Genome-guided molecular characterization of oil genes in coconut (Cocos nucifera l.)

Creator

Anand Noel C. Manohar, University of the Philippines Los Banos
Darlon V. Lantican, University of the Philippines Los Banos
Melvin P. Dancel, University of the Philippines Los Banos
Don Emanuel M. Cardona, University of the Philippines Los Banos
Alissa Carol M. Ibarra, University of the Philippines Los Banos
Cynthia R. Gulay, University of the Philippines Los Banos
Alma O. Canama, University of the Philippines Los Banos
Roanne R. Gardoce, University of the Philippines Los Banos
Hayde F. Galvez, University of the Philippines Los Banos

Abstract

© 2019, Department of Science and Technology. All rights reserved. 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 INGenomes).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.

Source or Periodical Title

Philippine Journal of Science

ISSN

317683

Page

183-198

Document Type

Article

Subject

Coconut, EcoTILLING, Genomics-assisted breeding, In silico gene prediction, Medium-chain fatty acid, SNP markers

Recommended Citation

Manohar, Anand Noel C.; Lantican, Darlon V.; Dancel, Melvin P.; Cardona, Don Emanuel M.; Ibarra, Alissa Carol M.; Gulay, Cynthia R.; Canama, Alma O.; Gardoce, Roanne R.; and Galvez, Hayde F., "Genome-guided molecular characterization of oil genes in coconut (Cocos nucifera l.)" (2021). Journal Article. 809.
https://www.ukdr.uplb.edu.ph/journal-articles/809