Philippine Journal of Science

148 (S1): 183-191, Special Issue on Genomics

ISSN 0031 - 7683
Date Received: 19 Mar 2019

Genome-guided Molecular Characterization

of Oil Genes in Coconut (Cocos nucifera L.)

Anand Noel C. Manohar1,3*, Darlon V. Lantican1,3, Melvin P. Dancel1,3,

Don Emanuel M. Cardona1,3, Alissa Carol M. Ibarra1, Cynthia R. Gulay1,3,
Alma O. Canama1, Roanne R. Gardoce1, and Hayde F. Galvez1,2

1
Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science,
University of the Philippines Los Baños, College, Laguna 4031 Philippines
2
Institute of Crop Science, College of Agriculture and Food Science,
University of the Philippines Los Baños, College, Laguna 4031 Philippines
3
Philippine Genome Center – Program for Agriculture, Livestock,
Fisheries and Forestry (PGC-Agriculture), University of the Philippines Los Baños,
College, Laguna 4031 Philippines

Coconut oil is a major source of medium chain fatty acids (MCFAs), which are health-promoting plant
compounds. The MCFAs of coconut oil have been reported to exhibit various health properties such as
antioxidant, antibacterial, antiviral, and cardiovascular benefits brought about by the multi-functionality
of these complex MCFAs. Six (6) candidate genes involved in oil and MCFA synthesis were identified in
the general seed oil biosynthetic pathway. The candidate gene sequences were mined using local BLAST
in the coconut genome assembly constructed based on 15× PacBio® and 50× Illumina® MiSeq sequence
reads of CATD coconut variety. Scaffolds harboring the candidate genes were mapped based on sequence
homology alignment. Gene structures of all genes were elucidated using evidence-based and ab initio
prediction algorithms. The coding DNA sequences of KasII and KasIII in coconut were characterized.
These MCFA genes have not been characterized nor reported in coconut. Gene-specific PCR primers
were designed targeting the coding regions of each gene. PCR conditions were optimized to mine
natural allele variants across 48 established coconut varieties in the Philippines through EcoTILLING
(Ecotype Targeting Induced Local Lesions IN Genomes).Asingle nucleotide polymorphism (SNP) on the
lysophosphatidic acid acyltransferase genes (LPAAT) was detected in the ‘West African Tall’(WAT) and
‘Aguinaldo Tall’ (AGDT) varieties. The partial LPAAT gene sequences of WAT and AGDT were cloned
and sequenced in order to characterize the SNP. Based on the identified SNPs, robust DNA markers
may be developed for high-throughput screening and selection of favorable alleles in genomics-assisted
coconut breeding for outstanding high-quality oil producing varieties.

Keywords: coconut, EcoTILLING, genomics-assisted breeding, in silico gene prediction, medium-

chain fatty acid, SNP markers

INTRODUCTION crop in around 86 countries. In the Philippines, coconut

The coconut (Cocos nucifera L.), dubbed as the “Tree of
Life,” is the most important palm in the humid tropics,
with approximately 12 million hectares planted with the
*Corresponding Author: acmanohar@up.edu.ph
is a major agricultural crop grown in around 3.6 million
hectares of farmland or 26% of the country’s agricultural
lands. The country produces an average of 13.8 million
tonnes of harvest per year derived from 340 million
bearing trees. As the second largest producer and exporter

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of coconut in the world, the industry provides employment
to approximately 1.4 million Filipino coconut farmers
who comprise 21.7% of the total number of farmers
directly engaged in agriculture (FAO 2018). Every part
of the coconut palm – from the leaves, all the way down
to the roots – have various economic uses. Copra oil (or
coconut oil), the coconut’s most economically important
product, used to be the most-traded vegetable oil in the
world (Purseglove 1985). However, there is a remarkable
global decline in the importance of coconut oil when used
for food based on consolidated values/reports from 1961
and 2011. One of the major reasons for this is the stigma
associated with the presence of long-chain fatty acids
(Nayar 2017).
MCFAs and long-chain fatty acids comprise around
83.92% of the total composition of copra oil, of which
lauric acid (C12:0) is the most predominant (Padolina
et al. 1987). The high proportion of saturated fatty acids
in coconut oil has been previously reported to increase
cholesterol levels in the body, thus increasing the risk of
cardiovascular diseases (Mensink et al. 2003). However,
this has been scientifically discredited by numerous
researches demonstrating several health benefits from
consuming high amounts of MCFAs in coconut oil,
particularly lauric acid extracted from the fruit endosperm
(Blackburn et al. 1989a, b; Kintanar and Castro 1988;
Müller et al. 2003; Dayrit et al. 2008; Orsasova et
al. 2015). MCFAs in coconut oil exhibit synergistic
cardioprotective, anti-thrombotic, anti-atherosclerotic,
anti-bacterial, anti-dermatophytic, and anti-viral effects
(Kaunitz et al. 1958, Bach and Babayan 1982, Scalfi et al.
1991, Fushiki et al. 1995). One of the primary objectives
in coconut breeding is to develop outstanding coconut
varieties not only based on yield/productivity but also
with improved copra oil quality by increasing MCFAs and
short-chain fatty acid content. To develop varieties with
improved fatty acid profile, the coconut oil biosynthesis
pathway must be elucidated. The general oil biosynthetic
pathway in seeds involves various organelles and
extensive lipid trafficking – requiring several enzymes.
It starts with the synthesis of fatty acids in the plastids,
while the triacylglycerides (TAGs) synthesized by LPAAT
are assembled outside the plastid – particularly in both
smooth and rough endoplasmic reticulum (Chapman and
Ohlrogge 2012). Assembly of fatty acids is initiated by
the acyl carrier protein (ACP) via a cycle of reactions that
elongate the acyl chain at a rate of two carbon atoms per
cycle. The processed fatty acid can either be hydrolyzed
by FatB or further elongated by KasII (Li-Beisson et
al. 2010). However, genes involved in the synthesis of
MCFAs in coconut oil are not yet well-characterized at
the gene structure level.
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Characterization of Oil Genes in Coconut
With the advent of next-generation sequencing
technologies and bioinformatics, a coconut genome
assembly has been constructed from the 15X PacBio®
and 50X Illumina® MiSeq sequence data of ‘Catigan
Green Dwarf’ (CATD) coconut (Lantican et al. 2019).
Using the appropriate bioinformatics tools, these genes
can be characterized at the genome level with the aid of
the genome assembly. Allele variations of these genes
across various ecotypes can be detected by EcoTILLING.
EcoTILLING is a modification of the Targeting Induced
Local Lesions IN Genomes (TILLING) protocol used
for the discovery of SNPs in natural populations instead
of chemically-induced mutant populations. It was first
used to identify and map SNPs detected in various
Arabidopsis ecotypes (Comai et al. 2004). A similar
approach was performed in the assessment of fatty acid
elongase 1 (FAE1) gene among Brassica species for the
development of DNA markers associated with seed erucic
acid (Wang et al. 2010). Identified polymorphisms using
this technique will be screened further for potential use
in marker-assisted breeding of coconut to improve copra
oil quality by manipulating any or a combination of these
coconut oil genes.
This paper reports coconut genes involved in coconut
endosperm oil biosynthesis that were characterized in
the CATD genome through in silico gene prediction. The
validation of the genes by EcoTILLING is also presented
and discussed, including its potential application in the
development of gene-markers in coconut marker-assisted
breeding procedures.
MATERIALS AND METHODS
Gene Mining
Candidate genes for variant detection were selected based
on their roles in the general endosperm oil biosynthesis
pathway of plant seeds (Bates et al. 2013). These genes
are acyl-ACP thioesterase A and B (FatA and FatB);
β-ketoacyl-ACP synthases I, II, and III (KasI, KasII, and
KasIII); and LPAAT genes. Equivalents of these genes
were mined in the Elaeis guineensis genome assembly
available in the NCBI database (https://www.ncbi.nlm.
nih.gov/). These are deposited E. guineensis genes with
NCBI accession nos. XM_010929397.2, AF147879.2,
XM_010917679.2, XM_010923620.2, XM_010907910.2,
and XM_010910594.1. The nucleotide sequences of the
genes were downloaded and, through local BLASTn
(e-value = 1e–150) analysis, the gene homologs on the
CATD coconut genome assembly (Lantican et al. 2019)
were mined using the E. guineensis sequences as a query.
Assembly scaffolds harboring the genes were identified
for subsequent analysis.
Special Issue on Genomics Manoharet al.: Genome-guided Molecular
Characterization of Oil Genes in Coconut

