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Highlights in BioScience                                                                       
 

 

 

Highlights in BioScience       DOI:10.36462/H.BioSci.20182                              August 2018 | Volume1 

 
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Citation: Rslan W. M. (2018) Sugar 

beet artificial seeds an overview. 

Highlights in BioScience, Volume 

1.Article ID 20182, dio:10.36462/ 

H.BioSci.20182 

 

 

 

 

 

 

 

Received: May 22, 2018 

 

Accepted: July 17, 2018 

 

Published: August 12, 2018 

 

Copyright:© 2018 Rslan. This is an 

open access article distributed under 

the terms of the Creative Commons 

Attribution License, which permits 

unrestricted use, distribution, and 

reproduction in any medium, provided 

the original author and source are 

credited. 

 

 

Data Availability Statement: All 

relevant data are within the paper 

 

Funding: The authors have no support 

or funding to report. 

 

 

 

 

 

 

Date Palm Biotechnology: Recent Research 

an Overview  

Wessam M. Rslan* 

Agricultural Genetic Engineering Research Institute; Agricultural Research 

Center, Egypt. 
 

*To whom correspondence should be addressed: wessam.rslan@ageri.sci.eg 

 

 

Abstract 

 

Date palm (Phoenix dactylifera L.) is among the earliest fruit crops 

cultivated in the arid Arab Peninsula, North Africa, and Middle 

East territories. Dates are a significant source of food and revenue 

for Middle East and North Africa's local communities. It has 

distinctive features of biology and development that require special 

methods of reproduction, culture and governance. In varying date-

growing regions, there are thousands of date plant cultivars and 

varieties. The lengthy life cycle, long juvenile lifespan, and date 

palm dioecism produce cultivation difficult. Every year, the 

percentage of crop genomes sequenced has continued to increase. 

The incredible rate at which DNA samples become accessible is 

mainly due to the enhancement in cost-and speed-related 

sequencing techniques. Modern sequencing techniques enable the 

sequencing at realistic price of various cultivars of tiny plant 

genomes. Although many of the published genomes are deemed 

incomplete, they have nevertheless proven to be useful instruments 

for understanding significant plant characteristics such as fruit 

maturation, grain characteristics and adaptation of flowering time, 

here we review date palm genomic studies and determine its 

genomics element. 

 

 
 

Keywords: Date palm, genome-wide association,  SNP, genomics element, 

genome annotation .  

 

 

 

Review Article                                                                                             Open Access   



 
 

                                                                                                                                         Date Palm Biotechnology an Overview 

 

 

 

Highlights in BioScience       DOI:10.36462/H.BioSci.20182                              August 2018 | Volume1 

 
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Introduction 

Several of the plant genome sequences have been fully 

sequenced (collected, annotated and released) and have been 

openly accessible in the database, such as Oryza sativa (1), 

Zea mays (2), Hordeum vulgare (3), Phoenix dactylifera (4), 

Triticum aestivum (5), Eucalyptus grandis (6), Capsicum 

annuum (7), Beta vulgaris (8) and Solanum  (9). Yang et al. 

(1) presented a full date palm chloroplast genome sequence 

of approximately 158,462 bp. They revealed that there are 

112 distinctive genes and 19 duplicated parts in the IR areas 

in the date palm chloroplast genome. They recognized 78 

SNPs within the population of a particular chloroplast 

genome as significant intravarietal polymorphisms, most of 

which were found in genes with essential tasks. They also 

discovered 18 polycistronic transcription blocks and 3 

extremely expression-based genes-atpF, trnA-UGC, and 

rrn23 based on RNA-sequencing records. 

Al-Dous et al. .(4) used the Illumina GAII sequencing 

platform to present the first date of the palm assembly draft 

genome sequence for the Khalas cultivar. They reported a 

date palm genome with size of 658 Mb, 58% assembled 

sequences (382 Mb) and forecast 25,059 genes. Among the 

nine cultivars of date palms trees (Deglet Noor, Deglet Noor 

BC5, Khalas, Khalas BC2, Medjool BC4, Medjool, Alrjfem, 

KhltMale, KhFxfem) they recorded more than 3.5 million 

polymorphic locations. In (http://qatar-weill.cornell.edu/ 

research/datepalmGenome/), this sequence was stored. 

