Date Palm - Genomics of Cultivated Palms - page 52

primers and 13 AFLP primer combinations, pointed to less than 3% genetic varia-
tion, confirming the genetic stability of tissue culture-derived dry date palm cultivars
[32] . Differences in the pattern of methylation of DNA were noticed in the dwarf
type of Medjool and the normal tall Medjool variety. Around 2000 genes differed in
expression pattern between normal and dwarf [33] . Genes involved were the biosyn-
thesis of gibberellins, auxins, brassinosteroids, and expansins, and WRKY transcrip-
tion factors were mainly shown in differential expression profiles. About 21 of these
genes [33] were verified by quantitative reverse transcriptase PCR (qRT-PCR).
Methylation of cytosine is an important phenomena affecting gene expression in
locations where C is methylated. A methylation-sensitive amplified polymorphism
(MSAP) technique was developed for date palm, using this feature to analyze the
DNA variation in offshoots and mother palm. Hypomethylation of DNA was found
in offshoots of date palm compared with mother plants. It may be related to gene
expression during offshoot development [34] .
DNA amplification fingerprinting (DAF) is another set of markers initially used in
Tunisian germplasm [35] . Restricted fragment length polymorphism (RFLP) analy-
sis [36] is used to complement the RAPD markers in cultivar identification of date
palm. RFLP using a cDNA probe of a zinc finger protein motif is useful to screen the
polymorphism among cultivars and to tag important traits (yield, fruit quality, and
resistance to disease) in date palm in different countries where it is grown [37] . Apart
from these, molecular markers were helpful to analyze the seedling of a rare ancient
date seed excavated [38] from Masada and radiocarbon-dated to the first century C.E.
The study provides insights into the historic date culture of the Dead Sea region as
representative of an extinct date palm population [38] .
4.7 Complete Genomes, SNPs, and Genomic Libraries
The genomic library was constructed from total cellular DNA, previously amplified
according to an RAPD [39] procedure and cloning. The resultant recombinant DNA
[40] is characterized by a size ranging from 200 to 1600 bp inserts. It constitutes a
large number of anonymous probes of potential application in Southern hybridiza-
tion experiments. It also generates markers for molecular characterization of date
palm varieties and those associated with fruit quality, resistance to Bayoud dis-
ease, and sex of trees. The complete genome of the chloroplast (cp) of date palm
is A  T rich, of 158 kb size, and is sequenced and available now [41] . About 78
SNPs were discovered as major intravarietal polymorphisms within the population
of a specific cp genome, most of which were located in genes with vital functions.
Based on RNA-sequencing data, 18 polycistronic transcription units and three highly
expression-biased genes—atpF, trnA-UGC, and rrn23—along with their tissue spe-
cific patterns, were found. The complete cp genome of date palm was compared with
the 81 available coding sequences of the oil palm cp genome to locate the intraSNPs.
Nevertheless, date palm and oil palm belong to two different genera and 19 sites,
whose cp minor genotypes in date palm became major genotypes in oil palm, or vice
versa. These SNPs have potential application in markers for palms.