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
1Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science,
University of the Philippines Los Baños, College, Laguna 4031 Philippines
2Institute of Crop Science, College of Agriculture and Food Science,
University of the Philippines Los Baños, College, Laguna 4031 Philippines
3Philippine 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). A single 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.
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 crop in around 86 countries. In the Philippines, coconut 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 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). . . . read more
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