Fang  et al. (12) provided date palm full sequence of 

mitochondrial genome with an estimated size of 

approximately 715.001 bp. Al-Mssallem et al. (13) 

introduced the second Khalas nuclear genome assembly, 

which is 605.4 Mb in size, spanning > 90% of the genome 

(~671 Mb) and > 96% of its functional genes (~41,660 

genes). This sequence was stored with BioProject ID 

PRJNA83433 in Genbank (http://www.ncbi.nlm.nih.gov/) 

and produced the first genetic map of the date palm (Phoenix 

dactylifera) and recognized the putative gender chromosome. 

They submitted ~4000 maps on the map using a total of 1293 

cM of nearly 1200 molecular markers. These molecular 

markers were divided into 18 linkage clusters (LG) and 

proposed that the sex chromosome could be LG12. 

Hazzouri et al. (14) launched an extensive catalog of 

about seven million single nucleotide polymorphisms in date 

palms based on a set of 62 cultivars re-sequencing the entire 

genome. Analysis of population structure suggested a 

significant genetic gap between North Africa and the date 

palms of Middle East/South Asia with proof of admixture in 

Egyptian and Sudanese cultivars. Candidate mutations for 

trait variation were recorded, including polymorphisms of 

nonsense and variety of presence/absence of gene material in 

important agronomic trait mechanisms. In the R2R3 myb-like 

orthologue of the oil palm virescens gene connected with 

fruit color variability, they also recognized a copy-like retro-

transposon insertion polymorphism. 

The first miRNA segments of the palm species Elaeis 

guineensis, Elaeis oleifera and Phoenix dactylifera were 

recorded by Silva et al. (15). In the genomes of these species, 

they recognized miRNA precursors and defined their 

potential biological functions proposed by the mature 

miRNA-based target gene regulation. Three hundred and 

thirty-eight precursors were recognized, varying in sequence 

size from 76 to 220 nucleotides dispersed in 33 households. 

In addition, they also recognized Musa acuminata 266 

miRNA precursors that were phylogenetically near to palm 

species.  

 

Detection of resistance genes in date palm 

Al-Mssallem et al. (13) monitored Phoenix dactylifera 

protein samples using the Pfam NBS (NB-ARC) family 

PF00931 databases (E-value cutoff of 1.0) Hidden Markov 

Models (HMMs). Using an HMM model with Pfam TIR 

PF01582 (E-value cutoff 1.0) domains as well as LRR motifs 

in the C-terminal domains, the 144 expected amino acid 

sequences were used to identify TIR domains. In total, 144 

non-redundant NBS-encoding proteins have been recognized 

and validated manually, accounting for about 0.35% of the 

gene designs in the Phoenix dactylifera genome. 

 

Simple sequence repeats in date palm 

Billotte et al. (16) built a library (GA) n enriched with 

microsatellite and described 16 nuclear simple sequence 

repetition (SSR) loci in Phoenix dactylifera. They studied 

amplification and genotyping across taxes. This experiment 

reveals the usefulness of most SSR indicators in 11 other 

Phoenix organisms and the applicability of some of them in 

Elaeis guineensis, 11 Pritchardia species, Pritchardiopsis 

jeanneneyi species, and six Astrocaryum species. 

Akkak et al. (17) separated from two microsatellite 

enriched date palm libraries forty-one easy sequence repeats 

(Phoenix dactylifera). Of the 41 SSRs, 17 chosen 

microsatellite loci were identified and assessed on a 

collection of 31 Algerian and Californian germplasm 

cultivars and clones. All primer pairs generated an 

amplification PCR pattern of the expected size and high 

polymorphism was detected among the samples analyzed. 

Tax amplification across the genus Phoenix indicates the 

usefulness of most SSR indicators in 14 other species. 

