Genetic linkage mapping and genetic analysis of QTL related to eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs

Aquaculture

Volumn 358-359, Issue , 2012, Pages 176-182

  Jin, Shubo ^a   Zhang, Xiaofeng ^a   Jia, Zhiying ^a   Fu, Hongtuo ^a   Zheng, Xianhu ^a,b   Sun, Xiaowen ^a  

^a SOUTH CHINA SEA FISHERIES RESEARCH INSTITUTE   (China)

^b SHANGHAI OCEAN UNIVERSITY   (China)

Author keywords

Breeding; Correlation analysis; Eye cross; Eye diameter; Mirror carp (Cyprinus carpio L.); Quantitative trait locus

Indexed keywords

BODY MASS; BREEDING; COMMERCIAL SPECIES; CYPRINID; EYE; FISH CULTURE; GENETIC ANALYSIS; GENETIC MARKER; GENOME; MAPPING; PHENOTYPIC PLASTICITY; SOFTWARE; WEIGHT;

CYPRINIDAE; CYPRINUS CARPIO;

EID: 84864401527     PISSN: 00448486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.aquaculture.2012.06.014     Document Type: Article

References (45)

1. Aliah R.S., Takagi M., Dong S., Taniguchi N. Isolation and inheritance of microsatellite markers in the common carp Cyprinus carpio. Fisheries Science 1999, 65:235-239.
2. Cai W., Morishima H. QTL clusters reflect character associations in wild and cultivated rice. Biological Science 2002, 104:1217-1228.
3. Castaño-Sánchez C., Fuji K., Ozaki A., Hasegawa O., Sakamoto T., Morishima K., Nakayama I., Fujiwara A., Masaoka T., Okamoto N. A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus). BMC Genomics 2010, 11:554.
4. Cheng L., Liu L., Yu X., Wang D., Tong J. A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers. Animal Genetics 2009, 41:191-198.
5. Cnaani A., Zilberman N., Tinman S., Hulata G., Ron M. Genome-scan analysis for quantitative trait loci in an F 2 tilapia hybrid. Molecular Genetics and Genomics 2004, 272:162-172.
6. Crooijmans R., Poel J.J., Groenen M.A.M., Bierbooms V.A.F., Komen J. Microsatellite markers in common carp (Cyprinus carpio L.). Animal Genetics 1997, 28:129-134.
7. David L., Rajasekaran P., Fang J., Hillel J., Lavi U. Polymorphism in ornamental and common carp strains (Cyprinus carpio L.) as revealed by AFLP analysis and a new set of microsatellite markers. Molecular Genetics and Genomics 2001, 266:353-362.
8. Guryev V., Koudijs M.J., Berezikov E., Johnson S.L., Plasterk R.H.A., van Eeden F.J.M., Cuppen E. Genetic variation in the zebrafish. Genome Research 2006, 16:491-497.
9. Hou N., Zhang Y., Lu C., Li Y., Li D., Ji X., Ding L., Sun X. Genetic potential analysis of Germany mirror carp (Cyprinus carpio L.) using microsatellite markers. Hereditas 2007, 29:1509-1518.
10. Jacobs J., Eck H.J., Arens P., Verkerk-Bakker B., Lintel Hekkert B., Bastiaanssen H., El-Kharbotly A., Pereira A., Jacobsen E., Stiekema W. A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers. Theoretical and Applied Genetics 1995, 91:289-300.
11. Kazumitsu O., Yuki H., Noriko I., Kyoko T., Naofumi I., Masamichi M., Yoshio S. A QTL Cluster for plant architecture and its ecological significance in Asian wild rice. Breeding Science 2007, 57:7-16.
12. Kucuktas H., Wang S., Li P., He C., Xu P., Sha Z., Liu H., Jiang Y., Baoprasertkul P., Somridhivej B. Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 2009, 181:1649-1660.
13. Lander E.S., Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989, 121:185-199.
14. Li W., Liu C., Zhang X., Zhang T., Wang X., Chu Z., Sun X. Mapping QTLs related to body weight of mirror carp (Cyprinus carpio L.). Genomics and Applied Biology 2011, 30:316-324.
15. Lien S., Lars G., Thomas M., Ben J.H., Paul R.B., William S.D., Stig W.O., Matthew P.K. A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. BMC Genomics 2011, 12:615.
16. Liu J., Zhang Y., Chang Y., Liang L., Lu C., Zhang X., Xu M., Sun X. Mapping QTLs related to head length, eye diameter and eye cross of common carp (Cyprinus carpio L.). Hereditas 2009, 31:508.
17. Liu S., Zhou Z., Lu J., Sun F., Wang S., Liu H., Jiang Y., Kucuktas H., Kaltenboeck L., Peatman E., Liu Z. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics 2011, 12:53.
18. Moen T., Hayes B., Baranski M., Berg P., Kj glum S., Koop B., Davidson W., Omholt S., Lien S. A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 2008, 9:223.
19. Naruse K., Tanaka M., Mita K., Shima A., Postlethwait J., Mitani H. A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Research 2004, 14:820-828.
20. Ragot M., Sisco P.H., Hoisington D.A., Stuber C.W. Molecularmarker-mediated characterization of favourable exotic alleles at quantitative trait loci in maize. Crop Science 1995, 35:1306-1315.
