Transcriptome-derived EST–SSR markers and their correlations with growth traits in crucian carp Carassius auratus

详细信息    查看全文

• 作者：Xianhu Zheng ; Youyi Kuang ; Weihua Lü ; Dingchen Cao ; Xiaowen Sun
• 关键词：Carassius auratus ; EST–SSR ; Growth trait ; Correlation
• 刊名：Fisheries Science
• 出版年：2014
• 出版时间：September 2014
• 年：2014
• 卷：80
• 期：5
• 页码：977-984
• 全文大小：311 KB
• 参考文献：1. Chen XL, Huang HJ (1982) Cyprininae. In: Wu XW (ed) Monographs of Cyprinidae in China. Shanghai People’s Press, Shanghai, pp 395-35
  2. Dong J, Murakami M, Fujimoto T, Yamaha E, Arai K (2013) Genetic characterization of the progeny of a pair of the tetraploid silver crucian carp / Carassius auratus langsdorfii. Fish Sci 79:935-41 CrossRef
  3. Xiao J, Zou T, Chen Y, Chen L, Liu S, Tao M, Zhang C, Zhao R, Zhou Y, Long Y (2011) Coexistence of diploid, triploid and tetraploid crucian carp ( / Carassius auratus) in natural waters. BMC Genet 12:20 CrossRef
  4. Gui JF, Zhou L (2010) Genetic basis and breeding application of clonal diversity and dual reproduction modes in polyploid / Carassius auratus gibelio. Sci China Life Sci 53:409-15 CrossRef
  5. Yue G, Orban L (2002) Polymorphic microsatellites from silver crucian carp ( / Carassius auratus gibelio Bloch) and cross-amplification in common carp ( / Cyprinus carpio L.). Mol Ecol Notes 2:534-36 CrossRef
  6. Jia ZY, Sun XW, Liang LQ, Lu CY, Lei QQ (2006) Isolation and characterization of microsatellite markers from Fangzheng silver crucian carp, / Carassius auratus gibelio (Bloch), and cross-amplification in the closely related species crucian carp, / Carassius auratus auratus (Linnaeus). Mol Ecol Notes 6:1141-143 CrossRef
  7. Guo W, Gui JF (2008) Microsatellite marker isolation and cultured strain identification in / Carassius auratus gibelio. Aquacult Int 16:497-10 CrossRef
  8. Zheng X, Lu C, Zhao Y, Lee C, Cao D, Chang Y, Liang L, Sun X (2010) A set of polymorphic trinucleotide and tetranucleotide microsatellite markers for silver crucian carp ( / Carassius auratus gibelio) and cross-amplification in crucian carp. Biochem Genet 48:624-35 CrossRef
  9. Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E (2011) Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genom 12:53 CrossRef
  10. Boussaha M, Guyomard R, Cabau C, Esquerré D, Quillet E (2012) Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout. BMC Genom 13:238 CrossRef
  11. Xu J, Ji P, Zhao Z, Zhang Y, Feng J, Wang J, Li J, Zhang X, Zhao L, Liu G (2012) Genome-wide SNP discovery from transcriptome of four common carp strains. PLoS ONE 7:e48140 CrossRef
  12. Ji P, Zhang Y, Li C, Zhao Z, Wang J, Li J, Xu P, Sun X (2012) High throughput mining and characterization of microsatellites from common carp genome. Int J Mol Sci 13:9798-807 CrossRef
  13. Zhou Z, Dong Y, Sun H, Yang A, Chen Z, Gao S, Jiang J, Guan X, Jiang B, Wang B (2013) Transcriptome sequencing of sea cucumber ( / Apostichopus japonicus) and the identification of gene-associated markers. Mol Ecol Resour 14:127-38 CrossRef
  14. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48-5 CrossRef
  15. Ellis J, Burke J (2007) EST–SSRs as a resource for population genetic analyses. Heredity 99:125-32 CrossRef
  16. 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. PLoS ONE 8:e62308 CrossRef
  17. You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinform 9:253 CrossRef
  18. Conesa A, G?tz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-676 CrossRef
  19. Emrich SJ, Barbazuk WB, Li L, Schnable PS (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17:69-3 CrossRef
  20. Roy SW, Penny D, Neafsey DE (2007) Evolutionary conservation of UTR intron boundaries in / Cryptococcus. Mol Biol Evol 24:1140-148 CrossRef
  21. Buschiazzo E, Gemmell NJ (2006) The rise, fall and renaissance of microsatellites in eukaryotic genomes. BioEssays 28:1040-050 CrossRef
  22. Wang D, Liao X, Cheng L, Yu X, Tong J (2007) Development of novel EST-SSR markers in common carp by data mining from public EST sequences. Aquaculture 271:558-74 CrossRef
  23. Kang JH, Park JY, Jo HS (2012) Rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish, the mottled skate, / Raja pulchra. Int J Mol Sci 13:7199-211 CrossRef
  24. Neff BD, Gross MR (2001) Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution 55:1717-733 CrossRef
  25. Luo W, Nie Z, Zhan F, Wei J, Wang W, Gao Z (2012) Rapid development of microsatellite markers for the endangered fish / Schizothorax biddulphi (Günther) using next generation sequencing and cross-species amplification. Int J Mol Sci 13:14946-4955 CrossRef
  26. Lü Z, Li H, Liu L, Cui W, Hu X, Wang C (2013) Rapid development of microsatellite markers from the large yellow croaker ( / Pseudosciaena crocea) using next generation DNA sequencing technology. Biochem Syst Ecol 51:314-19 CrossRef
  27. Schoreeret F, Ggartlar SM (1992) Analysis of CpGg suppression in methylated and nonmethylated species. Proc Natl Acad Sci USA 89:957-61 CrossRef
  28. Serapion J, Kucuktas H, Feng J, Liu Z (2004) Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish ( / Ictalurus punctatus). Mar Biotechnol 6:364-77 CrossRef
  29. Qu C, Liang X, Huang W, Cao L (2012) Isolation and characterization of 46 novel polymorphic EST-simple sequence repeats (SSR) markers in two Sinipercine fishes ( / Siniperca) and cross-species amplification. Int J Mol Sci 13:9534-544 CrossRef
  30. Wang J, Yu X, Zhao K, Zhang Y, Tong J, Peng Z (2012) Microsatellite development for an endangered bream / Megalobrama pellegrini (Teleostei, Cyprinidae) using 454 sequencing. Int J Mol Sci 13:3009-021 CrossRef
  31. Lee BY, Lee WJ, Streelman JT, Carleton KL, Howe AE, Hulata G, Slettan A, Stern JE, Terai Y, Kocher TD (2005) A second generation genetic linkage map of tilapia ( / Oreochromis spp.). Genetics 170:237-44 CrossRef
  32. Zhang Y, Xu P, Lu C, Kuang Y, Zhang X, Cao D, Li C, Chang Y, Hou N, Li H, Wang S, Sun X (2011) Genetic linkage mapping and analysis of muscle fiber-related QTLs in common carp ( / Cyprinus carpio L.). Mar Biotechnol 13:376-92 CrossRef
  33. Zheng X, Kuang Y, Zhang X, Lu C, Cao D, Li C, Sun X (2011) A genetic linkage map and comparative genome analysis of common carp ( / Cyprinus carpio L.) using microsatellites and SNPs. Mol Genet Genomics 286:261-77 CrossRef
  34. Lyttle TW (1991) Segregation distorters. Annu Rev Genet 25:511-57 CrossRef
  35. Xu SZ (2008) Quantitative trait locus mapping can benefit from segregation distortion. Genetics 180:2201-208 CrossRef
  36. Taylor DR, Ingvarsson PK (2003) Common features of segregation distortion in plants and animals. Genetica 117:27-5 CrossRef
  