Hamwieh et al. (18) researched the prevalence of 

microsatellite patterns in the first edition of the new genome 

profile of the date palm assembly produced by the next 

generation DNA sequencing of the entire genome shotgun. 

http://qatar-weill.cornell.edu/%20research/datepalmGenome/
http://qatar-weill.cornell.edu/%20research/datepalmGenome/
http://www.ncbi.nlm.nih.gov/


 
 

                                                                                                                                         Date Palm Biotechnology an Overview 

 

 

 

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They structured a total of 1,091 primer combinations in 

simple/perfect microsatellite motifs flanking regions. From it 

377 primers flanked dinucleotide, 352 primers flanked 

trinucleotide, and 362 primers pair flanked tetranucleotide 

repeats out of these primer combinations fifty primer pairs 

used for 8 Iraqi date palm varieties screening. Results 

showed that 28 combinations of primers were usable (56%) 

and 18 (36%) disclosed polymorphic alleles. Also (19) 

developed date palm molecular markers database. 

Elmeer et al. (20) constructed thirty primer pairs of 

microsatellite genomic DNA markers for SSR. These 

molecular markers were used for eleven date palm genotypes 

to evaluate genetic diversity. Results stated that the targeted 

PCR fragments were not amplified by only seven (23.3 

percent) of the thirty primers. While thirteen PCR primers 

(43.3%) enhanced monomorphic banding patterns and 

polymorphic banding motifs were produced by the remaining 

ten primers (33.4%). 

Arabnezhad  et al. (21) formed two SSR-enriched date 

palm genomic databases, including repeat motifs (AG) n and 

(AAG) n, using 22 SSR PCR primer pairs to evaluate the 

genetic connection between 16 date palm cultivars cultivated 

in separate geographic areas (Iran, Iraq and Africa). Based on 

Nei's genetic distance they used, the cluster analysis put 

African date palms in a group other than the genotypes of 

Iran and Iraq. They stated it appears that African date palms ' 

domestication has taken a distinct path than those cultivated 

in the Middle East. 

Bodian et al. (22) used easy sequence repeat markers to 

analyze genetic variation among 128 date palm specimens 

from the Figuig desert (Morocco). 121 females belonging to 

11 cultivars were among those palms, and 7 were males. 

Eighteen SSR primers have been used, but all samples have 

been effectively amplified by only 15 primers. The 

dendrogram acquired showed three populations and male and 

female genotypes did not detect any genetic distinctions.   

Zhao et al. (23) evaluated 28,889 samples of EST from 

the database of the date palm genome and recognized 4,609 

ESTs as SSRs. Trinucleotide patterns (69.7%) were the most 

common among these SSRs, followed by tetranucleotide 

(10.4%) and dinucleotide patterns (9.6%). They also 

engineered a total of 4,967 primer pairs from sequencing data 

for EST-SSR markers. Twenty of these primer pairs from 

twelve date palm cultivars were tested with genomic DNA. 

One-third of these primer pairs identified polymorphisms of 

DNA that distinguished the cultivars of the twelve date 

palms.  

Aberlenc-Bertossi  et al. (24) used the new sequence 

draft of the date palm genome Al-Dous et al. (11) to identify 

microsatellites and layout primers for SSR. They recognized 

204 genes with microsatellite coding sequences, 150 of 

which were appropriate for primer construction, but only 103 

had annealing locations that were not duplicated. With six or 

more repeats, such microsatellites had perfect trinucleotide 

motifs, and hexanucleotide motifs with at least four repeats. 

Of the 47 first pairs lastly maintained, 33 in a preliminary 

experiment with eight Phoenix dactylifera samples produced 

expected PCR amplification. The 33 loci have been further 

evaluated on 16 individuals comprising Phoenix roebelenii 

O'Brien(2), Phoenix dactylifera (7), Phoenix reclinata Jacq 

.(2), Phoenix rupicola T. Anderson (2), Phoenix theophrasti 

Greuter (2), and Phoenix canariensis interspecific hybrid 

phoenix sylvestris . 

Zehdi-Azouzi et al. (25) used both nuclear SSR and 

chloroplast microsatellites to evaluate the variety and genome 

composition of date palm accessions from Mauritania to 

Pakistan in ten regions. A total of 295 accessions were 

evaluated using 18 nuclear SSR loci revealing > 200 alleles 

for every locus. They recorded analyzes of the date palm 

population's genetic composition using the Bayesian 

clustering strategy, hierarchical ranking of NJ and DACP. 