Gene Annotation Table 1. Coconut varieties obtained from PCA-ZRC and used to
The sequence scaffolds harboring the coconut candidate screen for SNPs on identified coconut candidate oil genes.
oil genes were subsequently extracted from the CATD Code Variety Code Variety
genome assembly using a local Perl script (github.com/
PILD Pilipog Dwarf MVT Markham Talla
aubombarely/GenoToolBox/blob/master/SeqTools/
a
FastaExtract). Annotation was performed via ab initio, CRD Cameron Red Dwarf KKT Karkar Tall
cDNA/EST, and homology-based approaches – and TACD Tacunan Dwarf AGDT Aguinaldo Tall
integrated by the MAKER annotation pipeline (Cantarel MYD Malayan Yellow Dwarf a
WAT West African Talla
et al. 2008). The gene structures were predicted on the CATD Catigan Green Dwarf GATT Gatusan Tall
scaffold by ab initio gene prediction using AUGUSTUS a
MRD Malayan Red Dwarf BAYT Baybay Tall
and SNAP programs (Korf 2004) – revealing exon-intron
junctions, ORFs, and UTRs. These sets of predictions KIAD Kiamba Dwarf SNRT San Ramon Tall
were merged with BLASTx, BLASTn, and exonerate SGD Sri Lanka Green Dwarfa TPKT Tampakan Tall
alignments of oil biosynthesis gene homologs deposited EGD Equatorial Green Dwarf SCHT Sanchez Mira Tall
at the NCBI GenBank (www.ncbi.nlm.nih.gov/genbank/).
BAGD Baguer Dwarf VTT Vanuatu Talla
AROD Aromatic Green Dwarf TAGT Tagnanan Tall
Plant Materials
KIND Kinabalan Dwarf BAOT Bago Oshiro Tall
Forty-eight (48) accessions of coconuts established at the
Institute of Plant Breeding, University of the Philippines BAND Banga Dwarf GPT Gazelle Tall
Los Baños (IPB-UPLB) were used in this study. The MAKD Makilala Dwarf PYT Tahiti Talla
accessions included 24 Dwarf and 24 Tall coconut GALD Galas Dwarf VENT Venus Tall
varieties from both local and foreign sources, which were VICD La Victoria Green Dwarf RIT Rennel Island Talla
obtained from the germplasm collection of the Philippine
VIBD La Victoria Brown Dwarf AGAT Agta Tall
Coconut Authority - Zamboanga Research Center (PCA-
ZRC) through the Coconut Genomics Project 8 of IPB- TUPD Tupi Dwarf LONT Loong Tall
UPLB. The list of the varieties used is presented in Table 1. MAGD Magtuod Dwarf CULT Culaman Tall
TALD Talisay Dwarf KGT Katangawan Tall
Genomic DNA Extraction SNOD Sto. Niño Dwarf BNGT Banigan Tall
Leaf samples from the 48 Philippine coconut varieties BUSD New Buswang Dwarf SALT Salambuyan Tall
were harvested from the mini-germplasm collection of KAPD Kapatagan Dwarf PAGT Panda Tall
the Genetics Laboratory in IPB-UPLB. These are among
SNID San Isidro Dwarf LAGT Laguna Tall
the selected accessions from the PCA-ZRC coconut
a
genebank being established at IPB-UPLB for the coconut Foreign accession

genomics project 8 (Galvez 2016). Genomic DNA from

each variety was extracted using the modified Doyle and
Doyle (1990) protocol described by Cardona et al. (2015). Table 2. PCR temperature profile used in amplifying the candidate
Each accession consists of 4–10 individual genomic DNA oil genes in 48 coconut varieties
samples, which were pooled and normalized to 10 ng/μL Step Temperature (°C) Time
prior to polymerase chain reaction (PCR) analysis. Initial denaturation 95 3 min
Denaturation 95 1 min
PCR Annealing 50–60 1 min
The optimized amplification reaction mixture consisted Extension 72 2 mins
of 30 ng of DNA template; 1X PCR buffer (10 mM
Final Extension 72 5 mins
Tris-Cl pH 8.3, 50 mM KCl); 2.0mM MgCl2 (Vivantis
Technologies); 2.5 mM dNTPs (Promega Aust Ltd); Hold 12 ∞
0.2 μM of forward and reverse primers; and 0.4 U of
Taq polymerase (Vivantis Technologies). The samples
were amplified through PCR using different temperature products were electrophoresed in a 1% agarose gel in 1X
profiles based on corresponding optimum temperature TBE buffer (90 mM Tris-borate, 2 nM EDTA) at 100 V
in T100™ Thermal Cycler (Bio-rad Laboratories Inc., for 40 min. After electrophoresis, the gel was stained
Hercules, CA, USA). The temperature profiles used in with ethidium bromide for 20–30 min, after which was
amplifying the samples were similar except for annealing viewed under ultraviolet (UV) light using the Enduro
temperatures as presented in Table 2. The amplified PCR Gel Documentation System (Labnet International, Inc.).

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EcoTILLING involving natural population was performed
upon optimization of PCR amplification conditions.
Amplicons of the 48 coconut accessions were mixed in
equal parts of the amplicons of the reference genome
CATD. Running the admixture in a series of annealing
and denaturation causes the formation of heteroduplexes.
These were then subjected to a nuclease assay using Cel1,
which is composed of 194.4 μL of T-Digest buffer and 1.6
μL of dsDNA cleavage enzyme (Advanced Analytical) for
every 96 samples analyzed. Cel1 nuclease specifically
cleaves at regions where a mismatch bubble is formed,
thus revealing the presence and relative location of an
SNP (Barkley and Wang 2008). Resulting fragments were
resolved in Fragment AnalyzerTM (Advanced Analytical
Technologies, Inc., San Diego, CA, USA). Lanes that
showed cleaved fragments were considered for further
characterization as SNPs were detected in these regions.
Cloning and Sequencing
Ligation and transformation. Identified genes with
variants were cloned using the pGEM-T Easy Vector System
(Promega Aust Ltd), following the manufacturer’s instruction.
The transformed cells were incubated at 37 °C with shaking
for 90 min. A total of 100 and 150 μL of each transformation
culture was plated onto prewarmed Luria-Bertani (LB) agar
plates with ampicillin (100 μg/mL), overlaid with 50 μL of 100
mM IPTG and 20 μL of 80 mg/mL X-gal. The plates were
incubated overnight (16–24 h) at 37 °C.
Colony PCR and subculture. White colonies corresponding
to putative transformants were selected. Using a sterile
pipette tip, selected colony were pricked and mixed with
prepared PCR mixtures containing gene-specific primers.
Recommended PCR conditions were used in the PCR
analysis. In colonies that exhibited the expected amplicon,
a sterile toothpick was used to prick the corresponding
bacterial colony and placed in a culture tube containing
LB broth with ampicillin (100 μg/mL). The tubes were
incubated overnight at 37 °C in a shaking incubator.
Bacterial plasmid isolation. Purelink Plasmid Miniprep
Kit (Invitrogen) was used to isolate the plasmids
from bacterial cultures following the manufacturer’s
instructions. Resulting purified plasmids were sent for
double pass sequencing using T7 and SP6 primers.
Sequence Analysis and SNP Marker Development
Sequenced clones positive for putative SNPs were
analyzed using appropriate bioinformatics tools. Chromas
(Technelysium Pty. Ltd.) was used to determine the quality
of sequencing by checking the sequencing chromatogram
provided. Clustal Omega (www.ebi.ac.uk/Tools/
msa/clustalo/) was used for all pairwise and multiple
sequence alignments. Putative SNPs that are located in
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Manohar et al.: Genome-guided Molecular
Characterization of Oil Genes in Coconut
intronic regions were characterized by determining any
gene regulatory elements present in the sequences. The
miRBase (Kozomara and Griffiths-Jones 2014) was used
to check for any homologies with microRNAs deposited
in the database. Furthermore, PlantTFcat (Dai et al.
2013) was used to categorize transcription factors and/or
transcriptional regulators.
RESULTS AND DISCUSSION
All six (6) candidate MCFA genes were identified in the
CATD genome assembly by running a local BLASTn
search using E. guineensis cDNA sequences as a query
at e-value = 1e–150 (Table 3). High homology with these
genes indicates their presence within the CATD assembly.
Multiple contig hits for the case of AF147879.2 (EgFatB)
and XM_010917679.2 (EgKasI) is indicative of the
presence of gene homologs within the genome. This is
further supported by the high percent identity among the
contigs identified. Corresponding CATD contigs harboring
the genes were identified for annotation. The gene structure
of each sequence was determined by evidence-based and
ab initio gene prediction using MAKER. MAKER is a
genome annotation pipeline that makes use of homology-
based approaches incorporating BLAST, AUGUSTUS,
and SNAP within its pipeline (Cantarel et al. 2008). Using
the predicted gene sequence, alignment with the contig
revealed exon and introns. It has been observed that most
genes (KasII, KasIII, and LPAAT) exhibit large gene
lengths and abundant introns. This would explain why very
limited information are available for these genes as there
is a difficulty in characterizing large genes in the genome
level in the conventional approach. A summary of the data
gathered is presented in Table 4. The relative positions of
exons and introns along the gene are also shown in Figure 1.
Gene-specific primer design is a crucial step in performing
any TILLING procedure. Making use of the genome
assembly sequences as the basis for primer design ensures
the specificity of the primers developed for each gene. For
predicted full-length genes greater than 2000 bp, primers
with amplicons not exceeding 1500 bp were designed
at specific regions of the gene. As for small genes, such
as the FatA, primers capturing the whole length of the
gene were generated. All primers designed in each gene
successfully amplified the target gene region based on
estimated size. The optimized annealing temperature for
each primer pair ranges from 50 to 60 ºC via gradient PCR
using approximately 30 ng/μL of coconut CATD genomic
DNA as a template. PCR products were electrophoresed in
1% agarose gels and then stained in ethidium bromide. An
electrophoretogram of the amplicons is shown in Figure 2.
EcoTILLING results revealed no significant SNP cleavage
Special Issue on Genomics Manoharet al.: Genome-guided Molecular
Characterization of Oil Genes in Coconut

