1887
Volume 2026, Issue 1
  • EISSN: 2223-506X

Abstract

Date palm (.) is a dioecious perennial of significant agricultural and socio-economic value in arid regions, yet its genetic improvement is constrained by a long juvenile phase and separate male and female plants. Microsatellite markers have emerged as key tools to overcome these limitations. They aid in assessing genetic diversity, cultivar identification, population structure analysis, somaclonal variation detection, and early sex determination using male-specific markers, enhancing breeding and plantation management. The advent of genome sequencing has enabled detailed identification and characterization of microsatellite motifs. The genome contains approximately 105,183 microsatellite motifs, with a higher frequency of simple/imperfect repeats than perfect ones. Dinucleotide repeats are most abundant, particularly AG/TC, AT/TA, and AC/TG, while TAA and GAA dominate among trinucleotide motifs, jointly accounting for 52% of all trinucleotide types. To date, 87 functionally validated, polymorphic microsatellite primer pairs have been developed for polymerase chain reaction-based amplification in .

Loading

Article metrics loading...

/content/journals/10.5339/connect.2026.2
2026-01-26
2026-01-27

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/connect/2026/1/connect.2026.issue1.2.html?itemId=/content/journals/10.5339/connect.2026.2&mimeType=html&fmt=ahah

References

  1. Chao CT, Krueger RR. The date palm (Phoenix dactylifera L.): overview of biology, uses, and cultivation. HortScience. 2007; 42:(5):1077–1082. doi: 10.21273/HORTSCI.42.5.1077
    [Google Scholar]
  2. Ghnimi S, Umer S, Karim A, Kamal-Eldin A. Date fruit (Phoenix dactylifera L.): an underutilized food seeking industrial valorization. NFS Journal. 2017;6:1–10. doi: 10.1016/j.nfs.2016.12.001
    [Google Scholar]
  3. Zhao Y, Williams R, Prakash CS, He G. Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.). BMC Plant Biology. 2012;12:237. doi: 10.1186/1471-2229-12-237
    [Google Scholar]
  4. Food and Agriculture Organization of the United Nations (FAO). Agriculture Organization of the United Nations (FAO). FAOSTAT statistical database. Rome: FAO; 2023. Available from: https://www.fao.org/faostat
  5. Khoulassa S, Khurshid H, Fokar M, Eliddrissy H, Outeha Y, Elfadil J, et al. Genetic diversity of Moroccan date palm revealed by microsatellite markers. Genetics and Molecular Biology. 2023; 46:(2):e20220021. doi: 10.1590/1678-4685-GMB-2022-0021
    [Google Scholar]
  6. Ahmed W, Feyissa T, Tesfaye K, Farrakh S. Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers. Journal of Genetic Engineering and Biotechnology. 2021; 19:(1):64. doi: 10.1186/s43141-021-00168-5
    [Google Scholar]
  7. Rahman H, Vikram P, Hammami Z, Singh RK. Recent advances in date palm genomics: a comprehensive review. Frontiers in Genetics. 2022;13:959266. doi: 10.3389/fgene.2022.959266
    [Google Scholar]
  8. Awan FS, Maryam, Jaskani MJ, Sadia B. Gender identification in date palm using molecular markers. In: Jain SM, Al-Khayri JM, Johnson DV. (eds.) Date palm biotechnology protocols. Vol II. New York: Springer; 2017. p. 209–225. doi: 10.1007/978-1-4939-7159-6_18
    [Google Scholar]
  9. Wang Y, Ihase LO, Htwe YM, Shi P, Zhang D, Li D, et al. Development of sex-linked SSR marker in the genus Phoenix and validation in P. dactylifera. Crop Science. 2020; 60:(5):2452–2466. doi: 10.1002/csc2.20187
    [Google Scholar]
  10. Banjare R, Nidhi N, Sood A. Physiological aspects of flowering, fruit setting, fruit development and fruit drop, regulation and their manipulation: a review. International Journal of Environment and Climate Change. 2023; 13:(12):205–224. doi: 10.9734/ijecc/2023/v13i123677
    [Google Scholar]
  11. Elshibli S. Genetic diversity and adaptation of date palm (Phoenix dactylifera L.). PhD thesis. Helsinki: University of Helsinki; 2009.
  12. Maryam, Jaskani MJ, Awan FS, Ahmad S, Khan IA. Development of molecular method for sex identification in date palm (Phoenix dactylifera L.) plantlets using novel sex-linked microsatellite markers. 3 Biotech. 2016; 6:(1):22. doi: 10.1007/s13205-015-0321-6
