molecular markers development,researches in genetic diversity,genetic map construction and QTL mapping.
引文
陈春林,田易萍,陈林波,邓少春,徐丕忠,李朝云.2018.基于荧光标记的紫娟茶树转录组EST-SSR标记开发[J].江苏农业学报,34(4):747-753.[Chen C L,Tian Y P,Chen LB,Deng S C,Xu P Z,Li C Y.2018.EST-SSR marker development of Zijuan tea tree transcriptome based on the fluorescent labeling[J].Jiangsu Journal of Agricultural Sciences,34(4):747-753.]
李冰冰,赵振利,邓敏捷,曹亚兵,董焱鹏,范国强.2017.盐胁迫对南方泡桐基因表达的影响[J].河南农业大学学报,51(4):471-480.[Li B B,Zhao Z L,Deng M J,Cao YB,Dong Y P,Fan G Q.2017.Effect of salt stress on gene expressions of different genotypes of Paulownia australis[J].Journal of Henan Agricultural University,51(4):471-480.]
李盛文,贾智英,柏盈盈,李池陶,石连玉.2014.散鳞镜鲤两个保种群体的遗传多样性[J].水产学杂志,27(2):1-8.[Li S W,Jia Z Y,Bai Y Y,Li C T,Shi L Y.2014.Microsatellite marker analysis of genetic diversity in two scattered scale mirror carp populations[J].Chinese Journal of Fisheries,27(2):1-8.]
刘义新,肖祖国,徐振秋.2007.几种杂交鲤的形态学特征及主要经济性状[J].水产科学,26(11):619-621.[Liu Y X,Xiao Z G,Xu Z Q.2007.Morphological and main economic characteristics of several common carp(Cyprinus carpio L.)hybrids[J].Fisheries Science,26(11):619-621.]
楼允东.1999.我国鱼类育种研究五十年回顾[J].淡水渔业,29(9):1-3.[Lou Y D.1999.Review of fish breeding research in China in the past fifty years[J].Freshwater Fisheries,29(9):1-3.]
孙颖.2016.棕点石斑鱼(♀)×鞍带石斑鱼(♂)杂交F1代生长优势的转录组学研究[D].广州:中山大学.[Sun Y.2016.Transcriptomic studies on the growth superiorities in grouper hybrid(Epinephelus fuscogutatus♀)×(Epinephelus lanceolatus♂)[D].Guangzhou:Sun Yat-sen University.]
唐玉娟,黄国弟,罗世杏,周俊岸,莫永龙,李日旺,赵英,张宇,宋恩亮,宁琳.2018.芒果2个不同花芽分化时期转录组分析[J].南方农业学报,49(7):1257-1264.[Tang YJ,Huang G D,Luo S X,Zhou J A,Mo Y L,Li R W,Zhao Y,Zhang Y,Song E L,Ning L.2018.Transcriptome of Mangifera indica L.in two different flower bud differentiation stages[J].Journal of Southern Agriculture,49(7):1257-1264.]
王静,肖军,曾鸣,徐康,陶敏,张纯,段巍,刘文彬,罗凯坤,刘筠,刘少军.2015.白鲫×红鲫杂交后代的遗传变异[J].中国科学:生命科学,45(4):371-380.[Wang J,Xiao J,Zeng M,Xu K,Tao M,Zhang C,Duan W,Liu W B,Luo K K,Liu Y,Liu S J.2015.Genomic variation in the hybrids of white crucian carp and red crucian carp[J].Scientia Sinica(Vitae),45(4):371-380.]
武耀,贾智英,李池陶,葛会争,石连玉.2012.筛选杂交鲤亲子鉴定的微卫星标记(英文)[J].农业生物技术学报,20(5):549-559.[Wu Y,Jia Z Y,Li C T,Ge H Z,Shi L Y.2012.Microsatellite markers for parentage identification of cross-breeding carp(Cyprinus carpio)in a selective breeding programme[J].Journal of Agricultural Biotechnology,20(5):549-559.]
岳华梅,翟晴,宋明月,叶欢,杨晓鸽,李创举.2016.基于转录组测序的兴国红鲤微卫星标记筛选[J].淡水渔业,46(1):24-28.[Yue H M,Zhai Q,Song M Y,Ye H,Yang X G,Li C J.2016.Development of microsatellite markers in Cyprinus carpio var.singuonensis using next-generation sequencing[J].Freshwater Fisheries,46(1):24-28.]