Table 3. Local BLASTn results of Elaeis guineensis sequences against the CATD reference genome.
Query Query Subject Subject Bit
Query Scaffold ID % Identity Length e-value
start end start end score
XM_010929397.2:
PREDICTED: Elaeis guineensis oleoyl-acyl CONTIG1616_
91.17 419 1 416 711695 711280 4e–158 564
carrier protein thioesterase 1, chloroplastic PILON
(LOC105049664), mRNA

CONTIG201_ 93.32 584 187 770 1158940 1158366 0.0 854

AF147879.2:
Elaeis guineensis var. tenera palmitoyl-ac- PILON 92.57 565 1254 1811 1154251 1153690 0.0 802
yl carrier protein thioesterase (PTE) mRNA,
CONTIG117_
complete cds 86.17 564 211 770 1567971 1567414 4e–169 601
PILON
XM_010917679.2: 96.99 432 707 1138 2310007 2309576 0.0 726
PREDICTED: Elaeis guineensis 3-oxoacyl- CONTIG160_
[acyl-carrier-protein] synthase I, chloroplas- PILON 97.21 359 348 706 2310894 2310536 2e–171 608
tic-like (LOC105040922), mRNA
XM_010923620.2:
PREDICTED: Elaeis guineensis acyl car- CONTIG4419_
93.10 377 384 759 90586 90960 7e–154 549
rier protein 2, mitochondrial-like PILON
(LOC105045364), mRNA
X M _ 0 1 0 9 0 7 9 1 0 . 2 : P R E D I C T-
ED: Elaeis guineensis acyl carrier protein 3, CONTIG5102_
92.71 645 308 949 49028 48385 0.0 928
mitochondrial (LOC105033210), transcript PILON
variant X1, mRNA
XM_010910594.1:
PREDICTED: Elaeis guineensis 1-acyl-
CONTIG19_
sn-glycerol-3-phosphate acyltransferase 91.89 407 1005 1408 318719 318313 1e–158 566
PILON
(LOC105035151), transcript variant X2,
mRNA

Table 4. Gene structures of the selected coconut candidate oil genes.

Predicted transcript
Gene code Protein product Size (bp) No. of exons No. of introns
length (bp)
FatA Acyl-ACP thioesterase A 681 416 4 3
FatB Acyl-ACP thioesterase B 5016 1684 6 5
KasI Ketoacyl-ACP synthase I 4443 1808 7 6
KasII Ketoacyl-ACP synthase II 24342 1829 5 4
KasIII Ketoacyl-ACP synthase III 9686 949 7 6
LPAAT Lysophosphatidic acid acyltransferase 28262 1325 11 10

Figure 1. A graphical representation of the approximate

locations of the exons and introns within each
coconut candidate oil gene.
Figure 2. Electrophoretogram of the six coconut candidate oil genes:
Lanes 1 – 1 kb Plus DNA ladder (Invitrogen), 2 – FatA,
3 – FatB, 4 – KasI, 5 – KasII, 6 – KasIII, and 7 – LPAAT