    [Google Scholar]
  13. Elmeer K, Mattat I. Marker-assisted sex differentiation in date palm using simple sequence repeats. 3 Biotech. 2012; 2:(3):241–247. doi: 10.1007/s13205-012-0052-x
    [Google Scholar]
  14. Ibrahimi M, Brhadda N, Ziri R, Fokar M, Iraqi D, Gaboun F, et al. Analysis of genetic diversity and population structure of Moroccan date palm (Phoenix dactylifera L.) using SSR and DAMD molecular markers. Journal of Genetic Engineering and Biotechnology. 2023; 21:(1):66. doi: 10.1186/s43141-023-00516-7
    [Google Scholar]
  15. Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One. 2010; 5:(9):e12762. doi: 10.1371/journal.pone.0012762
    [Google Scholar]
  16. Fang Y, Wu H, Zhang T, Yang M, Yin Y, Pan L, et al. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS One. 2012; 7:(5):e37164. doi: 10.1371/journal.pone.0037164
    [Google Scholar]
  17. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, et al. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnology. 2011;29:521–527. doi: 10.1038/nbt.1860
    [Google Scholar]
  18. Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W, Tan J, et al. Genome sequence of the date palm Phoenix dactylifera L. Nature Communications. 2013;4:2274. doi: 10.1038/ncomms3274
    [Google Scholar]
  19. Hamwieh A, Farah J, Moussally S, Al-Sham’aa K, Almer K, Khierallah H, et al. Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome. Acta Horticulturae. 2010;882:29. doi: 10.17660/ActaHortic.2010.882.29
    [Google Scholar]
  20. Schlötterer C. Evolutionary dynamics of microsatellite DNA. Chromosoma. 2000; 109:(6):365–371. doi: 10.1007/s004120000089
    [Google Scholar]
  21. Ellegren H. Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics. 2004;5:435–445. doi: 10.1038/nrg1348
    [Google Scholar]
  22. Buschiazzo E, Gemmell NJ. The rise, fall and renaissance of microsatellites in eukaryotic genomes. BioEssays. 2006; 28:(10):1040–1050. doi: 10.1002/bies.20470
    [Google Scholar]
  23. Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review. Molecular Ecology. 2002; 11:(1):1–16. doi: 10.1046/j.0962-1083.2001.01418.x
    [Google Scholar]
  24. Tóth G, Gáspári Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research. 2000; 10:(7):967–981. doi: 10.1101/gr.10.7.967
    [Google Scholar]
  25. Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Research. 2000; 10:(1):72–80.
    [Google Scholar]
  26. Mokhtar MM, Adawy SS, El-Assal SE-DS, Hussei. EH. Genic and intergenic SSR database generation, SNPs determination and pathway annotations, in date palm (Phoenix dactylifera L.). PLoS One. 2016; 11:(7):e0159268. doi: 10.1371/journal.pone.0159268
    [Google Scholar]
  27. Manju KP, Manimekalai R, Naganeeswaran SA, Arunachalam V, Karun A. Microsatellites mining in date palm (Phoenix dactylifera L.) and their cross transferability across Arecaceae family. Plant Omics. 2016; 9:(3):191–197. doi: 10.21475/poj.16.09.03.p7793
    [Google Scholar]
  28. Tangphatsornruang S, Somta P, Uthaipaisanwong J, Chanprasert J, Sangsrakru D, Seehalak W, et al. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biology. 2009;9:137. doi: 10.1186/1471-2229-9-137
    [Google Scholar]
  29. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics. 2000; 156:(2):847–854. doi: 10.1093/genetics/156.2.847
    [Google Scholar]
  30. Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, et al. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics. 2010;11:569. doi: 10.1186/1471-2164-11-569
    [Google Scholar]
  31. Akkaya MS, Bhagwat AA, Cregan PB. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics. 1992; 132:(4):1131–1139. doi: 10.1093/genetics/132.4.1131
    [Google Scholar]
  32. Lagercrantz U, Ellegren H, Andersson L. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Research. 1993; 21:(5):1111–1115. doi: 10.1093/nar/21.5.1111
    [Google Scholar]
  33. Morgante M, Olivieri A. PCR-amplified microsatellites as markers in plant genetics. Plant Journal. 1993; 3:(1):175–182.
    [Google Scholar]
  34. Winter P, Pfaff T, Udupa S, Hüttel B, Sharma P, Sahi S, et al. Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Molecular and General Genetics. 1999;262:90–101. doi: 10.1007/s004380051063
