Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.)

BMC Plant Biology

Volumn 12, Issue , 2012, Pages

  Zhao, Yongli ^a   Williams, Roxanne ^a   Prakash, C S ^a   He, Guohao ^a  

^a TUSKEGEE UNIVERSITY   (United States)

Author keywords

Date palm; EST sequence; Gene ontology; Genic marker; Polymorphism

Indexed keywords

PHOENIX DACTYLIFERA;

MICROSATELLITE DNA; PLANT DNA;

ARECACEAE; ARTICLE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENETIC MARKER; GENETICS; MOLECULAR GENETICS;

ARECACEAE; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENETIC MARKERS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, DNA;

MLCS; MLOWN;

EID: 84870897244     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-12-237     Document Type: Article

References (46)

1. Barrow S. A monograph of phoenix L. (palmae: Coryphoideae). Kew Bull 1998, 53:513-575.
2. Jain SM, Al-Khayri J, Johnson DV, Jain SM, et al. Date palm biotechnology 2011, Dordrecht Heidelberg London New York: Springer Science+Business Media B.V.
3. Krueger RR, et al. Chapter 16 date palm germplasm in date palm biotechnology. Date palm biotechnology 2011, Springer Science+Business Media B.V, Jain SM.
4. Elhoumaizi MA, Saaidi M, Oihabi M, Cilas C. Phenotypic diversity of date-palm cultivars (Phoenix dactylifera L.) from Morocco. Genet Resour Crop Evol 2002, 49:483-490.
5. Sedra MH, Lashermes P, Trouslot P, et al. Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers. Euphytica 1998, 103:75-82.
6. Benkhalifa A. Gestion De La Diversite' Ge'Ne'Tique Du Palmier Dattier En Alge'Rie 1999, Marrakech, Morocco: Paper presented at the workshop constitution at organisation D'E' Quipesde Recherche Scientifique Dans Les Domainnes De Foresterie Et Des Arbres Fruitiers, 13-15 April.
7. Trifi M, Rhouma A, Marrakchi M. Phylogenetic relationships in Tunisian date-palm (Phoenix dactylifera L.) germplasm collection using DNA amplification fingerprinting. Agronomie 2000, 20:665-671.
8. Al-Khalifah NS, Askari E. Molecular phylogeny of date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia by DNA fingerprinting. Theor Appl Genet 2003, 107:1266-1270. 10.1007/s00122-003-1369-y, 12879257.
9. Soliman SS, Ali BA, Ahmed MMM. Genetic comparisons of Egyptian date palm cultivars (Phoenix dactylifera L.) by RAPD-PCR. Afr J Biotechnol 2003, 2:86-87.
10. Adawy SS, Hussein EHA, Ismail SEME, El-Itriby HA. Genomic diversity in date palm (Phoenix dactylifera L.) as revealed by AFLPs in comparison to RAPDs and ISSRs. Arab J Biotechnol 2005, 8:99-114.
11. Cao BR, Chao CT. Identification of date cultivars in California using AFLP markers. Hortic Sci 2002, 37:966-968.
12. El-Assar AM, Krueger RR, Devanad PS, Chao CT. Genetic analysis of Egyptian date (Phoenix dactylifera L.) accessions using AFLP markers. Genet Resour Crop Evol 2005, 52:601-607.
13. Soumaya RC, Ghada B, Sonia DD, Salwa ZA, Trifi M. Molecular research on the genetic diversity of Tunisian date palm (phoenix dactylifera L.) using the random amplified microsatellite polymorphism (RAMPO) and amplified fragment length polymorphism (AFLP) methods. Afr J Biotechnol 2011, 10(51):10352-10365.
14. Zehdi S, Sakka H, Rhouma A, Salem AOM, Marrakchi M, Trifi M. Analysis of Tunisian date palm germplasm using simple sequence repeat primers. Afr J Biotechnol 2004, 3:215-219.
15. Elshibli S, Korpelainen H. Microsallite markers reveal high genetic diversity in date palm (Phoenix dactylifera L.) germplasm from Sudan. Genetica 2007, 134:251-260.
16. Al-Ruqaishi IA, Davey M, Alderson P, Mayes S. Genetic relationships and genotype tracing in date palm (Phoenix dactylifera L.) in Oman based on microsatellite markers. Plant Genet Resour 2008, 61:70-72.
17. Ahmed TA, Al-Qaradawi A. Molecular phylogeny of Qatari date palm genotypes using simple sequence repeats markers. Biotechnology 2009, 8:126-131.
18. Malek JA. Next generation DNA sequencing applied to the Date palm tree (Phoenix dactylifera). Acta Hortic 2010, 882:249-252.
19. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J, Arondel V, Ohlrogge J, Saie IJ, Suliman-Elmeer K, Bennetzen JL, Kruegger RR, Malek JA. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 2011, 29:521-527. 10.1038/nbt.1860, 21623354.
20. Andersen JB, Lubberstedt T. Functional markers in plants. Trends Plant Sci 2003, 8(11):554-560. 10.1016/j.tplants.2003.09.010, 14607101.
21. Chen CX, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, Soneji JR, McCollum G, Gmitter FG. EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliate. Tree Genetics Genomes 2008, 4:1-10.
22. Durand J, Bodénès C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herrán A, Ikaran Z, Cabané C, Ueno S, Alberto F, Dumoulin PY, Guichoux E, de Daruvar A, Kremer A, Plomion C. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genom 2010, 11:570.