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for FatA, FatB, KasI, KasII, and KasIII. However, an
SNP was detected in the LPAAT gene of WAT and AGDT
coconut varieties at approximately 500–600 bp position of
the LPAAT amplicon. Figure 3 shows the chromatogram
and gel representative of the EcoTILLING results of
WAT. The red peak on the chromatogram corresponds
to the homoduplexes, while the orange peaks represent
the heteroduplexes formed during the endonuclease
digestion process. LPAAT is a major gene responsible
for the high lauric acid accumulation in coconut, as
previously demonstrated in the genetic transformation
experiments of this gene to Brassica rapus (Knutzon et
al. 1999). Moreover, recent transcriptome analysis of
developing coconut endosperm carried out by Reynolds
et al. (2019) confirmed the important role of LPAAT in
oil biosynthesis, particularly in the synthesis of TAGs.
The predicted sequence length of coconut LPAAT gene is
28,344 bp in reference to the CATD genome assembly.
This is shorter than the reported gene sequence of African
oil palm by 10,487 bp (Singh et al. 2013). Analysis of
its gene structure in coconut should provide an effective
reference to targeted gene editing and variation screening
Figure 3. Chromatogram and capillary gel electrophoretogram of the EcoTILLING results of the LPAAT gene in WAT coconut depicting
the cleaved heteroduplex of the PCR amplicon.
Figure 4. A graphical representation of the SNPs mined within the LPAAT amplicon (1400 bp) of WAT and AGDT coconut.
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Manoharet al.: Genome-guided Molecular
Characterization of Oil Genes in Coconut
towards improved copra oil quality (Lantican et al.
2019). Liang et al. (2014) has also reported the roles of
LPAAT in the fatty acid biosynthesis in coconut using
the Kyoto Encyclopedia of Genes and Genomes analysis
from suppression subtractive hybridization experiment.
However, none has been published regarding the degree
of variation of this gene in a natural coconut population.
The SNP was verified through cloning and sequencing
of the amplicon of LPAAT from WAT and AGDT coconut
DNA samples. Sequence data revealed that a pair of
SNPs (T/C and C/A, respectively) – 6 bp apart – is
inherent along the approximate Cel1 cleavage site in
the partial LPAAT sequence of WAT. Multiple sequence
alignment of the gene region is presented in Figure I. The
relative position of the SNPs along the gene is shown
in Figure 4. Coincidentally, WAT is a popular foreign
coconut cultivar known for its high oil yield. The pair
of SNPs is located in an intronic segment of the gene
and may harbor functional genetic elements that may
influence the expression of LPAAT and/or associated
genes in the metabolic network (Cooper 2010).
Special Issue on Genomics
Moreover, comparative gene analysis was carried out
between the CATD and ‘Hainan Tall’ (HAT) LPAAT
gene. Multiple sequence alignment was used to check for
similarities against the HAT genome assembly by Xiao
et al. (2017). The high similarity between the CATD
LPAAT (Scaffold ID: CONTIG19_PILON) and HAT
LPAAT (Scaffold ID: scaffold1063) was observed at 99.7%
homology. Few single base insertions were identified to be
present along both genes commonly found in nucleotide
base runs (i.e., AAAAA, TTTTT,GTGTGTGT).
Interestingly, comparative analysis reveals a sequence
discrepancy approximately 9286–10510 bp on the HAT
sequence assembly within the predicted first exon region
of LPAAT. Upon further characterization on the discrepant
locus, it was found out that it is comprised of ambiguous
base calls (i.e., NNNN) and runs of adenine bases, which
may be attributed to sequencing and/or scaffolding
errors. Nonetheless, further validation through wet lab
experiments is needed to confirm the polymorphisms
detected.
To check for possible affected regulatory elements within
the SNP/polymorphic region of coconut LPAAT, its
sequence homology was tested against miRbase (www.
mirbase.org) to determine any microRNA sequences in
the gene segment. Significant homology with miR172 was
detected in the presence of the two SNPs. The miR172
microRNA is responsible to modulate the expression of
mRNAs coding for APETALA2-like transcription factors
in Arabidopsis. APETALA2 is a member of a family of
transcription factors AP2/EREBP, which plays a major
role in plant hormone regulation, particularly those
involved in seed and flower development (Ogawa et al.
2007). Reverse genetics studies conducted by Ohto et al.
(2005) also showed that APETALA2 is directly involved in
the control of seed mass by changing the ratio of hexose
to sucrose during seed development. Using PlantTFcat
(plantgrn.noble.org/PlantTFcat/), 154 APETALA2
transcription factor family genes were detected in the
annotated CATD coconut genome assembly (Lantican et
al. 2019). The results of the transcription factor analysis of
the reference CATD coconut genome are shown in Table I.
This study is the first report of natural variation in LPAAT
in coconut. The identified SNPs within the LPAAT gene
region can be used as a basis in designing a DNA marker
potentially associated with improved copra oil quality
and/or yield. However, further EcoTILLING using larger
population samples i.e., more coconut varieties and
individual palms, is needed to validate the genetics of
these coconut LPAAT SNPs. There is also a need to validate
the correlation of the SNP to copra oil phenotype data in
a defined bi/multi-parent genetic mapping population.
Manohar et al.: Genome-guided Molecular
Characterization of Oil Genes in Coconut
CONCLUSION
The genome sequences and predictive structure of MCFA
synthesis-related genes in coconut were characterized
using appropriate bioinformatics analysis and in reference
to the CATD genome assembly. Gene-specific markers
were developed and used to analyze the genetic diversity
of at least 48 coconut accessions, Tall and, Dwarf varieties
through EcoTILLING and using a high-throughput
fragment analyzer platform. All the gene markers
positively amplified by PCR the expected fragment
sizes of the MCFA-related genes in all the coconut DNA
samples. This validates the good quality of the assembly
of coconut CATD as the reference genome in this study.
EcoTILLING analysis likewise revealed sequence
conservation of almost all the MCFA-related genes in the
48 coconut varieties based on the genomic regions tagged
by the markers. Except for LPAAT, no potential SNP was
detected in the other coconut genes mined in this study.
Among the coconut varieties screened, one SNP was
detected in the partial sequence (amplicons) of AGDT
and WAT coconut varieties. WAT is a foreign coconut
accession conserved in the Philippine Coconut Authority
(PCA) germplasm, while AGDT is a local variety
collection. Although no data is available for AGDT, WAT
has been a favorite genetic resource of the PCA breeders
for coconut oil yield. The potential association of this
sequence variant of LPAAT, specifically in AGDT and/
or WAT to improve the economic value of coconut oil,
is yet to be validated. In bay thioesterase-transformed
rapeseed, further introduction of coconut LPAAT resulted
in increased total lauric acid levels (Knutzon et al. 1999).
The LPAAT amplicons in selected palms/individuals of
coconut AGDT and WAT were cloned and sequenced,
which indeed all returned high homology to the reference
CATD sequence except for the characterized SNP. This
study has revealed a potential SNP marker that can be used
to determine coconut palms with outstanding oil quality.
However, phenotypic validation is still needed prior to
marker association. Moreover, other exons and/or introns
not characterized in this study, as well as promoter regions,
of the mined candidate MCFA-related genes may also be
screened for potential DNA sequence variation i.e., SNPs
and functional association to coconut oil quality.
ACKNOWLEDGMENTS
This study would not be possible without the generous
funding from the Department of Science and Technology
– Philippine Council for Agriculture, Aquatic and Natural
Resources Research and Development through PGC-
Agriculture. The authors extend their sincere gratitude to
Dr. Antonio C. Laurena, Dr. rer. nat. Lourdes B. Cardenas,
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and Dr. Consorcia E. Reaño for their guidance during the
conduct of the study. Also, to the authors’ colleagues at
PCA-ZRC – Mr. Ramon L. Rivera, Dr. Susan M. Rivera,
and Mr. Ernesto E. Emmanuel – for the source of the plant
materials used in this study. Equally, to the co-authors and
collaborators in the assembly of the reference genome, the
CATD coconut genome, especially Dr. Suzy Strickler and
Dr. Lukas A. Mueller of the Boyce Thompson Institute
for Plant Research, Ithaca, NY, USA. The high-quality
assembly of the reference genome was vital to the success
of this study.
STATEMENT ON CONFLICT OF
INTEREST
The authors declare no conflict of interest.
NOTES ON APPENDICES
The complete appendices section of the study is accessible
at http://philjournsci.dost.gov.ph
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Figure I. Clustal Omega alignment.

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Table I. PlantTFCat results.

Gene models Functional annotation

Cnu_07676-RA protein Name:"Similar to AIL5 AP2-like ethylene-responsive transcription factor AIL5 (Arabidopsis thaliana)"
AED:0.17 eAED:0.17 QI:0|0.71|0.5|1|0.85|0.75|8|0|443
Cnu_06751-RA protein Name:"Similar to DREB2C Dehydration-responsive element-binding protein 2C (Oryza sativa subsp.
japonica)" AED:0.02 eAED:0.01 QI:0|-1|0|1|-1|1|1|0|195
Cnu_07685-RA protein Name:"Similar to ERF003 Ethylene-responsive transcription factor ERF003 (Arabidopsis thaliana)"
AED:0.09 eAED:0.09 QI:73|1|0.5|1|1|1|2|0|151
Cnu_28685-RA protein Name:"Similar to ERF3 Ethylene-responsive transcription factor 3 (Arabidopsis thaliana)" AED:0.21
eAED:0.23 QI:0|-1|0|1|-1|1|1|0|220
Cnu_13245-RA protein Name:"Similar to RAP2-11 Ethylene-responsive transcription factor RAP2-11 (Arabidopsis thaliana)"
AED:0.01 eAED:0.01 QI:0|-1|0|1|-1|1|1|0|271
Cnu_06457-RA protein Name:"Similar to AP2 Floral homeotic protein APETALA 2 (Arabidopsis thaliana)" AED:0.12 eAED:0.12
QI:0|0.71|0.75|1|1|1|8|823|510
Cnu_06459-RA protein Name:"Similar to ERF010 Ethylene-responsive transcription factor ERF010 (Arabidopsis thaliana)"
AED:0.33 eAED:0.33 QI:0|0|0|0.5|1|1|2|0|137
Cnu_09318-RA protein Name:"Similar to RAP2-13 Ethylene-responsive transcription factor RAP2-13 (Arabidopsis thaliana)"
AED:0.07 eAED:0.07 QI:0|0|0|1|0|0.5|2|0|282
Cnu_16629-RA protein Name:"Similar to ERF110 Ethylene-responsive transcription factor ERF110 (Arabidopsis thaliana)"
AED:0.01 eAED:0.01 QI:380|1|1|1|1|1|2|0|313
Cnu_07492-RA protein Name:"Similar to ERF091 Ethylene-responsive transcription factor ERF091 (Arabidopsis thaliana)"
AED:0.03 eAED:0.02 QI:0|-1|0|1|-1|1|1|0|267
Cnu_07493-RA protein Name:"Similar to PTI5 Pathogenesis-related genes transcriptional activator PTI5 (Solanum lycopersicum)"
AED:0.13 eAED:0.13 QI:0|0|0|0.5|1|1|2|0|115
Cnu_08747-RA protein Name:"Similar to AIL1 AP2-like ethylene-responsive transcription factor AIL1 (Arabidopsis thaliana)"
AED:0.18 eAED:0.18 QI:194|0.83|1|1|0.83|0.71|7|221|364
Cnu_08831-RA protein Name:"Similar to EREBP1 Ethylene-responsive transcription factor 1 (Oryza sativa subsp. japonica)"
AED:0.10 eAED:0.10 QI:0|0.75|0.6|0.8|0.25|0.2|5|1025|338
Cnu_08855-RA protein Name:"Similar to ERF017 Ethylene-responsive transcription factor ERF017 (Arabidopsis thaliana)"
AED:0.03 eAED:0.01 QI:0|-1|0|1|-1|1|1|0|162
Cnu_08895-RA protein Name:"Similar to AIL1 AP2-like ethylene-responsive transcription factor AIL1 (Arabidopsis thaliana)"
AED:0.07 eAED:0.07 QI:32|0.71|0.62|1|0.28|0.5|8|189|612
Cnu_17567-RA protein Name:"Similar to ERF3 Ethylene-responsive transcription factor 3 (Nicotiana tabacum)" AED:0.26
eAED:0.59 QI:0|0|0|1|1|1|2|0|165
Cnu_05776-RA protein Name:"Similar to WRI1 Ethylene-responsive transcription factor WRI1 (Arabidopsis thaliana)" AED:0.12
eAED:0.12 QI:0|0|0|1|1|1|7|0|403
Cnu_08064-RA protein Name:"Similar to CRF2 Ethylene-responsive transcription factor CRF2 (Arabidopsis thaliana)" AED:0.11
eAED:0.11 QI:0|0|0|1|1|1|2|0|238
Cnu_32115-RA protein Name:"Similar to RAP2-11 Ethylene-responsive transcription factor RAP2-11 (Arabidopsis thaliana)"
AED:0.26 eAED:-0.21 QI:0|-1|0|1|-1|1|1|0|346
Cnu_17079-RA protein Name:"Similar to ERF019 Ethylene-responsive transcription factor ERF019 (Arabidopsis thaliana)"
AED:0.11 eAED:-0.13 QI:0|-1|0|1|-1|1|1|0|206
Cnu_03074-RA protein Name:"Similar to ANT AP2-like ethylene-responsive transcription factor ANT (Arabidopsis thaliana)"
AED:0.12 eAED:0.12 QI:0|0.85|0.62|1|0.71|0.62|8|277|674
Cnu_15889-RA protein Name:"Similar to ERF3 Ethylene-responsive transcription factor 3 (Arabidopsis thaliana)" AED:0.00
eAED:0.00 QI:0|-1|0|1|-1|1|1|0|203
Cnu_24426-RA protein Name:"Similar to WIN1 Ethylene-responsive transcription factor WIN1 (Arabidopsis thaliana)" AED:0.04
eAED:0.03 QI:0|0|0|1|0|0.5|2|0|203
Cnu_34216-RA protein Name:"Similar to ERF015 Ethylene-responsive transcription factor ERF015 (Arabidopsis thaliana)"
AED:0.14 eAED:-0.11 QI:0|-1|0|1|-1|1|1|0|195
Cnu_27083-RA protein Name:"Similar to DREB2F Dehydration-responsive element-binding protein 2F (Arabidopsis thaliana)"
AED:0.06 eAED:-0.06 QI:0|-1|0|1|-1|1|1|0|352