    [Google Scholar]
  35. Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, et al. EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genetics & Genomes. 2008; 4:1–10. doi: 10.1007/s11295-007-0083-3
    [Google Scholar]
  36. Ramchiary N, Nguyen VD, Li X, Hong CP, Dhandapani V, Choi SR, et al. Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives. DNA Research. 2011; 18:(5):305–320. doi: 10.1093/dnares/dsr017
    [Google Scholar]
  37. Squirrell J, Hollingsworth P, Woodhead M, Russell J, Lowe A, Gibby M, et al. How much effort is required to isolate nuclear microsatellites from plants?. Molecular Ecology. 2003; 12:(6):1339–1348. doi: 10.1046/j.1365-294X.2003.01825.x
    [Google Scholar]
  38. Kumar P, Gupta V, Misra A, Modi D, Pandey B. Potential of molecular markers in plant biotechnology. Plant Omics. 2009; 2:(4):141–162.
    [Google Scholar]
  39. Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity. 2011;107:1–15. doi: 10.1038/hdy.2010.152
    [Google Scholar]
  40. Hoffman JI, Nichols HJ. A novel approach for mining polymorphic microsatellite markers in silico. PLoS One. 2011; 6:(8):e23283. doi: 10.1371/journal.pone.0023283
    [Google Scholar]
  41. Robinson AJ, Love CG, Batley J, Barker G, Edwards D. Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics. 2004; 20:(9):1475–1476. doi: 10.1093/bioinformatics/bth104
    [Google Scholar]
  42. Xu X, Peng M, Fang Z, Xu X. The direction of microsatellite mutations is dependent upon allele length. Nature Genetics. 2000;24:396–399. doi: 10.1038/74238
    [Google Scholar]
  43. Thiel T, Michalek W, Varshney R, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics. 2003; 106:(3):411–422. doi: 10.1007/s00122-002-1031-0
    [Google Scholar]
  44. Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology. 2005; 23:(1):48–55. doi: 10.1016/j.tibtech.2004.11.005
    [Google Scholar]
  45. Billotte N, Marseillac N, Brottier P, Noyer J, Jacquemoud-Collet J, Moreau C, et al. Nuclear microsatellite markers for the date palm (Phoenix dactylifera L.): characterization and utility across the genus Phoenix and in other palm genera. Molecular Ecology Notes. 2004; 4:(2):256–258. doi: 10.1111/j.1471-8286.2004.00634.x
    [Google Scholar]
  46. Zehdi S, Trifi M, Billotte N, Marrakchi M, Pintaud JC. Genetic diversity of Tunisian date palms (Phoenixdactylifera L.) revealed by nuclear microsatellite polymprohism. Hereditas. 2004; 141:(3):278–287. doi: 10.1111/j.1601-5223.2004.01855.x
    [Google Scholar]
  47. Elshibli S, Korpelainen H. Microsatellite markers reveal high genetic diversity in date palm (Phoenix dactylifera L.) germplasm from Sudan. Genetica. 2007; 134:(2):251–260. doi: 10.1007/s10709-007-9232-8
    [Google Scholar]
  48. Al-Ruqaishi IA, Davey M, Alderson P, Mayes S. Genetic relationships and genotype tracing in date palms (Phoenix dactylifera L.) in Oman, based on microsatellite markers. Plant Genetic Resources. 2008; 6:(1):70–72. doi: 10.1017/S1479262108923820
    [Google Scholar]
  49. Elmeer K, Mattat I. Genetic diversity of Qatari date palm using SSR markers. Genetics and Molecular Research. 2015; 14:(141):1624–1635. doi: 10.4238/2015.March.6.9
    [Google Scholar]
  50. Akkak A, Scariot V, Marinoni DT, Boccacci P, Beltramo C, Botta R. Development and evaluation of microsatellite markers in Phoenix dactylifera L. and their transferability to other Phoenix species. Biologia Plantarum. 2009; 53:(1):164–166. doi: 10.1007/s10535-009-0026-y
    [Google Scholar]
  51. Malek J. Next generation DNA sequencing applied to the date palm tree (Phoenix dactylifera). Acta Horticulturae. 2010;882:249–252. doi: 10.17660/ActaHortic.2010.882.27
    [Google Scholar]
  52. Elmeer K, Sarwath H, Malek J, Baum M, Hamwieh A. New microsatellite markers for assessment of genetic diversity in date palm (Phoenix dactylifera L.). 3 Biotech. 2011;1:91–97. doi: 10.1007/s13205-011-0010-z
    [Google Scholar]
  53. Arabnezhad H, Bahar M, Mohammadi HR, Latifian M. Development, characterization and use of microsatellite markers for germplasm analysis in date palm (Phoenix dactylifera L.). Scientia Horticulturae. 2012;134:150–156. doi: 10.1016/j.scienta.2011.11.032
    [Google Scholar]
