Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection

Scientia Horticulturae

Volumn 128, Issue 3, 2011, Pages 220-227

  Amar, Mohamed Hamdy ^a,b   Biswas, Manosh Kumar ^a   Zhang, Zongwen ^c   Guo, Wen Wu ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b DESERT RESEARCH CENTER   (Egypt)

^c BIOVERSITY INTERNATIONAL   (Italy)

Author keywords

CAPS SNP; Citrus; Genetic diversity; PIC; SRAP; SSR

Indexed keywords

ASSESSMENT METHOD; CLUSTER ANALYSIS; DATA SET; DISCRIMINANT ANALYSIS; EVERGREEN TREE; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENETIC MARKER; GERMPLASM; MOLECULAR ANALYSIS; POLYMORPHISM;

CITRUS;

EID: 79952455920     PISSN: 03044238     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.scienta.2011.01.021     Document Type: Article

References (65)

1. Abkenar A.A., Isshiki S., Tashiro Y. Phylogenetic relationships in the true citrus fruit trees revealed by PCR-RFLP analysis of cpDNA. Sci. Hortic. 2004, 102:233-242.
2. Agarwal M., Shrivastava N., Padh H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 2008, 27:617-631.
3. Ahmad R., Potter D., Southwick M. Genotyping of peach and nectarine cultivars with SSR and SRAP molecular markers. J. Am. Soc. Hortic. Sci. 2004, 129:204-210.
4. Anderson J.A., Churchill G.A., Autrique J.E., Tanksley S.D., Sorrells M.E. Optimizing parental selection for genetic linkage maps. Genome 1993, 36:181-186.
5. Barkley N.A., Roose M.L., Krueger R.R., Federici C.T. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor. Appl. Genet. 2006, 112:1519-1531.
6. Batley J., Edwards D. Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree. Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology 2009, 537. pp. 303-321.
7. Belaj A., Satovic Z., Cipriani G., Baldoni L., Testolin R., Rallo L., Trujillo I. Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor. Appl. Genet. 2003, 107:736-744.
8. Bernet G.P., Mestre P.F., Pina J.A., Asins M.J. Molecular discrimination of lemon cultivars. HortScience 2004, 39:165-169.
9. Biswas, M.K., 2010a. Exploring SSR markers based on the BES and EST sequences for the linkage map of citrus. Ph.D Dissertation, Huazhong Agricultural University (HZAU).
10. Biswas M.K., Baig M.N.R., Cheng Y., Deng X.X. Retro-transposon based genetic similarity within the genus citrus and its relatives. Gen. Res. Crop Evol. 2010, 10:22-33.
11. Biswas M.K., Xu Q., Deng X.X. Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci. Hortic. 2010, 124:254-261.
12. Cao Q.Q., Meng H.J., Wen X.P., Yi H.L., Deng X.X. Genetic diversity of male sterile and low fertility germplasm of citrus revealed using SSR markers. Chinese J. Agric. Biotechnol. 2006, 14:937-941.
13. Chao S., Zhang W., Akhunov E., Sherman J., Ma Y., Luo M., Dubcovsky J. Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol. Breed. 2009, 23:23-33.
14. Chen C., Zhou P., Choi Y.A., Huang S., Gmitter F.J. Mining and characterizing microsatellites from citrus ESTs. Theor. Appl. Genet. 2006, 112:1248-1257.
15. Cheng Y.J., Guo W.W., Yi H.L., Pang X.M., Deng X.X. An efficient protocol for genomic DNA extraction from citrus species. Plant Mol. Biol. Rep. 2003, 21:177a-1177a.
16. Cristofani M., Machado M., Novelli V., Souza A., Targon M. Construction of linkage maps of Poncirus Trifoliate and citrus sunki based on microsatellite markers. Proceedings of the 9th International Society of Citriculture Congress 2003, 175-178.
17. Demey J.R., Gamez E., Molina S., infante D. Comparative study of the discriminating capacity of AFLP and ISTR markers for genetic analysis of agave fourcroydes. Plant Mol. Biol. Rep. 2004, 22:29-35.
18. Dice L.R. Measures of the amount of ecologic association between species. Ecology 1945, 26:297-302.