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Table I continued . . . .

Cnu_00637-RA protein Name:"Similar to DREB2A Dehydration-responsive element-binding protein 2A (Oryza sativa subsp.
indica)" AED:0.06 eAED:0.06 QI:258|1|1|1|1|1|2|489|319
Cnu_00788-RA protein Name:"Similar to AP2 Floral homeotic protein APETALA 2 (Arabidopsis thaliana)" AED:0.20 eAED:0.20
QI:0|0.8|0.72|1|0.8|0.90|11|464|474
Cnu_30312-RA protein Name:"Similar to ERF053 Ethylene-responsive transcription factor ERF053 (Arabidopsis thaliana)"
AED:0.01 eAED:-0.01 QI:0|-1|0|1|-1|1|1|0|479
Cnu_17504-RA protein Name:"Similar to RAP2-7 Ethylene-responsive transcription factor RAP2-7 (Arabidopsis thaliana)"
AED:0.30 eAED:0.30 QI:0|0.81|0.75|1|0.72|0.75|12|370|456
Cnu_10507-RA protein Name:"Similar to DREB1A Dehydration-responsive element-binding protein 1A (Arabidopsis thaliana)"
AED:0.01 eAED:0.01 QI:0|-1|0|1|-1|1|1|0|237
Cnu_01904-RA protein Name:"Similar to ERF012 Ethylene-responsive transcription factor ERF012 (Arabidopsis thaliana)"
AED:0.13 eAED:0.12 QI:0|-1|0|1|-1|1|1|0|167
Cnu_02062-RA protein Name:"Similar to CRF2 Ethylene-responsive transcription factor CRF2 (Arabidopsis thaliana)" AED:0.03
eAED:0.03 QI:0|0.5|0.33|1|0.5|0.66|3|481|466
Cnu_34292-RA protein Name:"Similar to DREB1F Dehydration-responsive element-binding protein 1F (Oryza sativa subsp.
japonica)" AED:0.04 eAED:0.03 QI:0|-1|0|1|-1|1|1|0|208
Cnu_24281-RA protein Name:"Similar to ERF071 Ethylene-responsive transcription factor ERF071 (Arabidopsis thaliana)"
AED:0.04 eAED:0.04 QI:37|1|0.5|1|1|1|2|0|204
Cnu_24282-RA protein Name:"Similar to ERF113 Ethylene-responsive transcription factor ERF113 (Arabidopsis thaliana)"
AED:0.28 eAED:0.28 QI:0|0|0|0.33|1|1|3|0|154
Cnu_11116-RA protein Name:"Similar to ERF118 Ethylene-responsive transcription factor ERF118 (Arabidopsis thaliana)"
AED:0.13 eAED:0.13 QI:266|0.66|0.5|1|0|0|4|0|292
Cnu_26511-RA protein Name:"Similar to CRF4 Ethylene-responsive transcription factor CRF4 (Arabidopsis thaliana)" AED:0.09
eAED:0.09 QI:0|-1|0|1|-1|1|1|0|344
Cnu_01404-RA protein Name:"Similar to RAP2-4 Ethylene-responsive transcription factor RAP2-4 (Arabidopsis thaliana)"
AED:0.02 eAED:0.00 QI:0|-1|0|1|-1|1|1|0|195
Cnu_09067-RA protein Name:"Similar to DREB3 Dehydration-responsive element-binding protein 3 (Arabidopsis thaliana)"
AED:0.03 eAED:0.02 QI:0|-1|0|1|-1|1|1|0|227
Cnu_19675-RA protein Name:"Protein of unknown function" AED:0.17 eAED:0.17 QI:0|0|0|0.5|1|1|2|0|243
Cnu_17656-RA protein Name:"Similar to ERF071 Ethylene-responsive transcription factor ERF071 (Arabidopsis thaliana)"
AED:0.08 eAED:0.05 QI:32|1|0.5|1|1|1|2|0|250
Cnu_17652-RA protein Name:"Similar to RAP2-3 Ethylene-responsive transcription factor RAP2-3 (Arabidopsis thaliana)"
AED:0.13 eAED:0.12 QI:0|0.5|0|0.66|0.5|0.33|3|0|338
Cnu_13415-RA protein Name:"Similar to EREBP1 Ethylene-responsive transcription factor 1 (Oryza sativa subsp. japonica)"
AED:0.29 eAED:0.35 QI:0|0.2|0|0.83|0.2|0.5|6|0|677
Cnu_13436-RA protein Name:"Protein of unknown function" AED:0.35 eAED:0.35 QI:0|-1|0|1|-1|1|1|0|177
Cnu_13437-RA protein Name:"Similar to ERF056 Ethylene-responsive transcription factor ERF056 (Arabidopsis thaliana)"
AED:0.17 eAED:-0.12 QI:0|-1|0|1|-1|1|1|0|190
Cnu_13439-RA protein Name:"Similar to ERF017 Ethylene-responsive transcription factor ERF017 (Arabidopsis thaliana)"
AED:0.11 eAED:-0.09 QI:0|0|0|0.5|1|1|2|0|176
Cnu_13441-RA protein Name:"Similar to ERF011 Ethylene-responsive transcription factor ERF011 (Arabidopsis thaliana)"
AED:0.39 eAED:0.23 QI:0|-1|0|1|-1|1|1|0|185
Cnu_13440-RA protein Name:"Protein of unknown function" AED:0.40 eAED:0.27 QI:0|-1|0|1|-1|1|1|0|158
Cnu_13443-RA protein Name:"Protein of unknown function" AED:0.09 eAED:0.05 QI:0|-1|0|1|-1|1|1|0|158
Cnu_30526-RA protein Name:"Protein of unknown function" AED:0.21 eAED:0.21 QI:477|1|1|1|0|0.5|2|285|184
Cnu_30527-RA protein Name:"Similar to At1g16060 AP2-like ethylene-responsive transcription factor At1g16060 (Arabidopsis
thaliana)" AED:0.44 eAED:0.41 QI:10|0.6|0.66|0.83|1|1|6|0|129
Cnu_32725-RA protein Name:"Similar to ERF4 Ethylene-responsive transcription factor 4 (Nicotiana sylvestris)" AED:0.09
eAED:-0.02 QI:0|-1|0|1|-1|1|1|0|232
Cnu_08572-RA protein Name:"Similar to AP2 Floral homeotic protein APETALA 2 (Arabidopsis thaliana)" AED:0.13 eAED:0.13
QI:408|1|1|1|1|1|10|856|479

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Table I continued . . . .