朱健,柴学森,李冰,张成锋.2014.建鲤和黑龙江野鲤自交以及正反交子代生长比较[J].渔业科学进展,35(2):35-41.[Zhu J,Chai X S,Li B,Zhang C F.2014.Growth comparison of inbreeds of Cyprinus carpio var.Jian,Cyprinus carpio haermatopterus and the reciprocal F1hybrid[J].Progress in Fishery Sciences,35(2):35-41.]
朱健,王建新,龚永生,郁桐炳.2000.我国鲤鱼遗传改良研究概况[J].浙江海洋学院学报(自然科学版),19(3):266-271.[Zhu J,Wang J X,Gong Y S,Yu T B.2000.An introduction to the studies on common carp genetic improvement in China[J].Journal of Zhejiang Ocean University(Natural Science),19(3):266-271.]
Arcella T E,Perry W L,Lodge D M,Feder J L.2014.The role of hybridization in a species invasion and extirpation of resident fauna:Hybrid vigor and breakdown in the rusty crayfish,Orconectes Rusticus[J].Journal of Crustacean Biology,34(2):157-164.
Bougas B,Granier S,Audet C,Bernatchez L.2010.The transcriptional landscape of cross-specific hybrids and its possible link with growth in brook charr(Salvelinus fontinalis Mitchill)[J].Genetics,186(1):97-107.
Chen X,Mei J,Wu J,Jing J,Ma W,Zhang J,Dan C,Wang W,Gui J.2015.A comprehensive transcriptome provides candidate genes for sex determination/differentiation and SSR/SNP markers in yellow catfish[J].Marine Biotechnology,17(2):190-198.
Davey J W,Hohenlohe P A,Etter P D,Boone J Q,Catchen JM,Blaxter M L.2011.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J].Nature Reviews Genetics,12:499-510.
Firdaus R F,S L L,Kawamura G,Shapawi R.2016.Assessment on the acceptability of hybrid grouper,Epinephelus fuscoguttatus♀×Epinephelus lanceolatus♂to soybean meal-based diets[J].AACL Bioflux,9(2):284-290.
Fu B D,He S P.2012.Transcriptome analysis of silver carp(Hypophthalmichthys molitrix)by paired-end RNA sequencing[J].DNA Research,19(2):131-142.
Gao B Q,Liu P,Li J,Wang Q Y,Li X P.2014.Genetic diversity of different populations and improved growth in the F1hybrids in the swimming crab(Portunus trituberculatus)[J].Genetics&Molecular Research,13(4):10454-10463.
Gao Y,Zhang H,Gao Q,Wang L L,Zhang F C,Siva V S,Zhou Z,Song L S,Zhang S.2013.Transcriptome analysis of artificial hybrid pufferfish Jiyan-1 and its parental species:Implications for pufferfish heterosis[J].PLoS One,8(3):e58453.
Huang Q,Dong S,Fang C,Wu X,Ye T,Lin Y.2012.Deep sequencing-based transcriptome profiling analysis of Oryzias melastigma exposed to PFOS[J].Aquatic Toxicology,120-121:54-58.doi:10.1016/j.aquatox.2012.04.013.
Ji P F,Liu G M,Xu J,Wang X M,Li J T,Zhao Z X,Zhang X F,Zhang Y,Xu P,Sun X W.2012.Characterization of common carp transcriptome:Sequencing,de Novo assembly,annotation and comparative genomics[J].PLoS One,7(4):e35152.
Jia Z Y,Shi L Y,Liu X F,Sun X W.2008.The genetic diversity of diploid and triploid crucian carp from six populations in Heilongjiang River System[J].Hereditas,30(11):1459-1465.
Jin J J,Sun Y W,Qu J,Syah R,Lim C H,Alfiko Y,Rahman N,Suwanto A,Yue G,Wong L,Chua N H,Ye J.2017.Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm[J].Scientific Reports,7(1):439.doi:10.1038/s41598-017-00438-8.
Li B,Dewey C N.2011.RSEM:Accurate transcript quantification from RNA-seq data with or without a reference genome[J].BMC Bioinformatics,12:323.doi:10.1186/1471-2105-12-323.