• 作者单位：Xianhu Zheng (1)
  Youyi Kuang (1)
  Weihua Lü (1)
  Dingchen Cao (1)
  Xiaowen Sun (1)
  
  1. National Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.43, Songfa Street, Daoli District, Harbin, 150070, Heilongjiang, China
  
• ISSN：1444-2906

文摘

In our previous study, transcriptomes of crucian carp were sequenced using 454 Sequencing, which generated many expressed sequence tag (EST) sequences that are useful to develop gene-based markers. In this study, from these ESTs, 5505 simple sequence repeats (SSRs) were identified, among which dinucleotide repeats (43.6?%) and AC/GT motifs (39.6?%) were the most frequent, followed by AAT/ATT (15.5?%). We designed 3932 primers with sufficient amplified flanking sequences. To verify the identified EST–SSRs, 500 primers were randomly selected for polymerase chain reaction (PCR), of which 408 (81.6?%) were successfully amplified, among which 151 (30.2?%) were polymorphic. These polymorphic markers were further surveyed among an F1 population. The results showed that 148 loci were informative in both parents, with segregation ratios of 1:1:1:1 (23, 15.5?%), 1:1 (59, 39.9?%), and 1:2:1 (66, 44.6?%). In addition, the general linear model (GLM) procedure in the SPSS software package was used to analyze the correlations between these 148 loci and two growth traits. Twelve loci were discovered to be significantly (P?P?P?P?