Their findings were obviously compatible with a two-cluster 

geographic structure. The first, called the Eastern pool, 

includes Djibouti, Iraq, Oman, Pakistan, and the UAE date 

palm accessions. While the Western pool was appointed the 

second cluster, it included the residual accessions from 

Africa, including Egypt, Algeria, Mauritania, Tunisia and 

Morocco (26).   

 

SNPs studies in date palm  

Al-Dous et al. (11) analyzed 3.5 million SNP across the 

genomes of male and female date palms trees to recognize 

gender-segregating polymorphisms. The findings noted best 

fit an XY sex-determination model with the heterogamous 

sex being males. Using a male heterogamete model 1,605 

SNPs were noted segregating with gender. Analyzing two 

scaffolds with the most gender-segregating SNPs, they noted 

an estimated threefold distinction in divergence between 

male and female haplotypes from the reference sequence. 

Across all genome sequences in these regions, the 

cultivars of 867 polymorphic sites have been observed. 

Comparing the females of Deglet Noor and Medjool with the 

female reference of Khalas disclosed that 253 and 271 sites 

varied from the reference of Khalas and that only 24 (9%) 

and 19 (7%) locations were heterozygous. At the same sites, 

their backcrossed males illustrated 736 and 770 different 

locations from the Khalas reference, of which 584 (79%) and 

578 (75%) were heterozygous, respectively. 

Al-Mssallem et al. (27) researched genetic variety of 

SNPs between many date tree species (Khalas, Fahal, Sukry, 

Agwa, Deglet Noor, Deglet Noor BC5, Medjool, Medjool 

BC4, KhalsFx, AlrijalF and Khalt) and recognized SNP 



 
 

                                                                                                                                         Date Palm Biotechnology an Overview 

 

 

 

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(indel) abundances of 6.10 (0.25), 5.51 (0.15) and 6.24 

(0.20) per kb. They explored how evolutionary selection left 

its marks in genomes of various date palm species by first 

assessing the allocation of SNPs on big scaffolds and then 

pinning down obviously chosen functional genes, particularly 

those strongly engaged in the metabolisms of sugar and 

energy. They found that there is no random distribution of 

SNPs, but a bimodal curve. Depending on SNPs and the 

frequency distributions, they built the phylogenetic tree of 11 

Phoenix dactylifera cultivars. 

In nine Saudi Arabian date plant cultivars (Sukkariat 

Al-Madinah Perny Al-Riyadh, Sukkariat Qassim, Rabia Al-

Madinah, Dekhaini Al-Riyadh, Ajwa Al-Madinah,, Shalaby 

Al-Madinah, Moshwaq Al-Riyadh and Moshwaq Hada Al-

Sham), Sabir et al. (28) evaluated the entire maternal and 

plastid genome SNPs. They detected 188 SNPs in the 

mitochondrial genome at 37 distinct locations. For all nine 

cultivars, the amount of mutual SNPs was 16. While there 

were 30 of the nine date palm cultivars in the amount of 

plastid SNPs, they were situated in 20 distinct genome 

locations with 13 in genes, 2 in introns, and 5 in intergenic 

spacers. 

Hazzouri et al. (14) established an extensive catalog of 

about seven million SNPs in date palms depending on a set 

of 62 cultivars re-sequencing of the entire genome. 

Assessment of population structure indicates a significant 

genetic divide between North Africa and Middle East/South 

Asian date palms, with evidence of admixture in Egyptian 

and Sudanese cultivars. At least 56 genomic regions 

correlated with selective sweeps which may underlie regional 

adaptation were proposed by genome-wide selection scans. 

Candidate mutations for trait variety were recorded, 

including polymorphisms of nonsense and variety of 

presence/absence of gene material in important agronomic 

trait mechanisms. In the R2R3 myb-like orthologist of the oil 

palm virescens gene connected with fruit color variability, 

they also recognized a copy-like retro-transposon insertion 

polymorphism. 

 

 

 

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