Li C,Zhang Y,Wang R,Lu J,Nandi S,Mohanty S,Terhune J,Liu Z,Peatman E.2012.RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish,Ictalurus punctatus[J].Fish&Shellfish Immunology,32(5):816-827.
Li F B,Gui J F.2007.Clonal diversity and genealogical relationships of gibel carp in four hatcheries[J].Animal Genetics,39(1):28-33.
Li J Q,Wang M L,Fang J G,Liu X,Mao Y Z,Liu G M,Bian D P.2017.Reproductive performance of one-yearold Pacific abalone(Haliotis discus hannai)and its crossbreeding effect on offspring growth and survival[J].Aquaculture,473:110-114.
Liao X,Cheng L,Xu P,Lu G,Wachholtz M,Sun X,Chen S.2013.Transcriptome analysis of crucian carp(Carassius auratus),an important aquaculture and hypoxia-tolerant species[J].PLoS One,8(4):e62308.
Liu Q,Qi Y,Liang Q,Xu X,Hu F,Wang J,Xiao J,Wang S,Li W,Tao M,Qin Q,Zhao R,Yao Z,Liu S.2018.The chimeric genes in the hybrid lineage of Carassius auratus cuvieri(♀)×Carassius auratus red var.(♂)[J].Science China.Life Sciences,61(9):1079-1089.
Liu X J,Liang H W,Li Z,Liang Y J,Lu C,Li C,Chang Y,Zou G,Hu G.2017.Performances of the hybrid between CyCa nucleocytplasmic hybrid fish and scattered mirror carp in different culture environments[J].Scientific Reports,7:46329.doi:10.1038/srep46329.
Liu Y F,Ma D Y,Zhao C Y,Wang W Q,Zhang X L,Liu X,Liu Y,Xiao Z Z,Xu S H,Xiao Y S,Liu Q H,Li J.2014.Histological and enzymatic responses of Japanese flounder(Paralichthys olivaceus)and its hybrids(P.olivaceus♀×P.dentatus♂)to chronic heat stress[J].Fish Physiology and Biochemistry,40(4):1031-1041.
Mao X Z,Cai T,Olyarchuk J G,Wei L.2005.Automated genome annotation and pathway identification using the KEGG Orthology(KO)as a controlled vocabulary[J].Bioinformatics,21(19):3787-3793.
Rauw W.2012.Immune response from a resource allocation perspective[J].Frontiers in Genetics,3:267.doi:10.3389/fgene.2012.00267.
Schaeffer H J,Weber M J.1999.Mitogen-activated protein kinases:Specific messages from ubiquitous messengers[J].Molecular and Cellular Biology,19(4):2435-2444.
Sinhorin V D G,Sinhorin A P,Teixeira J M D S,Miléski KM L,Hansen P C,Moreira P S A,Kawashita N H,Baviera A M,Loro V L.2014.Effects of the acute exposition to glyphosate-based herbicide on oxidative stress parameters and antioxidant responses in a hybrid Amazon fish surubim(Pseudoplatystoma sp)[J].Ecotoxicology and Environmental Safety,106:181-187.
Tian C X,Liang X F,Yang M,Dou Y Q,Zheng H Z,Cao L,Yuan Y C,Zhao C.2014.New microsatellite loci for the mandarin fish Siniperca chuatsi and their application in population genetic analysis[J].Genetics and Molecular Research,13(1):546-558.
Wang Z W,Zhu H P,Wang D,Jiang F F,Guo W,Zhou L,Gui J F.2011.A novel nucleo-cytoplasmic hybrid clone formed via androgenesis in polyploid gibel carp[J].BMCResearch Notes,4(1):82.doi:10.1186/1756-0500-4-82.
Xiao T Q,Lu C Y,Xu Y L,Li C,Zheng X H,Cao D C,Cheng L,Mahboob S,Sun X.2015.Screening of SSRmarkers associated with scale cover pattern and mapped to a genetic linkage map of common carp(Cyprinus carpio L.)[J].Journal of Applied Genetics,56(2):261-269.
Yan L L,Su J Q,Wang Z P,Yan X W,Yu R H,Ma P,Li Y,Du J.2017.Transcriptomic analysis of Crassostrea sikamea×Crassostrea angulata hybrids in response to low salinity stress[J].PLoS One,12(2):e0171483.