Cnu_06358-RA protein Name:"Similar to ERF096 Ethylene-responsive transcription factor ERF096 (Arabidopsis thaliana)"
AED:0.19 eAED:0.19 QI:0|0|0|1|1|1|2|0|141
Cnu_22517-RA protein Name:"Similar to AP2 Floral homeotic protein APETALA 2 (Arabidopsis thaliana)" AED:0.16 eAED:0.16
QI:554|1|1|1|0.66|0.8|10|73|527
Cnu_22556-RA protein Name:"Similar to ERF3 Ethylene-responsive transcription factor 3 (Arabidopsis thaliana)" AED:0.00
eAED:0.00 QI:0|-1|0|1|-1|1|1|0|221
Cnu_06398-RA protein Name:"Similar to BBM2 AP2-like ethylene-responsive transcription factor BBM2 (Brassica napus)"
AED:0.09 eAED:0.09 QI:0|0|0|1|0.71|0.87|8|0|710
Cnu_18333-RA protein Name:"Similar to ERF003 Ethylene-responsive transcription factor ERF003 (Arabidopsis thaliana)"
AED:0.06 eAED:0.06 QI:117|1|1|1|1|1|2|295|187
Cnu_12746-RA protein Name:"Similar to DREB1F Dehydration-responsive element-binding protein 1F (Oryza sativa subsp.
japonica)" AED:0.13 eAED:-0.03 QI:0|0|0|0.33|1|1|3|0|291
Cnu_24731-RA protein Name:"Similar to At4g13040 Ethylene-responsive transcription factor-like protein At4g13040 (Arabidopsis
thaliana)" AED:0.21 eAED:0.21 QI:0|0|0|0.6|1|1|5|0|190
Cnu_02813-RA protein Name:"Similar to AIL5 AP2-like ethylene-responsive transcription factor AIL5 (Arabidopsis thaliana)"
AED:0.14 eAED:0.14 QI:51|1|0.87|1|1|1|8|189|471
Cnu_02837-RA protein Name:"Similar to ERF003 Ethylene-responsive transcription factor ERF003 (Arabidopsis thaliana)"
AED:0.14 eAED:0.14 QI:0|1|0|1|1|0.5|2|0|174
Cnu_31422-RA protein Name:"Similar to ERF114 Ethylene-responsive transcription factor ERF114 (Arabidopsis thaliana)"
AED:0.24 eAED:0.05 QI:0|0|0|0.5|1|1|2|0|260
Cnu_12539-RA protein Name:"Similar to ERF026 Ethylene-responsive transcription factor ERF026 (Arabidopsis thaliana)"
AED:0.04 eAED:-0.04 QI:0|-1|0|1|-1|1|1|0|236
Cnu_12538-RA protein Name:"Similar to DREB1E Dehydration-responsive element-binding protein 1E (Oryza sativa subsp.
japonica)" AED:0.02 eAED:0.02 QI:0|-1|0|1|-1|1|1|0|212
Cnu_04667-RA protein Name:"Similar to AIL1 AP2-like ethylene-responsive transcription factor AIL1 (Arabidopsis thaliana)"
AED:0.15 eAED:0.07 QI:0|0|0|0.85|0.16|0.28|7|0|648
Cnu_18444-RA protein Name:"Similar to At4g13040 Ethylene-responsive transcription factor-like protein At4g13040 (Arabidopsis
thaliana)" AED:0.17 eAED:0.17 QI:865|1|0.85|1|0.5|0.42|7|383|121
Cnu_30019-RA protein Name:"Similar to ERF9 Ethylene-responsive transcription factor 9 (Arabidopsis thaliana)" AED:0.10
eAED:-0.04 QI:0|0|0|1|1|1|2|0|236
Cnu_09400-RA protein Name:"Similar to ERF021 Ethylene-responsive transcription factor ERF021 (Arabidopsis thaliana)"
AED:0.06 eAED:0.06 QI:0|0|0|0.5|1|1|2|0|188
Cnu_34164-RA protein Name:"Similar to ERF12 Ethylene-responsive transcription factor 12 (Arabidopsis thaliana)" AED:0.25
eAED:-0.15 QI:0|-1|0|1|-1|1|1|0|166
Cnu_11457-RA protein Name:"Similar to ERF023 Ethylene-responsive transcription factor ERF023 (Arabidopsis thaliana)"
AED:0.01 eAED:0.01 QI:60|1|1|1|0|0|2|8|224
Cnu_09596-RA protein Name:"Protein of unknown function" AED:0.12 eAED:0.12 QI:0|0.5|0|1|1|1|3|0|231
Cnu_09597-RA protein Name:"Similar to RAP2-3 Ethylene-responsive transcription factor RAP2-3 (Arabidopsis thaliana)"
AED:0.02 eAED:0.01 QI:0|1|0.5|1|1|0.5|2|407|249
Cnu_15237-RA protein Name:"Similar to PLT2 AP2-like ethylene-responsive transcription factor PLT2 (Arabidopsis thaliana)"
AED:0.13 eAED:0.13 QI:0|0|0|1|0.85|0.75|8|0|405
Cnu_23095-RA protein Name:"Similar to CRF4 Ethylene-responsive transcription factor CRF4 (Arabidopsis thaliana)" AED:0.14
eAED:0.30 QI:7|0.5|0.33|1|0.5|0.33|3|0|354
Cnu_34187-RA protein Name:"Similar to ERF062 Ethylene-responsive transcription factor ERF062 (Arabidopsis thaliana)"
AED:0.35 eAED:-0.50 QI:0|0|0|0.5|1|1|2|0|412
Cnu_05056-RA protein Name:"Similar to DREB3 Dehydration-responsive element-binding protein 3 (Arabidopsis thaliana)"
AED:0.02 eAED:0.02 QI:0|-1|0|1|-1|1|1|0|244
Cnu_25804-RA protein Name:"Similar to ERF14 Ethylene-responsive transcription factor 14 (Arabidopsis thaliana)" AED:0.04
eAED:0.02 QI:0|-1|0|1|-1|1|1|0|121
Cnu_25805-RA protein Name:"Similar to ERF1B Ethylene-responsive transcription factor 1B (Arabidopsis thaliana)" AED:0.04
eAED:0.03 QI:0|-1|0|1|-1|1|1|0|190
Cnu_14580-RA protein Name:"Similar to ABI4 Ethylene-responsive transcription factor ABI4 (Arabidopsis thaliana)" AED:0.23
eAED:0.23 QI:0|0|0|0.5|1|1|2|0|216

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Characterization of Oil Genes in Coconut

Table I continued . . . .