21. Rasaei A., Ghobadi M.E., Ghobadi M., Abdi-niya K., Rasaei A., Ghobadi M.E., Ghobadi M., Abdi-niya K. The study of traits correlation and path analysis of the grain yield of the peas in semi-dry conditions in Kermanshah. International Conference on Food Engineering and Biotechnology 2011, vol. 9:246-249. IACSIT Press.
22. Sambrook J., Russell D. Molecular Cloning: a laboratory manual 2001, Cold Spring Harbor Press, Cold Spring Harbor, NY. 3rd edn.
23. Sun X., Liang L. A genetic linkage map of common carp (Cyprinus carpio L.) and mapping of a locus associated with cold tolerance. Aquaculture 2004, 238:165-172.
24. Sun X., Jia Z., Wei D., Lu C., Liang L. Comparison between magnetic beads enriched and small inserted fragment library for microsatellite sequences of common carp. Journal of Fishery Sciences of China 2005, 12:126-132.
25. Tanck M.W.T., Palstra A.P., Weerd M., Leffering C.P., Poel J.J., Bovenhuis H., Komen J. Segregation of microsatellite alleles and residual heterozygosity at single loci in homozygous androgenetic common carp (Cyprinus carpio L.). Genome 2001, 44:743-751.
26. Ulgen A., Han Z., Li W. Correlation between quantitative traits and correlation between corresponding LOD scores: detection of pleiotropic effects. BMC Genetics 2003, 4:S60.
27. Van Ooijen MAPQTL5.0, software for the mapping of quantitative trait loci in experimental population 2004, Plant Research International, Wageningen, The Netherlands.
28. Van Ooijen J., Boer M., Jansen R., Maliepaard C. MapQTL 4.0: software for the calculation of QTL positions on genetic maps (user manual) 2000, University of Wageningen, The Netherlands.
29. Viruel M.A., Messeguer R., Vicente M.C., Garcia-Mas J., Puigdomènech P., Vargas F., Arús P. A linkage map with RFLP and isozyme markers for almond. Theoretical and Applied Genetics 1995, 91:964-971.
30. Wang D.G., Fan J.B., Siao C.J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998, 280:1077-1082.
31. Wang D., Liao X., Cheng L., Yu X., Tong J. Development of novel EST-SSR markers in common carp by data mining from public EST sequences. Aquaculture 2007, 271:558-574.
32. Wang X., Zhang X., Li W., Zhang T., Sun X. Analysis of feed conversion ratio, bodyweight, body thickness traits of common carp (Cyprinus carpio L.) using SSR, EST-SSR, SNP markers. J. Fish. Sci. China 2011, 18:565-573.
33. Wei D., Lou Y., Sun X., Shen J. Isolation of microsatellite markers in the common carp (Cyprinus carpio). Zoological Research 2001, 22:238-241.
34. Xiao J., Li J., Grandillo S., Ahn S.N., Yuan L., Tanksley S.D., McCouch S.R. Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 1998, 150:899-909.
35. Xie Q. Practical Tutorial of Excel 2007 spreadsheet (M) 2010, Tsinghua University Press.
36. Xu P., Li J., Li Y., Cui R., Wang J., Zhang Y., Zhao Z., Sun X. Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences. BMC Genomics 2011, 12:188-193.
37. Yan X., Liang L., Sun X., Cao D. Comparison of the morphological characteristics between two types of backcross progenies from the common carp and crucian carp. Journal of Northeast Agricultural University 2007, 38(6):797-800.
38. Chromosomes of Chinese Fresh-water Fishes 1989, Sciences Press, Beijing, China. X. Yu, T. Zhou, Y. Li, K. Li, M. Zhou (Eds.).
39. Yue G., Ho M., Orban L., Komen J. Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp. Aquaculture 2004, 234:85-98.
40. Zhang Y., Xu P., Lu C., Kuang Y., Zhang X., Cao D., Li C., Chang Y., Hou N., Li H., Wang S., Sun X. Genetic linkage mapping and analysis of muscle fiber-related QTLs in common carp (Cyprinus carpio L.). Marine Biotechnology 2010, 13:376-392.
41. Zhang Y., Stupka E., Henkel C.V., Jansen H.J., Spaink H.P., Verbeek F.J. Identification of common carp innate immune genes with whole-genome sequencing and RNA-seq data. Journal of Integrative Bioinformatics 2011, 8:169-179.
42. Zheng X., Kuang Y., Zhang X., Lu C., Cao D., Li C., Sun X. A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs. Molecular Genetics and Genomics 2011, 286:261-277.
43. Zheng X., Kuang Y., Lu C., Wang X., Li W., Lv W., Sun X. Quantitative trait locus analysis of standard length, body depth and body thickness in mirror carp (Cyprinus carpio L.). Hereditas 2011, 12:1366-1373.
44. Zhou Y., Zheng D. A new calculation method of correlation coefficient test table. Annals of Shanghai Observatory Academia Sinica 1997, 18:18-23.
45. Zimdahl H., Nyakatura G., Brandt P., Schulz H., Hummel O., Fartmann B., Brett D., Droege M., Monti J., Lee Y. A SNP map of the rat genome generated from cDNA sequences. Science 2004, 303:807.