Young M D,Wakefield M J,Smyth G K,Oshlack A.2010.Gene ontology analysis for RNA-seq:Accounting for selection bias[J].Genome Biology,11(2):R14.doi:10.1186/gb-2010-11-2-r14.
Yu F X,Zhao B,Panupinthu N,Jewell J L,Lian I,Wang L H,Zhao J,Yuan H,Tumaneng K,Li H,Fu X D,Mills G B,Guan K L.2012.Regulation of the Hippo-YAP pathway by G-protein-coupled receptor signaling[J].Cell,150(4):780-791.
Zhai R R,Feng Y,Wang H M,Zhan X D,Shen X,Wu W,Zhang Y,Chen D,Dai G,Yang Z,Cao L,Cheng S.2013.Transcriptome analysis of rice root heterosis by RNA-seq[J].BMC Genomics,14:19.doi:10.1186/1471-2164-14-19.
Zhang C B,Lin C J,Fu F Y,Zhong X,Peng B,Yan H,Zhang J,Zhang W,Wang P,Ding X,Zhang W,Zhao L.2017a.Comparative transcriptome analysis of flower heterosis in two soybean F1hybrids by RNA-seq[J].PLoS One,12(7):e0181061.
Zhang H,Xu X,He Z,Zheng T,Shao J.2017b.De novo transcriptome analysis reveals insights into different mechanisms of growth and immunity in a Chinese soft-shelled turtle hybrid and the parental varieties[J].Gene,605:54-62.
Zhang Y Q,Liu J H,Fu W,Xu W T,Zhang H,Chen S,Liu W,Peng L,Xiao Y.2017c.Comparative transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in crucian carp(Carassius carassius L.)[J].BMC Genetics,18(1):95.doi:10.1186/s12863-017-0564-9.
Zhang Z H,Chen J,Ling L I,Tao M,Zhang C,Qin Q B,Xiao J,Liu Y,Liu S J.2014.Research advances in animal distant hybridization[J].Science China.Life Sciences,57(9):889-902.
Zhou Z C,Dong Y,Sun H J,Yang A F,Chen Z,Gao S,Jiang J W,Guan X Y,Jiang B,Wang B.2013.Transcriptome sequencing of sea cucumber(Apostichopus japonicus)and the identification of gene-associated markers[J].Molecular Ecology Resources,14(1):127-138.
李冰冰,赵振利,邓敏捷,曹亚兵,董焱鹏,范国强.2017.盐胁迫对南方泡桐基因表达的影响[J].河南农业大学学报,51(4):471-480.[Li B B,Zhao Z L,Deng M J,Cao YB,Dong Y P,Fan G Q.2017.Effect of salt stress on gene expressions of different genotypes of Paulownia australis[J].Journal of Henan Agricultural University,51(4):471-480.]
李盛文,贾智英,柏盈盈,李池陶,石连玉.2014.散鳞镜鲤两个保种群体的遗传多样性[J].水产学杂志,27(2):1-8.[Li S W,Jia Z Y,Bai Y Y,Li C T,Shi L Y.2014.Microsatellite marker analysis of genetic diversity in two scattered scale mirror carp populations[J].Chinese Journal of Fisheries,27(2):1-8.]
刘义新,肖祖国,徐振秋.2007.几种杂交鲤的形态学特征及主要经济性状[J].水产科学,26(11):619-621.[Liu Y X,Xiao Z G,Xu Z Q.2007.Morphological and main economic characteristics of several common carp(Cyprinus carpio L.)hybrids[J].Fisheries Science,26(11):619-621.]
楼允东.1999.我国鱼类育种研究五十年回顾[J].淡水渔业,29(9):1-3.[Lou Y D.1999.Review of fish breeding research in China in the past fifty years[J].Freshwater Fisheries,29(9):1-3.]
孙颖.2016.棕点石斑鱼(♀)×鞍带石斑鱼(♂)杂交F1代生长优势的转录组学研究[D].广州:中山大学.[Sun Y.2016.Transcriptomic studies on the growth superiorities in grouper hybrid(Epinephelus fuscogutatus♀)×(Epinephelus lanceolatus♂)[D].Guangzhou:Sun Yat-sen University.]
