Parentage determination of yellow catfish (Pelteobagrus Fulvidraco) based on microsatellite DNA markers

详细信息    查看全文

• 作者：Jin Zhang ; Wenge Ma ; Weimin Wang ; Jian-Fang Gui ; Jie Mei
• 关键词：Parentage determination ; Pelteobagrus fulvidraco ; Microsatellite marker ; Genetic selection breeding
• 刊名：Aquaculture International
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：24
• 期：2
• 页码：567-576
• 全文大小：711 KB
• 参考文献：Abdul-Muneer PM (2014) Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies. Genet Res Int 2014:691759PubMed PubMedCentral
  Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMed PubMedCentral
  Chen X, Mei J, Wu J, Jing J, Ma W, Zhang J, Dan C, Wang W, Gui JF (2015) A comprehensive transcriptome provides candidate genes for sex determination/differentiation and SSR/SNP markers in yellow catfish. Mar Biotechnol 17:190–198CrossRef PubMed
  Coman GJ, Crocos PJ, Preston NP, Fielder D (2002) The effects of temperature on the growth, survival and biomass of different families of juvenile Penaeus japonicus Bate. Aquaculture 214:185–199CrossRef
  Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity 93:504–509CrossRef PubMed
  Dan C, Mei J, Wang D, Gui JF (2013) Genetic differentiation and efficient sex-specific marker development of a pair of Y- and X-linked markers in yellow catfish. Int J Biol Sci 9:1043–1049CrossRef PubMed PubMedCentral
  Dong SR, Kong J, Zhang TS, Meng XH, Wang RC (2006) Parentage determination of Chinese shrimp (Fenneropenaeus chinensis) based on microsatellite DNA markers. Aquaculture 258:283–288CrossRef
  Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445CrossRef PubMed
  Gjedrem T (2005) Selection and breeding programs in aquaculture. Springer, Dordrecht, pp 89–111CrossRef
  Gui J, Zhu Z (2012) Molecular basis and genetic improvement of economically important traits in aquaculture animals. Chin Sci Bull 57:1751–1760CrossRef
  Harrison HB, Feldheim KA, Jones GP, Ma K, Mansour H, Perumal S, Williamson DH, Berumen ML (2014) Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae). Ecol Evol 4:2046–2057PubMed PubMedCentral
  Hauser L, Baird M, Hilborn R, Seeb LW, Seeb JE (2011) An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Mol Ecol Resour 11(Suppl 1):150–161CrossRef PubMed
  Hubner K, Gonzalez-Wanguemert M, Diekmann OE, Serrao EA (2013) Genetic evidence for polygynandry in the black-striped pipefish Syngnathus abaster: a microsatellite-based parentage analysis. J Hered 104:791–797CrossRef PubMed
  Janhunen M, Kause A, Vehvilainen H, Nousiainen A, Koskinen H (2013) Accounting for early rearing density effects on growth in the genetic evaluation of rainbow trout, Oncorhynchus mykiss. J Anim Sci 91:5144–5152CrossRef PubMed
  Jerry DR, Preston NP, Crocos PJ, Keys S, Meadows JRS, Li YT (2004) Parentage determination of Kuruma shrimp Penaeus (Marsupenaeus) japonicus using microsatellite markers (Bate). Aquaculture 235:237–247CrossRef
  Jones AG, Small CM, Paczolt KA, Ratterman NL (2010) A practical guide to methods of parentage analysis. Mol Ecol Resour 10:6–30CrossRef PubMed
  Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRef PubMed
  Lind CE, Ponzoni RW, Nguyen NH, Khaw HL (2012) Selective breeding in fish and conservation of genetic resources for aquaculture. Reprod Domest Anim 47(Suppl 4):255–263CrossRef PubMed
  Liu P, Xia JH, Lin G, Sun F, Liu F, Lim HS, Pang HY, Yue GH (2012) Molecular parentage analysis is essential in breeding Asian seabass. PLoS One 7:e51142CrossRef PubMed PubMedCentral
  Liu XD, Zhao GT, Cai MY, Wang ZY (2013) Estimated genetic parameters for growth-related traits in large yellow croaker Larimichthys crocea using microsatellites to assign parentage. J Fish Biol 82:34–41CrossRef PubMed
  Ma QQ, Ma HY, Chen JH, Ma CY, Feng NN, Xu Z, Li SJ, Jiang W, Qiao ZG, Ma LB (2013) Parentage assignment of the mud crab (Scylla paramamosain) based on microsatellite markers. Biochem Syst Ecol 49:62–68CrossRef
  Mei J, Gui J (2015) Genetic basis and biotechnological manipulation of sexual dimorphism and sex determination in fish. Sci China Life Sci 58:124–136CrossRef PubMed
  Norris AT, Bradley DG, Cunningham EP (2000) Parentage and relatedness determination in farmed Atlantic salmon Salmo salar using microsatellite markers. Aquaculture 182:73–83CrossRef
  Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRef PubMed PubMedCentral
  Wang D, Mao HL, Chen HX, Liu HQ, Gui JF (2009) Isolation of Y- and X-linked SCAR markers in yellow catfish and application in the production of all-male populations. Anim Genet 40:978–981CrossRef PubMed
  Wang ZW, Zhu HP, Wang D, Jiang FF, Guo W, Zhou L, Gui JF (2011) A novel nucleo-cytoplasmic hybrid clone formed via androgenesis in polyploid gibel carp. BMC Res Notes 4:82CrossRef PubMed PubMedCentral
  Xiao M, Bao F, Cui F (2014) Pattern of genetic variation of yellow catfish Pelteobagrus fulvidraco Richardso in Huaihe river and the Yangtze river revealed using mitochondrial DNA control region sequences. Mol Biol Rep 41:5593–5606CrossRef PubMed
  Yang M, Tian CX, Liang XF, Lv LY, Zheng HZ, Yuan YC, Zhao C, Huang W (2014) Parentage determination of mandarin fish (Siniperca chuatsi) based on microsatellite DNA markers. Biochem Syst Ecol 54:285–291CrossRef
  Zhang J, Ma W, Song X, Lin Q, Gui JF, Mei J (2014) Characterization and development of EST-SSR markers derived from transcriptome of yellow catfish. Molecules 19:16402–16415CrossRef PubMed
  