Cnu_22340-RA protein Name:"Similar to ERF019 Ethylene-responsive transcription factor ERF019 (Arabidopsis thaliana)"
AED:0.11 eAED:-0.05 QI:0|-1|0|1|-1|1|1|0|158\
Cnu_19544-RA protein Name:"Similar to ERF071 Ethylene-responsive transcription factor ERF071 (Arabidopsis thaliana)"
AED:0.02 eAED:0.01 QI:109|1|0.5|1|1|1|2|0|205
Cnu_03156-RA protein Name:"Similar to ERF023 Ethylene-responsive transcription factor ERF023 (Arabidopsis thaliana)"
AED:0.15 eAED:0.15 QI:0|-1|0|1|-1|1|1|0|182
Cnu_03309-RA protein Name:"Similar to WRI1 Ethylene-responsive transcription factor WRI1 (Arabidopsis thaliana)" AED:0.12
eAED:0.17 QI:0|0|0|1|0.33|0.71|7|0|404
Cnu_33408-RA protein Name:"Similar to ERF9 Ethylene-responsive transcription factor 9 (Arabidopsis thaliana)" AED:0.13
eAED:-0.18 QI:0|-1|0|1|-1|1|1|0|242
Cnu_12485-RA protein Name:"Similar to AP2 Floral homeotic protein APETALA 2 (Arabidopsis thaliana)" AED:0.22 eAED:0.15
QI:0|0.83|0.69|0.92|0.75|0.61|13|55|485
Cnu_12486-RA protein Name:"Similar to ERF010 Ethylene-responsive transcription factor ERF010 (Arabidopsis thaliana)"
AED:0.06 eAED:0.09 QI:380|0.5|0.33|1|0|0|3|0|159
Cnu_04554-RA protein Name:"Similar to ERF110 Ethylene-responsive transcription factor ERF110 (Arabidopsis thaliana)"
AED:0.19 eAED:0.18 QI:320|0.33|0.5|1|0|0|4|0|361
Cnu_24714-RA protein Name:"Similar to PTI5 Pathogenesis-related genes transcriptional activator PTI5 (Solanum lycopersicum)"
AED:0.05 eAED:0.05 QI:0|-1|0|1|-1|1|1|0|180
Cnu_24717-RA protein Name:"Similar to ERF091 Ethylene-responsive transcription factor ERF091 (Arabidopsis thaliana)"
AED:0.03 eAED:-0.03 QI:0|-1|0|1|-1|1|1|0|282
Cnu_26361-RA protein Name:"Similar to ANT AP2-like ethylene-responsive transcription factor ANT (Arabidopsis thaliana)"
AED:0.09 eAED:0.09 QI:112|0.85|0.75|1|1|0.87|8|319|659
Cnu_06945-RA protein Name:"Similar to DREB1E Dehydration-responsive element-binding protein 1E (Oryza sativa subsp.
japonica)" AED:0.11 eAED:-0.14 QI:0|-1|0|1|-1|1|1|0|298
Cnu_06946-RA protein Name:"Similar to ERF025 Ethylene-responsive transcription factor ERF025 (Arabidopsis thaliana)"
AED:0.18 eAED:0.17 QI:0|0|0|0.5|1|1|2|0|300
Cnu_14405-RA protein Name:"Similar to ERF019 Ethylene-responsive transcription factor ERF019 (Arabidopsis thaliana)"
AED:0.08 eAED:-0.03 QI:0|-1|0|1|-1|1|1|0|131
Cnu_14400-RA protein Name:"Similar to ERF021 Ethylene-responsive transcription factor ERF021 (Arabidopsis thaliana)"
AED:0.04 eAED:0.04 QI:0|-1|0|1|-1|1|1|0|174
Cnu_31507-RA protein Name:"Similar to ERF109 Ethylene-responsive transcription factor ERF109 (Arabidopsis thaliana)"
AED:0.20 eAED:0.20 QI:0|0|0|0.66|1|1|3|0|161
Cnu_25532-RA protein Name:"Similar to ERF012 Ethylene-responsive transcription factor ERF012 (Arabidopsis thaliana)"
AED:0.01 eAED:0.01 QI:0|-1|0|1|-1|1|1|0|208
Cnu_08225-RA protein Name:"Similar to ERF039 Ethylene-responsive transcription factor ERF039 (Arabidopsis thaliana)"
AED:0.11 eAED:0.11 QI:0|0|0|0.5|1|1|2|0|244
Cnu_08246-RA protein Name:"Similar to ERF5 Ethylene-responsive transcription factor 5 (Nicotiana sylvestris)" AED:0.13
eAED:0.13 QI:0|-1|0|1|-1|1|1|0|213
Cnu_08247-RA protein Name:"Similar to ERF1 Ethylene-responsive transcription factor 1 (Solanum lycopersicum)" AED:0.08
eAED:0.04 QI:0|0|0|1|1|1|2|0|282
Cnu_17812-RA protein Name:"Similar to ERF1B Ethylene-responsive transcription factor 1B (Arabidopsis thaliana)" AED:0.00
eAED:0.00 QI:0|-1|0|1|-1|1|1|0|227
Cnu_12326-RA protein Name:"Similar to AIL1 AP2-like ethylene-responsive transcription factor AIL1 (Arabidopsis thaliana)"
AED:0.08 eAED:0.08 QI:0|0|0|0.77|0.5|0.66|9|0|623
Cnu_21842-RA protein Name:"Similar to ERF008 Ethylene-responsive transcription factor ERF008 (Arabidopsis thaliana)"
AED:0.00 eAED:0.00 QI:0|-1|0|1|-1|1|1|0|168
Cnu_04041-RA protein Name:"Similar to ERF9 Ethylene-responsive transcription factor 9 (Arabidopsis thaliana)" AED:0.50
eAED:-0.04 QI:0|0|0|0.5|1|1|2|0|196
Cnu_18862-RA protein Name:"Similar to ERF017 Ethylene-responsive transcription factor ERF017 (Arabidopsis thaliana)"
AED:0.30 eAED:0.04 QI:0|0|0|0.33|1|1|3|0|353
Cnu_18950-RA protein Name:"Similar to DREB1C Dehydration-responsive element-binding protein 1C (Oryza sativa subsp.
japonica)" AED:0.01 eAED:0.01 QI:0|-1|0|1|-1|1|1|0|233

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Characterization of Oil Genes in Coconut

Table I continued . . . .

Cnu_18957-RA protein Name:"Similar to RAP2-11 Ethylene-responsive transcription factor RAP2-11 (Arabidopsis thaliana)"
AED:0.03 eAED:-0.00 QI:0|-1|0|1|-1|1|1|0|266
Cnu_26752-RA protein Name:"Similar to RAP2-11 Ethylene-responsive transcription factor RAP2-11 (Arabidopsis thaliana)"
AED:0.35 eAED:0.22 QI:0|0|0|0.5|1|1|2|0|355
Cnu_06218-RA protein Name:"Similar to ERF105 Ethylene-responsive transcription factor ERF105 (Arabidopsis thaliana)"
AED:0.13 eAED:-0.04 QI:0|0|0|1|1|1|2|0|234
Cnu_25405-RA protein Name:"Similar to ANT AP2-like ethylene-responsive transcription factor ANT (Arabidopsis thaliana)"
AED:0.11 eAED:0.09 QI:0|0.83|0.57|1|0.83|0.71|7|40|660
Cnu_20463-RA protein Name:"Similar to PTI6 Pathogenesis-related genes transcriptional activator PTI6 (Solanum lycopersicum)"
AED:0.11 eAED:0.07 QI:0|-1|0|1|-1|1|1|0|251
Cnu_25420-RA protein Name:"Similar to ERF012 Ethylene-responsive transcription factor ERF012 (Arabidopsis thaliana)"
AED:0.15 eAED:0.13 QI:0|0|0|1|1|1|2|0|172
Cnu_20503-RA protein Name:"Similar to ERF071 Ethylene-responsive transcription factor ERF071 (Arabidopsis thaliana)"
AED:0.07 eAED:0.07 QI:0|1|0|1|1|1|2|0|241
Cnu_28657-RA protein Name:"Similar to WRI1 Ethylene-responsive transcription factor WRI1 (Arabidopsis thaliana)" AED:0.13
eAED:0.32 QI:0|0|0|0.71|0.16|0|7|0|325
Cnu_07931-RA protein Name:"Similar to ERF113 Ethylene-responsive transcription factor ERF113 (Arabidopsis thaliana)"
AED:0.01 eAED:0.01 QI:117|1|1|1|1|1|2|126|233
Cnu_11926-RA protein Name:"Similar to RAP2-4 Ethylene-responsive transcription factor RAP2-4 (Arabidopsis thaliana)"
AED:0.14 eAED:0.14 QI:0|-1|0|1|-1|1|1|0|251
Cnu_23164-RA protein Name:"Similar to PLT2 AP2-like ethylene-responsive transcription factor PLT2 (Arabidopsis thaliana)"
AED:0.30 eAED:0.35 QI:0|0.5|0.28|1|1|1|7|0|414
Cnu_22768-RA protein Name:"Similar to ERF084 Ethylene-responsive transcription factor ERF084 (Arabidopsis thaliana)"
AED:0.27 eAED:0.20 QI:0|0|0|1|1|1|2|0|205
Cnu_22782-RA protein Name:"Similar to ERF003 Ethylene-responsive transcription factor ERF003 (Arabidopsis thaliana)"
AED:0.01 eAED:0.01 QI:97|1|1|1|1|1|2|198|188
Cnu_00071-RA protein Name:"Similar to ERF14 Ethylene-responsive transcription factor 14 (Arabidopsis thaliana)" AED:0.07
eAED:0.06 QI:0|-1|0|1|-1|1|1|0|125
Cnu_00134-RA protein Name:"Similar to DREB2C Dehydration-responsive element-binding protein 2C (Oryza sativa subsp.
japonica)" AED:0.43 eAED:0.43 QI:0|-1|0|1|-1|1|1|0|201
Cnu_05246-RA protein Name:"Similar to AIL5 AP2-like ethylene-responsive transcription factor AIL5 (Arabidopsis thaliana)"
AED:0.16 eAED:0.15 QI:0|0.5|0.22|0.88|0.75|0.66|9|0|468
Cnu_33633-RA protein Name:"Similar to ERF110 Ethylene-responsive transcription factor ERF110 (Arabidopsis thaliana)"
AED:0.24 eAED:0.28 QI:0|0.33|0|0.75|1|0.75|4|0|267
Cnu_16571-RA protein Name:"Similar to LEP Ethylene-responsive transcription factor LEP (Arabidopsis thaliana)" AED:0.06
eAED:0.02 QI:0|-1|0|1|-1|1|1|0|281
Cnu_16597-RA protein Name:"Similar to ERF114 Ethylene-responsive transcription factor ERF114 (Arabidopsis thaliana)"
AED:0.06 eAED:0.05 QI:0|0|0|0.5|1|1|2|0|180
Cnu_16598-RA protein Name:"Similar to ERF113 Ethylene-responsive transcription factor ERF113 (Arabidopsis thaliana)"
AED:0.30 eAED:0.30 QI:41|0|0.33|0.66|0.5|0.66|3|0|182
Cnu_01626-RA protein Name:"Similar to DREB2C Dehydration-responsive element-binding protein 2C (Arabidopsis thaliana)"
AED:0.16 eAED:0.16 QI:215|1|1|1|1|1|2|333|321
Cnu_18081-RA protein Name:"Similar to ANT AP2-like ethylene-responsive transcription factor ANT (Arabidopsis thaliana)"
AED:0.14 eAED:0.14 QI:106|0.71|0.5|1|0.85|0.75|8|0|643
Cnu_02451-RA protein Name:"Similar to DREB3 Dehydration-responsive element-binding protein 3 (Arabidopsis thaliana)"
AED:0.00 eAED:0.00 QI:0|-1|0|1|-1|1|1|0|222
Cnu_30010-RA protein Name:"Similar to CRF4 Ethylene-responsive transcription factor CRF4 (Arabidopsis thaliana)" AED:0.09
eAED:0.09 QI:0|-1|0|1|-1|1|1|0|326
Cnu_20112-RA protein Name:"Similar to BBM2 AP2-like ethylene-responsive transcription factor BBM2 (Brassica napus)"
AED:0.13 eAED:0.11 QI:0|0|0|1|1|1|7|0|719
Cnu_01836-RA protein Name:"Similar to ERF016 Ethylene-responsive transcription factor ERF016 (Arabidopsis thaliana)"
AED:0.15 eAED:-0.16 QI:0|0|0|0.5|1|1|2|0|285