唐玉娟,黄国弟,罗世杏,周俊岸,莫永龙,李日旺,赵英,张宇,宋恩亮,宁琳.2018.芒果2个不同花芽分化时期转录组分析[J].南方农业学报,49(7):1257-1264.[Tang YJ,Huang G D,Luo S X,Zhou J A,Mo Y L,Li R W,Zhao Y,Zhang Y,Song E L,Ning L.2018.Transcriptome of Mangifera indica L.in two different flower bud differentiation stages[J].Journal of Southern Agriculture,49(7):1257-1264.]
王静,肖军,曾鸣,徐康,陶敏,张纯,段巍,刘文彬,罗凯坤,刘筠,刘少军.2015.白鲫×红鲫杂交后代的遗传变异[J].中国科学:生命科学,45(4):371-380.[Wang J,Xiao J,Zeng M,Xu K,Tao M,Zhang C,Duan W,Liu W B,Luo K K,Liu Y,Liu S J.2015.Genomic variation in the hybrids of white crucian carp and red crucian carp[J].Scientia Sinica(Vitae),45(4):371-380.]
武耀,贾智英,李池陶,葛会争,石连玉.2012.筛选杂交鲤亲子鉴定的微卫星标记(英文)[J].农业生物技术学报,20(5):549-559.[Wu Y,Jia Z Y,Li C T,Ge H Z,Shi L Y.2012.Microsatellite markers for parentage identification of cross-breeding carp(Cyprinus carpio)in a selective breeding programme[J].Journal of Agricultural Biotechnology,20(5):549-559.]
岳华梅,翟晴,宋明月,叶欢,杨晓鸽,李创举.2016.基于转录组测序的兴国红鲤微卫星标记筛选[J].淡水渔业,46(1):24-28.[Yue H M,Zhai Q,Song M Y,Ye H,Yang X G,Li C J.2016.Development of microsatellite markers in Cyprinus carpio var.singuonensis using next-generation sequencing[J].Freshwater Fisheries,46(1):24-28.]
朱健,柴学森,李冰,张成锋.2014.建鲤和黑龙江野鲤自交以及正反交子代生长比较[J].渔业科学进展,35(2):35-41.[Zhu J,Chai X S,Li B,Zhang C F.2014.Growth comparison of inbreeds of Cyprinus carpio var.Jian,Cyprinus carpio haermatopterus and the reciprocal F1hybrid[J].Progress in Fishery Sciences,35(2):35-41.]
朱健,王建新,龚永生,郁桐炳.2000.我国鲤鱼遗传改良研究概况[J].浙江海洋学院学报(自然科学版),19(3):266-271.[Zhu J,Wang J X,Gong Y S,Yu T B.2000.An introduction to the studies on common carp genetic improvement in China[J].Journal of Zhejiang Ocean University(Natural Science),19(3):266-271.]
Arcella T E,Perry W L,Lodge D M,Feder J L.2014.The role of hybridization in a species invasion and extirpation of resident fauna:Hybrid vigor and breakdown in the rusty crayfish,Orconectes Rusticus[J].Journal of Crustacean Biology,34(2):157-164.
Bougas B,Granier S,Audet C,Bernatchez L.2010.The transcriptional landscape of cross-specific hybrids and its possible link with growth in brook charr(Salvelinus fontinalis Mitchill)[J].Genetics,186(1):97-107.
Chen X,Mei J,Wu J,Jing J,Ma W,Zhang J,Dan C,Wang W,Gui J.2015.A comprehensive transcriptome provides candidate genes for sex determination/differentiation and SSR/SNP markers in yellow catfish[J].Marine Biotechnology,17(2):190-198.
Davey J W,Hohenlohe P A,Etter P D,Boone J Q,Catchen JM,Blaxter M L.2011.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J].Nature Reviews Genetics,12:499-510.
Firdaus R F,S L L,Kawamura G,Shapawi R.2016.Assessment on the acceptability of hybrid grouper,Epinephelus fuscoguttatus♀×Epinephelus lanceolatus♂to soybean meal-based diets[J].AACL Bioflux,9(2):284-290.
Fu B D,He S P.2012.Transcriptome analysis of silver carp(Hypophthalmichthys molitrix)by paired-end RNA sequencing[J].DNA Research,19(2):131-142.
