Stocktake Sale on now: wide range of books at up to 70% off!
Register      Login
Functional Plant Biology Functional Plant Biology Society
Plant function and evolutionary biology
Shopping Cart: ( empty )
You are here: Home > Journals > FP > FP25021
REVIEW
Contents Vol 52(6)

Shaping the future of date palm (Phoenix dactylifera) through new genetic improvement strategies

Nasser Abdullah Ghdayer Al Kaabi A , Karthishwaran Kandhan A , Faisal Hayat https://orcid.org/0000-0001-8762-9693 A , Saif Ali Matar Al Blooshi A , Mohamed S. Sheteiwy A and Mohammed Alyafei A *
+ Author Affiliations
- Author Affiliations

A Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.

* Correspondence to: mohammed.s@uaeu.ac.ae

Handling Editor: Sajid Fiaz

Functional Plant Biology 52, FP25021 https://doi.org/10.1071/FP25021
Submitted: 15 January 2025  Accepted: 13 May 2025  Published: 5 June 2025

© 2025 The Author(s) (or their employer(s)). Published by CSIRO Publishing

Abstract

Conventional breeding of date palm (Phoenix dactylifera) is inherently challenging due to its long generation time, dioecious nature, and high genetic heterogeneity. However, current developments in genomics and molecular biology offer promising avenues for accelerating breeding programs, particularly through high-throughput technologies including functional genomics. This article reviews genomic tools such as like CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated protein 9) that may bring significant changes in date palm breeding. The CRISPR-Cas9 system enables scientists to accurately target genomic regions, which helps enhance breeding accuracy by adding advantageous traits and eliminating unfavorable genes through precision editing. Transcriptome and metabolome analyses have also explained the regulation of thousands of differentially expressed genes (DEGs) and metabolic pathways under environmental stress. These studies contribute to enhance the knowledge of stress tolerance mechanisms, which include the secondary metabolic process of flavonoids. Genomic studies illustrating single nucleotide polymorphism (SNP)-based diversity between cultivars from north African and the Arabian Gulf provide new genetic resources for selective breeding. The work relates genome-wide association studies (GWAS) and miRNA profiling to elucidate key regulatory networks involved in fruit development and stress resilience. The integration of such advanced technologies, especially the CRISPR-Cas9 system, is revolutionizing the landscape of date palm breeding, opening new avenues for accelerated development of superior cultivars that meet the needs of modern agriculture.

Keywords: CRISPR-Cas9, date palm breeding, date palm sex determination, disease management, functional genomics, genomic tools, SNP diversity, stress tolerance.

References

Abdul-Hamid NA, Mustaffer NH, Maulidiani M, Mediani A, Ismail IS, Tham CL, Shadid K, Abas F (2020) Quality evaluation of the physical properties, phytochemicals, biological activities and proximate analysis of nine Saudi date palm fruit varieties. Journal of the Saudi Society of Agricultural Sciences 19, 151-160.
| Crossref | Google Scholar |

Ahmad M, Abdul Aziz M, Sabeem M, Kutty MS, Sivasankaran SK, Brini F, Xiao TT, Blilou I, Masmoudi K (2024) Date palm transcriptome analysis provides new insights on changes in response to high salt stress of colonized roots with the endophytic fungus Piriformospora indica. Frontiers in Plant Science 15, 1400215.
| Crossref | Google Scholar | PubMed |

Ahmed W, Feyissa T, Tesfaye K, Farrakh S (2021) Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers. Journal of Genetic Engineering and Biotechnology 19, 64.
| Crossref | Google Scholar |

Al-Khayri JM, Naik PM, Jain SM, Johnson DV (2018) Advances in date palm (Phoenix dactylifera L.) breeding. In ‘Advances in plant breeding strategies: fruits’. (Eds J Al-Khayri, S Jain, D Johnson) pp. 727–771. (Springer: Cham) 10.1007/978-3-319-91944-7_18

Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W, Tan J, Yu X, Liu J, Pan L, Zhang T, Yin Y, Xin C, Wu H, Zhang G, Ba Abdullah MM, Huang D, Fang Y, Alnakhli YO, Jia S, Yin A, Alhuzimi EM, Alsaihati BA, Al-Owayyed SA, Zhao D, Zhang S, Al-Otaibi NA, Sun G, Majrashi MA, Li F, Wang J, Yun Q, Alnassar NA, Wang L, Yang M, Al-Jelaify RF, Liu K, Gao S, Chen K, Alkhaldi SR, Liu G, Zhang M, Guo H, Yu J (2013) Genome sequence of the date palm Phoenix dactylifera L. Nature Communications 4, 2274.
| Crossref | Google Scholar |