19. Dong J., Qing-liang Y., Fu-sheng W., Li C. The mining of citrus EST-SNP and its application in cultivar discrimination. Agric. Sci. China 2010, 9:179-190.
20. Dong P., Wei Y., Chen G., Li W., Wang J., Nevo E., Zheng Y. Sequence related amplified polymorphism (SRAP) of wild emmer wheat (Triticum dicoccoides) in Israel and its ecological association. Biochem. Syst. Ecol. 2010, 38:1-11.
21. Du X.Y., Zhang Q.L., Luo Z.R. Comparison of four molecular markers for genetic analysis in Diospyros L. (Ebenaceae). Plant Syst. Evol. 2009, 281:171-181.
22. Duran C., Appleby N., Edwards D., Batley J. Molecular genetic markers: discovery, applications, data storage and visualisation. Curr. Bioinformatics 2009, 4:16-27.
23. FAOSTAT, 2010. http://faostat.fao.org/site/339/default.aspx.
24. Fu J., Peng Z.J., Cai X.D., Guo W.W. Regeneration and molecular characterization of interspecific somatic hybrids between Satsuma mandarin and two seedy sweet oranges for scion improvement. Plant Breed. 2010, 01773. 10.1111/j.1439-0523.
25. Gaudet M., Fara A., Sabatti M., Kuzminsky E., Mugnozza G.S. Single reaction for SNP genotyping on agarose gel by allele-specific PCR in black poplar (Populus nigra L.). Plant Mol. Biol. Rep. 2007, 25:1-9.
26. Ghanbari A., Jelodar N.B., Rahiman H. Studying of genetic diversity in satsuma (Citrus unshiu) mandarin utilizing microsatellite markers. Int. J. Agric. Res. 2009, 4:88-96.
27. Gmitter F.G. Origin, evolution, and breeding of the Grapefruit. Plant Breed. 1995, 13:345-363.
28. Golein B., Talaie A., Zamani Z., Moradi B. Development and characterization of new microsatellite loci from lemon (Citrus limon). Int. J. Agric. Biol. 2006, 8:172-174.
29. Green R.M., Vardi A., Galun E. The plastome of Citrus. Physical map, variation among citrus cultivars and species and comparison with related genera. Theor. Appl. Genet. 1986, 72:170-177.
30. Gulsen O., Roose M.L. Chloroplast and nuclear genome analysis of the parentage of lemons. J. Am. Soc. Hortic. Sci. 2001, 126:210-215.
31. Gulsen O., Uzun A., Canan I., Seday U., Canihos E. A new citrus linkage map based on SRAP, SSR, ISSR, POGP, RGA and RAPD markers. Euphytica 2010, 173:265-277.
32. Gut I.G. Automation in genotyping of single nucleotide polymorphisms. Hum. Mutat. 2001, 17:475-492.
33. Handa T., Ishizawa Y., Oogaki C. Phylogenetic study of fraction I protein in the genus citrus and its close related genera. Jpn. J. Genet. 1986, 61:15-24.
34. Holton T.A., Christopher J.T., McClure L., Harker N., Henry R.J. Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol. Breed. 2002, 9:63-71.
35. Jannati M., Fotouhi R., Pourjan A., Salehi A.Z. Genetic diversity analysis of Iranian citrus varieties using microsatellite (SSR) based markers. J. Hortic. For. 2009, 1:120-125.
36. Kijas J.M.H., Fowler J.C.S., Garbett C.A., Thomas M.R. Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. BioTechniques 1994, 16:656-662.
37. Li G., Quiros F. Sequence related amplified polymorphisim (SRAP). A new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 2001, 103:455-461.
38. Li Y.H., Li W., Zhang C., Yang L., Chang R., Gaut B.S., Qiu L. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol. 2010, 188:242-253.
39. Lin Z., Zhang X., Nie Y., He D., Wu M. Construction of a genetic linkage map for cotton based on SRAP. Chinese Sci. Bull. 2003, 48:2064-2068.
40. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967, 27:209-220.
41. Maras M., Jelka S.V., Branka J., Vladimir M. The efficiency of AFLP and SSR markers in genetic diversity estimation and gene pool classification of common bean (Phaseolus vulgaris L.). Acta Agric. Slovenica 2008, 91:87-96.
42. McKinnon G.E., Vaillancourt R.E., Steane D.A., Potts B.M. An AFLP marker approach to lower-level systematics in Eucalyptus (Myrtaceae). Am. J. Bot. 2008, 95:368-380.