Gao B Q,Liu P,Li J,Wang Q Y,Li X P.2014.Genetic diversity of different populations and improved growth in the F1hybrids in the swimming crab(Portunus trituberculatus)[J].Genetics&Molecular Research,13(4):10454-10463.
Gao Y,Zhang H,Gao Q,Wang L L,Zhang F C,Siva V S,Zhou Z,Song L S,Zhang S.2013.Transcriptome analysis of artificial hybrid pufferfish Jiyan-1 and its parental species:Implications for pufferfish heterosis[J].PLoS One,8(3):e58453.
Huang Q,Dong S,Fang C,Wu X,Ye T,Lin Y.2012.Deep sequencing-based transcriptome profiling analysis of Oryzias melastigma exposed to PFOS[J].Aquatic Toxicology,120-121:54-58.doi:10.1016/j.aquatox.2012.04.013.
Ji P F,Liu G M,Xu J,Wang X M,Li J T,Zhao Z X,Zhang X F,Zhang Y,Xu P,Sun X W.2012.Characterization of common carp transcriptome:Sequencing,de Novo assembly,annotation and comparative genomics[J].PLoS One,7(4):e35152.
Jia Z Y,Shi L Y,Liu X F,Sun X W.2008.The genetic diversity of diploid and triploid crucian carp from six populations in Heilongjiang River System[J].Hereditas,30(11):1459-1465.
Jin J J,Sun Y W,Qu J,Syah R,Lim C H,Alfiko Y,Rahman N,Suwanto A,Yue G,Wong L,Chua N H,Ye J.2017.Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm[J].Scientific Reports,7(1):439.doi:10.1038/s41598-017-00438-8.
Li B,Dewey C N.2011.RSEM:Accurate transcript quantification from RNA-seq data with or without a reference genome[J].BMC Bioinformatics,12:323.doi:10.1186/1471-2105-12-323.
Li C,Zhang Y,Wang R,Lu J,Nandi S,Mohanty S,Terhune J,Liu Z,Peatman E.2012.RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish,Ictalurus punctatus[J].Fish&Shellfish Immunology,32(5):816-827.
Li F B,Gui J F.2007.Clonal diversity and genealogical relationships of gibel carp in four hatcheries[J].Animal Genetics,39(1):28-33.
Li J Q,Wang M L,Fang J G,Liu X,Mao Y Z,Liu G M,Bian D P.2017.Reproductive performance of one-yearold Pacific abalone(Haliotis discus hannai)and its crossbreeding effect on offspring growth and survival[J].Aquaculture,473:110-114.
Liao X,Cheng L,Xu P,Lu G,Wachholtz M,Sun X,Chen S.2013.Transcriptome analysis of crucian carp(Carassius auratus),an important aquaculture and hypoxia-tolerant species[J].PLoS One,8(4):e62308.
Liu Q,Qi Y,Liang Q,Xu X,Hu F,Wang J,Xiao J,Wang S,Li W,Tao M,Qin Q,Zhao R,Yao Z,Liu S.2018.The chimeric genes in the hybrid lineage of Carassius auratus cuvieri(♀)×Carassius auratus red var.(♂)[J].Science China.Life Sciences,61(9):1079-1089.
Liu X J,Liang H W,Li Z,Liang Y J,Lu C,Li C,Chang Y,Zou G,Hu G.2017.Performances of the hybrid between CyCa nucleocytplasmic hybrid fish and scattered mirror carp in different culture environments[J].Scientific Reports,7:46329.doi:10.1038/srep46329.
Liu Y F,Ma D Y,Zhao C Y,Wang W Q,Zhang X L,Liu X,Liu Y,Xiao Z Z,Xu S H,Xiao Y S,Liu Q H,Li J.2014.Histological and enzymatic responses of Japanese flounder(Paralichthys olivaceus)and its hybrids(P.olivaceus♀×P.dentatus♂)to chronic heat stress[J].Fish Physiology and Biochemistry,40(4):1031-1041.
Mao X Z,Cai T,Olyarchuk J G,Wei L.2005.Automated genome annotation and pathway identification using the KEGG Orthology(KO)as a controlled vocabulary[J].Bioinformatics,21(19):3787-3793.