Al-Shwyeh HA (2019) Date palm (Phoenix dactylifera L.) fruit as potential antioxidant and antimicrobial agents. Journal of Pharmacy and Bioallied Sciences 11, 1-11.
| Crossref | Google Scholar |

Belhaj K, Chaparro-Garcia A, Kamoun S, Nekrasov V (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9, 39.
| Crossref | Google Scholar |

Boudeffeur S, Ameur Ameur A, Aci MM, Khelafi H, Laaboudi A, Khersi M, Makhzoum A, Khelifi L (2021) Phenotypic and genetic characterization of date palm cultivars resistant to bayoud disease. Plant Science Today 8, 804-814.
| Crossref | Google Scholar |

Bourgis F, Kilaru A, Cao X, Ngando-Ebongue GF, Drira N, Ohlrogge JB, Arondel V (2011) Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning. Proceedings of the National Academy of Sciences of the United States of America 108, 12527-12532.
| Crossref | Google Scholar |

Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D (2023) A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Current Research in Food Science 7, 100579.
| Crossref | Google Scholar |

De Mori G, Cipriani G (2023) Marker-assisted selection in breeding for fruit trait improvement: a review. International Journal of Molecular Sciences 24, 8984.
| Crossref | Google Scholar |

El Modafar C (2010) Mechanisms of date palm resistance to Bayoud disease: current state of knowledge and research prospects. Physiological and Molecular Plant Pathology 74, 287-294.
| Crossref | Google Scholar |

El-Mounadi K, Morales-Floriano ML, Garcia-Ruiz H (2020) Principles, applications, and biosafety of plant genome editing using CRISPR-Cas9. Frontiers in Plant Science 11, 56.
| Crossref | Google Scholar |

Fang Y, Wu H, Zhang T, Yang M, Yin Y, Pan L, Yu X, Zhang X, Hu S, Al-Mssallem IS, Yu J (2012) A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS ONE 7, e37164.
| Crossref | Google Scholar |

Giovino A, Bertolini E, Fileccia V, Al Hassan M, Labra M, Martinelli F (2015) Transcriptome analysis of phoenix canariensis chabaud in response to Rhynchophorus ferrugineus olivier attacks. Frontiers in Plant Science 6, 817.
| Crossref | Google Scholar |

Gros-Balthazard M, Hazzouri KM, Flowers JM (2018) Genomic insights into date palm origins. Genes 9, 502.
| Crossref | Google Scholar |

Hadrami IE, Hadrami AE (2009) Breeding date palm. ‘Breeding plantation tree crops: tropical species’. (Eds S Mohan Jain, PM Priyadarshan) pp. 191–216. (Springer: Newyork, NY, USA) 10.1007/978-0-387-71201-7_6

Hasan M, Abdullah HM, Hasibuzzaman ASM, Ali MA (2022) Date palm genetic resources for breeding. In ‘Cash crops: genetic diversity, erosion, conservation and utilization’. (Eds P Priyadarshan, SM Jain) pp. 479–503. 10.1007/978-3-030-74926-2_12

Hazzouri KM, Flowers JM, Visser HJ, Khierallah HSM, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD (2015) Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nature Communications 6, 8824.
| Crossref | Google Scholar |

Hazzouri KM, Gros-Balthazard M, Flowers JM, Copetti D, Lemansour A, Lebrun M, Masmoudi K, Ferrand S, Dhar MI, Fresquez ZA, Rosas U, Zhang J, Talag J, Lee S, Kudrna D, Powell RF, Leitch IJ, Krueger RR, Wing RA, Amiri KMA, Purugganan MD (2019) Genome-wide association mapping of date palm fruit traits. Nature Communications 10, 4680.
| Crossref | Google Scholar |

He Z, Zhang C, Liu W, Lin Q, Wei T, Aljohi HA, Chen WH, Hu S (2017) DRDB: An online date palm genomic resource database. Frontiers in Plant Science 8, 1889.
| Crossref | Google Scholar |

Iqbal Z, Sattar MN, Al-Khayri JM (2021) Whole-genome mapping of date palm (Phoenix Dactylifera L.). In ‘The date palm genome, Vol. 1. Compendium of plant genomes’. (Eds JM Al-Khayri, SM Jain, DV Johnson) pp. 181–199. (Springer: Cham) 10.1007/978-3-030-73746-7_8

Jamil S, Shahzad R, Kanwal S, Yasmeen E, Rahman SU, Iqbal MZ (2020) DNA fingerprinting and population structure of date palm varieties grown in Punjab Pakistan using simple sequence repeat markers. International Journal of Agriculture and Biology 23, 943-950.
| Crossref | Google Scholar |

