Oil Palm - Genomics of Cultivated Palms - page 36

were found to be useful in cultivar identification. High genetic diversity exists in
West African germplasm, especially in Nigeria [58,61,67] . Genetic diversity of
American oil palm in Caiaue accessions of Amazon Brazil [57] is moderate,
whereas it is lowest in accessions from Ghana [58] . Most of the diversity studies
use Deli dura as a control to compare with other germplasm accessions. Deli dura
lacks many rare alleles and is found to have lost 36 [58] to 45 [62] more alleles than
natural populations. Economics of marker-aided breeding over conventional breed-
ing indicated time and money savings from using markers in genome-wide selection
[70] ( Table 3.3 ).
3.5 Genes and Promoters of Oil Palm
Important genes and promoters are cloned from oil palm and sequenced to improve
the traits of interest. Transcription factors, the master switches regulating the genes
of the MADS-box family [72] , Knotted gene [73] , AP2 domain [75] , and Myb-1
[79] of oil palm, are known. Other important genes related to oil yield are accD;
ACCase [71] , a gene-regulating beta-carotene pathway; beta-carotene hydroxylase
[74] , a gene involved in early isoprenoid pathway; and ketothiolase [76] , and they
have been studied in detail in oil palm. Ganoderma wilt, a fungal disease, is a seri-
ous problem in oil palm. Chitinases play a crucial role in defense against such fun-
gal diseases. Recently, three chitinases were cloned and sequenced in oil palm [77] .
Drought and salinity are major abiotic stress factors reducing productivity in oil
palm. A proline transport gene was recently analyzed with potential role in salinity
resistance [78] . Specific leaf tissue promoters [80] developed from oil palm have a
potential role in the cultivation of transgenic plants in addition to mesocarp-specific
[26] and metal-inducible [27,28] ones. Accession numbers of the sequences and
details of important genes of oil palm are given in Table 3.4 .
3.6 Bioinformatics
Bioinformatics is an emerging field combining information technology and bio-
logical sciences. Bioinformatics or in silico analysis helps to retrieve, handle, store,
and analyze the large-scale sequence data. In oil palm, large-scale annotation of
sequences led to the identification of many useful genes. Genomic resources, mark-
ers, and linkage map position details of oil palm are available as user-friendly, web-
enabled databases [82] . MicroRNA (miRNAs) are short snippets of single-stranded
RNA molecules of length 20-22 nucleotides encoded in the genomes. miRNAs
negatively regulate the target genes by binding at specific sites and post-translational
cleavage. Computational tools are helpful in the prediction and identification of
miRNA regions from the genomes. Combined homology and structural analysis in
sequences of oil palm expressed in apical meristem, immature, and mature flower
tissues were found to contain five potential miRNA-encoding sequences [83] .