43. Mondini L., Noorani A., Pagnotta M.A. Assessing plant genetic diversity by molecular tools. Diversity 2009, 1:19-35.
44. Neff M.M., Neff J.D., Chory J., Pepper A.E. dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms experimental applications in Arabidopsis thaliana genetics. Plant J. 1998, 14:387-392.
45. Nemri A., Neff M.M., Burrell M., Jones J.D.G., Studholme D.J. Marker development for the genetic study of natural variation in Arabidopsis thaliana. Bioinformatics 2007, 23:3108-3109.
46. Novelli V.M., Takita M.A., Machado M.A. Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus. Euphytica 2004, 138:227-237.
47. Oliveira A.C., Garcia A.N., Cristofani M., Machado M.A. Identification of citrus hybrids through the combination of leaf apex morphology and SSR markers. Euphytica 2002, 128:397-403.
48. Palmieri D.A., Novelli V.M., Bastianel M., Cristofani-Yaly M., Astúa-Monge G., Carlos E.F., Carlos de Oliveira A., Machado M.A. Frequency and distribution of microsatellites from ESTs of citrus. Genet. Mol. Biol. 2007, 30:1009-1018.
49. Pang X., Hu C., Deng X.X. Phylogenetic relationships among citrus and its relatives as revealed by SSR markers. Acta Genet. Sin. 2003, 30:81-87.
50. Pang X.M., Hu C.G., Deng X.X. Phylogenetic relationships within citrus and its related genera as inferred from AFLP markers. Genet. Res. Crop Evol. 2007, 54:429-436.
51. Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey S., Rafalski A. The comparison of RFLP, RAPD, AFLP and SSR markers for germplasm analysis. Mol. Breed. 1996, 2:225-238.
52. Rohlf F.J. NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1 2000, Exeter Software, New York.
53. Ruan C. Germplasm-regression-combined marker-trait association identification in plants. Afr. J. Biotechnol. 2010, 9:573-580.
54. Scariot V., De Keyser E., Handa T., De Riek J. Comparative study of the discriminating capacity and effectiveness of AFLP, STMS and EST markers in assessing genetic relationships among evergreen azales. Plant Breed. 2007, 126:207-212.
55. Smith J.S.C., Chin E.C.L., Shu H., Smith O.S., Wall S.J., Senior M.L., Mitchell S.E., Kresovich S., Ziegle J. An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor. Appl. Genet. 1997, 95:163-173.
56. Sokal R.R., Rohlf F.J. The comparison of dendrograms by objective methods. Taxon 1962, 11:30-40.
57. Spaniolas S., May S.T., Bennett M.J., Tucker G.A. Authentication of coffee by means of PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis. J. Agric. Food Chem. 2006, 54:7466-7470.
58. Ujino-Ihara T., Taguchi Y., Moriguchi Y., Tsumura Y. An efficient method for developing SNP markers based on EST data combined with high resolution melting (HRM) analysis. BMC 2010, 3:51.
59. Uzun A., Yesiloglu T., Aka-Kacar Y., Tuzcu O., Gulsen O. Genetic diversity and relationships within citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Sci. Hortic. 2009, 121:306-312.
60. Varshney R.K., Chabane K., Hendre P.S., Aggarwal R.K., Graner A. Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci. 2007, 173:638-649.
61. Xu S.B., Tao Y.F., Yang Z.Q., Chu J.Y. A simple and rapid method used for silver staining and gel preservation. Hereditas 2002, 24:335-336.
62. Zaefizadeh M., Goliev R. Diversity and relationships among durum wheat landraces (subconvars) by SRAP and phenotypic marker polymorphism. Res. Biol. Sci. 2009, 4:960-966.
63. Zane L., Bargelloni L., Patarnello T. Strategies for microsatellite isolation. Mol. Ecol. 2002, 11:1-16.
64. Zerihun D., Vashist U., Boora K.S. Molecular characterization of citrus cultivars using DNA markers. IJBB 2009, 5:3.
65. Zhao W., Fang R., Pan Y., Yang Y., Chung J.W., Chung I.M., Park Y.J. Analysis of genetic relationships of mulberry (Morus L.) germplasm using sequence-related amplified polymorphism (SRAP) markers. Afr. J. Biotechnol. 2009, 8:2604-2610.