Kassem HS, Alotaibi BA, Ahmed A, Aldosri FO (2020) Sustainable management of the red palm weevil: the nexus between farmers’ adoption of integrated pest management and their knowledge of symptoms. Sustainability 12, 9647.
| Crossref | Google Scholar |

Kaur N, Alok A, Ahmed ZFR (2024) Future perspective on CRISPR-Cas9-based targeted genome editing in date palms. In ‘Genetic engineering of crop plants for food and health security: Volume 2’. (Eds S Tiwari, B Koul) pp. 445–468. (Springer)

Khan FS, Goher F, Zhang D, Shi P, Li Z, Htwe YM, Wang Y (2022) Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits. Frontiers in Plant Science 13, 1042828.
| Crossref | Google Scholar |

Kharb P, Mitra C (2017) Early sex identification in date palm by male-specific sequence-characterized amplified region (SCAR) markers. In ‘Date palm biotechnology protocols Volume II. Methods in molecular biology’. (Eds J Al-Khayri, S Jain, D Johnson) pp. 199–207. (Humana Press: New York, NY, USA) 10.1007/978-1-4939-7159-6_17

Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar V V., Zheng Z, Joung JK (2015) Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nature Biotechnology 33, 1293-1298.
| Crossref | Google Scholar |

Kordrostami M, Mafakheri M, Al-Khayri JM (2022) Date palm (Phoenix dactylifera L.) genetic improvement via biotechnological approaches. Tree Genet Genomes 18, 26.
| Crossref | Google Scholar |

Lee CM, Cradick TJ, Fine EJ, Bao G (2016) Nuclease target site selection for maximizing on-target activity and minimizing off-target effects in genome editing. Molecular Therapy 24, 475-487.
| Crossref | Google Scholar |

Maher M, Ahmad H, Nishawy E, Li Y, Luo J (2021) Novel transcriptome study and detection of metabolic variations in UV-B-treated date palm (Phoenix dactylifera cv. khalas). International Journal of Molecular Sciences 22, 2564.
| Crossref | Google Scholar |

Mathew LS, Seidel MA, George B, Mathew S, Spannagl M, Haberer G, Torres MF, Al-Dous EK, Al-Azwani EK, Diboun I, Krueger RR, Mayer KFX, Mohamoud YA, Suhre K, Malek JA (2015) A genome-wide survey of date palm cultivars supports two major subpopulations in Phoenix dactylifera. G3: Genes, Genomes, Genetics 5, 1429-1438.
| Crossref | Google Scholar |

Montecillo JAV, Chu LL, Bae H (2020) CRISPR-Cas9 system for plant genome editing: current approaches and emerging developments. Agronomy 10, 1033.
| Crossref | Google Scholar |

Naqvi SA, Shafqat W, Haider MS, Awan FS, Khan IA, Jaskani MJ (2021) Gender determination of date palm. In ‘The date palm genome, vol 1: phylogeny, biodiversity and mapping’. (Eds JM Al-Khayri, S. Mohan Jain, DV Johnson) pp. 161–177. (Springer: Cham) 10.1007/978-3-030-73746-7_7

Nishad R, Ahmed TA (2020) Survey and identification of date palm pathogens and indigenous biocontrol agents. Plant Disease 104, 2498-2508.
| Crossref | Google Scholar |

Noutfia Y, Ropelewska E (2023) Comprehensive characterization of date palm fruit ‘Mejhoul’ (Phoenix dactylifera L.) using image analysis and quality attribute measurements. Agriculture 13, 74.
| Crossref | Google Scholar |

Othmani A, Hamza H, Kadri K, Sellemi A, Leus L, Werbrouck SPO (2024) The promising potential of triploidy in date palm (Phoenix dactylifera L.) breeding. Plants 13, 815.
| Crossref | Google Scholar |

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183.
| Crossref | Google Scholar |

Radwan O, Arro J, Keller C, Korban SS (2015) RNA-Seq transcriptome analysis in date palm suggests multi-dimensional responses to salinity stress. Tropical Plant Biology 8, 74-86.
| Crossref | Google Scholar |

Rahman H, Vikram P, Hammami Z, Singh RK (2022) Recent advances in date palm genomics: A comprehensive review. Frontiers in Genetics 13, 959266.
| Crossref | Google Scholar |

Rasheed A, Gill RA, Hassan MU, Mahmood A, Qari S, Zaman QU, Ilyas M, Aamer M, Batool M, Li H, Wu Z (2021) A critical review: recent advancements in the use of crispr/cas9 technology to enhance crops and alleviate global food crises. Current Issues in Molecular Biology 43, 1950-1976.
| Crossref | Google Scholar |

Rekik I, Chaabene Z, Grubb CD, Drira N, Cheour F, Elleuch A (2015) In silico characterization and molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour. Theoretical Biology and Medical Modelling 12, 23.
| Crossref | Google Scholar |