23. Ramchiary N, Nguyen VD, Li XN, Hong CP, Dhandapani V, Choi SR, Yu G, Piao ZY, Lim YP. Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica ralatives. DNA Res 2011, 18(5):305-320. 10.1093/dnares/dsr017, 3190952, 21768136.
24. Qi XL, Cui F, Li Y, Ding AM, Li J, Chen GL, Wang HG. Molecular tagging wheat powdery mildew resistance gene pm21 by EST-SSR and STS markers. Mol Plant Breed 2010, 1(4).
25. Zhang J, Yang W, Cui X, Yu H, Jin H, Chen Z, Shen T. Breeding strains of Panax notoginsent by using EST-SSR markers. Zhongquo Zhong Yao Za Zhi 2011, 36(2):97-101.
26. Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends Biotechnol 2005, 23(1):48-55. 10.1016/j.tibtech.2004.11.005, 15629858.
27. Billotte N, Marseilla N, Brottier P, Noyer JL, Jacquemoud-Collet JP, Moreau C, Couvreur T, Chevallier MH, Pintaud JC, Risterucci AM. Nuclear microsatellite markers for the date palm (Phoenix dactylifera L.): characterization, utility across the genus Phoenix and in other palm genera. Mol Ecol Notes 2004, 4:256-258.
28. Akkak A, Scariot V, Torello Marinoni D, Boccacci P, Beltramo C, Botta R. Development and evaluation of microsatellite markers in Phoenix dactylifera L. and their transferability to other Phoenix species. Biol Plant 2009, 53:164-166.
29. Elmeer K, Sarwath H, Malek J, Baum M, Hamwieh A. New microsatellite markers for assessment of genetic diversity in date palm (Phoenix dactylifera L.). Biotech 2011, 1(2):91-97.
30. Palmieri DA, Novelli VM, Bastianel M, Cristofani-Yaly M, Astua-Monge G, Carlos EF, de Oliveira AC, Machado MA. Frequency and distribution of microsatellites from ESTs of citrus. Genet Mol Biol 2007, 30(3):1009-1018.
31. Qiu L, Yang C, Tian B, Yang JB, Liu A. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol 2010, 10:278. 10.1186/1471-2229-10-278, 3017068, 21162723.
32. Tang S, Okashah RA, Cordonnier-Pratt MM, Pratt LH, Ed Johnson V, Taylor CA, Arnold ML. Knapp SJ: EST and EST-SSR marker resources for Iris. BMC Plant Biol 2009, 9:72. 10.1186/1471-2229-9-72, 2703627, 19515254.
33. Ting NC, Zaki NM, Rosli R, Low ET, Ithnin M, Cheah SC, Tan SG, Singh R. SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. J Genet 2010, 89(2):135-145. 10.1007/s12041-010-0053-7, 20861564.
34. Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ. Analyses of expressed sequence tags from Apple. Plant Physiol 2006, 141:147-166. 10.1104/pp.105.076208, 1459330, 16531485.
35. Mun JH, Kim DJ, Choi HK, Gish J, Debelle F, Mudge J, Denny R, Endre G, Saurat O, Dudez AM, Kiss GB, Roe B, Young ND, Cook DR. Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps. Genetics 2006, 172:2541-2555. 1456377, 16489220.
36. Ellis JR, Burke JM. EST-SSRs as a resource for population genetic analyses. Heredity 2007, 99:125-132. 10.1038/sj.hdy.6801001, 17519965.
37. Saker MM, Moursy HA. Molecular characterization of Egyptian date palm: 11 RAPD fingerprints. Proceeding first international conference on date palms, Al-Ain, United Arab Emirates, March 8-10 1998, 173-182.
38. Adawy SS, Hussein EHA, El-Khishin D, Saker MM, El-Itriby HA. Genetic variability studies and molecular fingerprinting of some Egyptian date palm (Phoenix dactylifera L.) cultivars II-RAPD and ISSR profiling. Arab J Biotechnol 2002, 5:225-236.
39. Hussein EHA, Adawy SS, El Khishin D, Moharam H, El-Itriby HA. Genetic variability studies and molecular fingerprinting of some Egyptian date palm (Phoenix dactylifera L.) cultivars. 1-A preliminary study using RAPD markers. Arab J Biotechnol 2002, 5(2):217-224.
40. Hussein Ebtissam HA, Adawy SS, Ismail SEM, El-Itriby HA. Molecular characterization of some Egyptian date palm germplasm using RAPD and ISSR markers. Arab J Biotech 2005, 8(1):83-98.
41. Ahmed MMM, Soliman SS, Elsayed EH. Molecular identification of some Egyptian date palm males by females varieties (Phoenix dactylifera L.) using DNA markers. J Appl Sci Res 2006, 2:270-275.
42. Wen MF, Wang HY, Xia ZQ, Zou ML, Lu C, Wang WQ. Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. BMC Res Notes 2010, 3:42. 10.1186/1756-0500-3-42, 2844395, 20181259.
43. Emebiri LC. An EST-SSR marker tightly linked to the barley male sterility gene (msg6) located on chromosome 6H. J Hered 2010, 101:769-774. 10.1093/jhered/esq083, 20650932.
44. Wang HZ, Li SJ, Yang RH, Guan W. EST-SSR marker linked to cucumber target leaf spot resistance-related gene. Acta Hort (ISHS) 2010, 871:49-56.
45. You Frank M, Huo N, Gu YQ, Luo MC, Ma YQ, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: a high throughput web application for PCR and sequencing primer designi. BMC Bioinforma 2008, 9:253.
46. Conesa A, Götz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676. 10.1093/bioinformatics/bti610, 16081474.