Rauw W.2012.Immune response from a resource allocation perspective[J].Frontiers in Genetics,3:267.doi:10.3389/fgene.2012.00267.
Schaeffer H J,Weber M J.1999.Mitogen-activated protein kinases:Specific messages from ubiquitous messengers[J].Molecular and Cellular Biology,19(4):2435-2444.
Sinhorin V D G,Sinhorin A P,Teixeira J M D S,Miléski KM L,Hansen P C,Moreira P S A,Kawashita N H,Baviera A M,Loro V L.2014.Effects of the acute exposition to glyphosate-based herbicide on oxidative stress parameters and antioxidant responses in a hybrid Amazon fish surubim(Pseudoplatystoma sp)[J].Ecotoxicology and Environmental Safety,106:181-187.
Tian C X,Liang X F,Yang M,Dou Y Q,Zheng H Z,Cao L,Yuan Y C,Zhao C.2014.New microsatellite loci for the mandarin fish Siniperca chuatsi and their application in population genetic analysis[J].Genetics and Molecular Research,13(1):546-558.
Wang Z W,Zhu H P,Wang D,Jiang F F,Guo W,Zhou L,Gui J F.2011.A novel nucleo-cytoplasmic hybrid clone formed via androgenesis in polyploid gibel carp[J].BMCResearch Notes,4(1):82.doi:10.1186/1756-0500-4-82.
Xiao T Q,Lu C Y,Xu Y L,Li C,Zheng X H,Cao D C,Cheng L,Mahboob S,Sun X.2015.Screening of SSRmarkers associated with scale cover pattern and mapped to a genetic linkage map of common carp(Cyprinus carpio L.)[J].Journal of Applied Genetics,56(2):261-269.
Yan L L,Su J Q,Wang Z P,Yan X W,Yu R H,Ma P,Li Y,Du J.2017.Transcriptomic analysis of Crassostrea sikamea×Crassostrea angulata hybrids in response to low salinity stress[J].PLoS One,12(2):e0171483.
Young M D,Wakefield M J,Smyth G K,Oshlack A.2010.Gene ontology analysis for RNA-seq:Accounting for selection bias[J].Genome Biology,11(2):R14.doi:10.1186/gb-2010-11-2-r14.
Yu F X,Zhao B,Panupinthu N,Jewell J L,Lian I,Wang L H,Zhao J,Yuan H,Tumaneng K,Li H,Fu X D,Mills G B,Guan K L.2012.Regulation of the Hippo-YAP pathway by G-protein-coupled receptor signaling[J].Cell,150(4):780-791.
Zhai R R,Feng Y,Wang H M,Zhan X D,Shen X,Wu W,Zhang Y,Chen D,Dai G,Yang Z,Cao L,Cheng S.2013.Transcriptome analysis of rice root heterosis by RNA-seq[J].BMC Genomics,14:19.doi:10.1186/1471-2164-14-19.
Zhang C B,Lin C J,Fu F Y,Zhong X,Peng B,Yan H,Zhang J,Zhang W,Wang P,Ding X,Zhang W,Zhao L.2017a.Comparative transcriptome analysis of flower heterosis in two soybean F1hybrids by RNA-seq[J].PLoS One,12(7):e0181061.
Zhang H,Xu X,He Z,Zheng T,Shao J.2017b.De novo transcriptome analysis reveals insights into different mechanisms of growth and immunity in a Chinese soft-shelled turtle hybrid and the parental varieties[J].Gene,605:54-62.
Zhang Y Q,Liu J H,Fu W,Xu W T,Zhang H,Chen S,Liu W,Peng L,Xiao Y.2017c.Comparative transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in crucian carp(Carassius carassius L.)[J].BMC Genetics,18(1):95.doi:10.1186/s12863-017-0564-9.
Zhang Z H,Chen J,Ling L I,Tao M,Zhang C,Qin Q B,Xiao J,Liu Y,Liu S J.2014.Research advances in animal distant hybridization[J].Science China.Life Sciences,57(9):889-902.
Zhou Z C,Dong Y,Sun H J,Yang A F,Chen Z,Gao S,Jiang J W,Guan X Y,Jiang B,Wang B.2013.Transcriptome sequencing of sea cucumber(Apostichopus japonicus)and the identification of gene-associated markers[J].Molecular Ecology Resources,14(1):127-138.