  54. Al-Faifi SA, Migdadi HM, Algamdi SS, Khan MA, Ammar MH, Al-Obeed RS, et al. Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars. Electronic Journal of Biotechnology. 2016;21:18–25. doi: 10.1016/j.ejbt.2016.01.006
    [Google Scholar]
  55. Faqir N, Muhammad A, Hyder MZ. Diversity assessment and cultivar identification in date palm through molecular markers- a review. Turkish Journal of Agriculture - Food Science and Technology. 2017; 5:(12):1516–1523. doi: 10.24925/turjaf.v5i12.1516-1523.1331
    [Google Scholar]
  56. Naqvi SA, Shafqat W, Haider MS, Awan FS, Khan IA, Jaskani MJ. Gender determination of date palm. In: Al-Khayri JM, Jain SM, Johnson DV. (eds.) The date palm genome. Vol. 1: Phylogeny, biodiversity and mapping. Cham: Springer; 2021. p. 161–177. doi: 10.1007/978-3-030-73746-7_7
  57. Salameh A, Hamdan YA, Aslan K. Use of microsatellite markers for sex determination in date palm (Phoenix dactylifera L.) cv. Medjool. Genetic Resources and Crop Evolution. 2024; 71:(7):3575–3581. doi: 10.1007/s10722-024-01880-0
    [Google Scholar]
  58. Mahdy EM, El-Sharabasy SF. Date palm genetic identification and improvement utilizing molecular markers and DNA barcoding. In: Al-Khayri JM, Jain SM, Johnson DV. (eds.) The date palm genome. Vol. 1: Phylogeny, biodiversity and mapping. Cham: Springer; 2021. p. 101–134. doi: 10.1007/978-3-030-73746-7_5
    [Google Scholar]
  59. Ahmed HA, Basry MA, Zakaria HM, Ibrahim SD, Radwan KH. Genetic marker identification and functional genomics in date palm (Phoenix dactylifera L.) for economic trait improvement and resilience enhancement. International Journal of Agriculture and Biology. 2025; 33:(06):1–8. doi: 10.17957/IJAB/15.2324
    [Google Scholar]
  60. Khierallah HSM, Bader SM, Baum M, Hamwieh A. Genetic diversity of Iraqi date palms revealed by microsatellite polymorphism. Journal of the American Society for Horticultural Science. 2011; 136:(4):282–287. doi: 10.21273/JASHS.136.4.282
    [Google Scholar]
  61. Elmeer K, Mattat I, Al-Malki A, Al-Mamari AG, Al-Jabri A, Buhendi A, et al. Intra-cultivar variability at microsatellite loci in date palm cultivars across the GCC countries. QScience Connect. 2020; 2020:(1):3. doi: 10.5339/connect.2020.3
    [Google Scholar]
  62. Elmeer K, Ahmed A, Mattat I. Genetic diversity of South Libyan elite date palm using SSR markers. Jordan Journal of Biological Sciences. 2025; 18:(1):155–161. doi: 10.54319/jjbs/180117
    [Google Scholar]
  63. Takele D, Tsegaw M, Indracanti M. Genetic diversity assessment in some landraces and varieties of date palm (Phoenix dactylifera L.) from Afar Region, Ethiopia, using ISSR markers. Ecological Genetics and Genomics. 2021;19:100085. doi: 10.1016/j.egg.2021.100085
    [Google Scholar]
  64. Johnson DV. Introduction: date palm biotechnology from theory to practice. In: SM Jain, Al-Khayri JM, Johnson DV. (eds.) Date palm biotechnology. Dordrecht: Springer; 2011. p. 1–11. doi: 10.1007/978-94-007-1318-5
    [Google Scholar]
  65. Khanam S, Sham A, Bennetzen JL, Aly MA. Molecular marker-based genetic variation in date palm. Australian Journal of Crop Science. 2012; 6:(8):1236–1244.
    [Google Scholar]
  66. Mirani AA, Teo CH, Markhand GS, Abul-Soad AA, Harikrishna JA. Detection of somaclonal variations in tissue cultured date palm (Phoenix dactylifera L.) using transposable element-based markers. Plant Cell, Tissue and Organ Culture. 2020; 141:(1):119–130. doi: 10.1007/s11240-020-01772-y
    [Google Scholar]
  67. Mesbahi Q, Alla A, Boulida Z, Mzabri I, Lafdil M, Kouddane N, et al. Genetic improvement of the date palm (Phoenix dactylifera L.): strategies and analysis techniques: review. E3S Web of Conferences. 2025;632:01032. doi: 10.1051/e3sconf/202563201032
    [Google Scholar]
  68. Hasan M, Abdullah HM, Hasibuzzaman ASM, Ali MA. Date palm genetic resources for breeding. In: Priyadarshan PM, Jain SM. (eds.) Cash crops: genetic diversity, conservation and utilization. Cham: Springer; 2021. p. 479–503. doi: 10.1007/978-3-030-74926-2_12
    [Google Scholar]
/content/journals/10.5339/connect.2026.2
Loading
/content/journals/10.5339/connect.2026.2
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error