Rekik I, Chaâbene Z, Kriaa W, Rorat A, Franck V, Hafedh M, Elleuch A (2019) Transcriptome assembly and abiotic related gene expression analysis of date palm reveal candidate genes involved in response to cadmium stress. Comparative Biochemistry and Physiology Part - C: Toxicology and Pharmacology 225, 108569.
| Crossref | Google Scholar |

Sabir JSM, Arasappan D, Bahieldin A, Abo-Aba S, Bafeel S, Zari TA, Edris S, Shokry AM, Gadalla NO, Ramadan AM, Atef A, Al-Kordy MA, El-Domyati FM, Jansen RK (2014) Whole mitochondrial and plastid genome SNP analysis of nine date palm cultivars reveals plastid heteroplasmy and close phylogenetic relationships among cultivars. PLoS ONE 9, e94158.
| Crossref | Google Scholar |

Safronov O, Kreuzwieser J, Haberer G, Alyousif MS, Schulze W, Al-Harbi N, Arab L, Ache P, Stempfl T, Kruse J, Mayer KX, Hedrich R, Rennenberg H, Salojarvi J, Kangasjarvi J (2017) Detecting early signs of heat and drought stress in Phoenix dactylifera (date palm). PLoS ONE 12, e0177883.
| Crossref | Google Scholar |

Saleh AA, Sharafaddin AH, El_Komy MH, Ibrahim YE, Hamad YK (2021) Molecular and physiological characterization of Fusarium strains associated with different diseases in date palm. PLoS ONE 16, e0254170.
| Crossref | Google Scholar |

Sattar MN, Iqbal Z, Tahir MN, Shahid MS, Khurshid M, Al-Khateeb AA, Al-Khateeb SA (2017) CRISPR/Cas9: A practical approach in date palm genome editing. Frontiers in Plant Science 8, 1469.
| Crossref | Google Scholar |

Sattar MN, Iqbal Z, Al-Khayri JM (2021) CRISPR-Cas based precision breeding in date palm: future applications. In ‘The date palm genome, Vol. 2. Compendium of plant genomes’. (Eds JM Al-Khayri, SM Jain, DV Johnson) pp. 169–199. (Springer: Cham) 10.1007/978-3-030-73750-4_9

Shan S, Soltis PS, Soltis DE, Yang B (2020) Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. Applications in Plant Sciences 8, e11314.
| Crossref | Google Scholar |

Swarup S, Cargill EJ, Crosby K, Flagel L, Kniskern J, Glenn KC (2021) Genetic diversity is indispensable for plant breeding to improve crops. Crop Science 61, 839-852.
| Crossref | Google Scholar |

Wang Y, Ihase LO, Htwe YM, Shi P, Zhang D, Li D, Emoghene BO, Iserhienrhien A (2020) Development of sex-linked SSR marker in the genus Phoenix and validation in P. dactylifera. Crop Science 60, 2452–2466. 10.1002/csc2.20187

Xiao Y, Xia W, Yang Y, Mason AS, Lei X, Ma Z (2013) Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera). PLoS ONE 8, e71435.
| Crossref | Google Scholar |

Xie K, Zhang J, Yang Y (2014) Genome-wide prediction of highly specific guide RNA spacers for CRISPR-Cas9-mediated genome editing in model plants and major crops. Molecular Plant 7, 923-926.
| Crossref | Google Scholar |

Xin C, Liu W, Lin Q, Zhang X, Cui P, Li F, Zhang G, Pan L, Al-Amer A, Mei H, Al-Mssallem IS, Hu S, Al-Johi HA, Yu J (2015) Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development. Genomics 105, 242-251.
| Crossref | Google Scholar |

Yaish MW, Sunkar R, Zheng Y, Ji B, Al-Yahyai R, Farooq SA (2015) A genome-wide identification of the miRNAome in response to salinity stress in date palm (Phoenix dactylifera L.). Frontiers in Plant Science 6, 946.
| Crossref | Google Scholar |

Yarra R, Cao H, Jin L, Mengdi Y, Zhou L (2020) CRISPR/Cas mediated base editing: a practical approach for genome editing in oil palm. 3 Biotech 10, 306.
| Crossref | Google Scholar |

Yin Y, Zhang X, Fang Y, Pan L, Sun G, Xin C, Abdullah MMB, Yu X, Hu S, Al-Mssallem IS, Yu J (2012) High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.). Plant Molecular Biology 78, 617-626.
| Crossref | Google Scholar |

Zheng X, Yang S, Zhang D, Zhong Z, Tang X, Deng K, Zhou J, Qi Y, Zhang Y (2016) Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism. Plant Cell Reports 35, 1545-1554.
| Crossref | Google Scholar |