• 作者单位：Jin Zhang (1)
  Wenge Ma (1)
  Weimin Wang (1)
  Jian-Fang Gui (1) (2)
  Jie Mei (1)
  
  1. College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
  2. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Hydrobiology
  
• 出版者：Springer Netherlands
• ISSN：1573-143X

文摘

The application of microsatellite (SSR) markers for parentage determination is a booming science for selective breeding as it can track the ancestry and lineage of fish and maintain pedigree information. This study was initiated to assess the feasibility of SSR markers for parentage determination in yellow catfish (Pelteobagrus fulvidraco) by using simulation and real data analysis. A panel of nine polymorphic SSR markers was chosen from our 454 pyrosequencing transcriptomes to genotype 180 progenies in eighteen yellow catfish full-sib families. These markers were highly polymorphic with a mean of 16.9 alleles per locus and an expected average heterozygosity value of 0.891 in 180 individuals. The allele frequency date-based simulation indicated that the combined exclusion probability values would be over 99 and 99.9 %, respectively, when six and eight SSRs were used. Based on the simulation, all progenies were unambiguously assigned to their putative parental pairs when six SSRs were used, whereas the rate of assignment success for the real data set was only 98.9 %. Moreover, when the number of SSRs was up to nine, all progenies from the eighteen full-sib families were 100 % allocated to their parents. The double-blind test demonstrated that 96 % of the randomly selected progeny can be clustered into their own families. This study demonstrated that the microsatellite-based approach is effective for parentage assignment in yellow catfish and has a significant application in selective breeding in this species.