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Table I continued . . . .

Cnu_01859-RA protein Name:"Similar to EREBP1 Ethylene-responsive transcription factor 1 (Oryza sativa subsp. japonica)"
AED:0.02 eAED:0.02 QI:191|1|1|1|0.5|0.33|3|1010|385
Cnu_04338-RA protein Name:"Similar to AIL5 AP2-like ethylene-responsive transcription factor AIL5 (Arabidopsis thaliana)"
AED:0.17 eAED:0.17 QI:491|0.8|0.66|1|0.8|0.83|6|348|384
Cnu_04392-RA protein Name:"Similar to ERF088 Ethylene-responsive transcription factor ERF088 (Arabidopsis thaliana)"
AED:0.42 eAED:0.42 QI:0|0|0|0.33|1|1|3|0|118
Cnu_14777-RA protein Name:"Similar to ERF061 Ethylene-responsive transcription factor ERF061 (Arabidopsis thaliana)"
AED:0.00 eAED:-0.00 QI:0|-1|0|1|-1|1|1|0|275
Cnu_14805-RA protein Name:"Similar to CRF4 Ethylene-responsive transcription factor CRF4 (Arabidopsis thaliana)" AED:0.06
eAED:0.06 QI:0|0|0|1|1|1|2|0|251
Cnu_23607-RA protein Name:"Similar to WRI1 Ethylene-responsive transcription factor WRI1 (Arabidopsis thaliana)" AED:0.09
eAED:0.09 QI:127|0.8|1|1|0.8|0.83|6|205|339
Cnu_23610-RA protein Name:"Protein of unknown function" AED:0.25 eAED:0.21 QI:0|0.46|0.37|0.81|1|1|16|0|953
Cnu_23915-RA protein Name:"Similar to RAP2-3 Ethylene-responsive transcription factor RAP2-3 (Arabidopsis thaliana)"
AED:0.02 eAED:0.02 QI:61|1|0.5|1|1|1|2|0|206
Cnu_24775-RA protein Name:"Similar to WIN1 Ethylene-responsive transcription factor WIN1 (Arabidopsis thaliana)" AED:0.00
eAED:0.00 QI:103|1|1|1|1|1|2|312|205
Cnu_16178-RA protein Name:"Similar to PLT2 AP2-like ethylene-responsive transcription factor PLT2 (Arabidopsis thaliana)"
AED:0.16 eAED:0.16 QI:0|0.5|0.28|1|0.83|0.71|7|0|388
Cnu_28838-RA protein Name:"Similar to ERF062 Ethylene-responsive transcription factor ERF062 (Arabidopsis thaliana)"
AED:0.30 eAED:-0.35 QI:0|-1|0|1|-1|1|1|0|374
Cnu_01025-RA protein Name:"Similar to WRI1 Ethylene-responsive transcription factor WRI1 (Arabidopsis thaliana)" AED:0.16
eAED:0.23 QI:0|0|0|1|0.6|0.66|6|0|298
Cnu_01179-RA protein Name:"Similar to DREB2C Dehydration-responsive element-binding protein 2C (Arabidopsis thaliana)"
AED:0.16 eAED:-0.06 QI:0|-1|0|1|-1|1|1|0|259
Cnu_01240-RA protein Name:"Similar to AP2 Floral homeotic protein APETALA 2 (Arabidopsis thaliana)" AED:0.09 eAED:0.09
QI:208|0.71|0.75|1|0.71|0.87|8|349|483
Table I continued…
Cnu_33344-RA protein Name:"Similar to ERF3 Ethylene-responsive transcription factor 3 (Arabidopsis thaliana)" AED:0.00
eAED:-0.00 QI:0|-1|0|1|-1|1|1|0|200
Cnu_19486-RA protein Name:"Similar to ERF2 Ethylene-responsive transcription factor 2 (Arabidopsis thaliana)" AED:0.14
eAED:0.14 QI:0|-1|0|1|-1|1|1|0|181
Cnu_03725-RA protein Name:"Similar to ERF1A Ethylene-responsive transcription factor 1A (Arabidopsis thaliana)" AED:0.41
eAED:0.49 QI:0|0|0|0.5|1|1|6|0|383
Cnu_03727-RA protein Name:"Similar to ERF5 Ethylene-responsive transcription factor 5 (Nicotiana sylvestris)" AED:0.32
eAED:0.27 QI:0|0|0|1|0|0.5|2|0|331
Cnu_03728-RA protein Name:"Similar to RAP2-2 Ethylene-responsive transcription factor RAP2-2 (Arabidopsis thaliana)"
AED:0.41 eAED:0.43 QI:0|0|0|0.5|1|1|4|0|332
Cnu_03777-RA protein Name:"Similar to ERF034 Ethylene-responsive transcription factor ERF034 (Arabidopsis thaliana)"
AED:0.08 eAED:0.08 QI:0|0|0|0.5|1|1|2|0|220
Cnu_03347-RA protein Name:"Similar to ERF109 Ethylene-responsive transcription factor ERF109 (Arabidopsis thaliana)"
AED:0.07 eAED:0.02 QI:0|-1|0|1|-1|1|1|0|245
Cnu_03506-RA protein Name:"Similar to RAP2-4 Ethylene-responsive transcription factor RAP2-4 (Arabidopsis thaliana)"
AED:0.13 eAED:0.13 QI:0|-1|0|1|-1|1|1|0|263

198