Sex: Male
Education:
- Master of Science in Molecular Biology and Biotechnology, University of the Philippines Los Baños, 2018
- Bachelor of Science in Agricultural Biotechnology, Molecular Makers, University of the Philippines Los Baños, 2012
Field of Specialization:
Agricultural Biotechnology
Plant Biotechnology
Plant Breeding
Plant Molecular Biology
Plant Genetics
Molecular Plant Breeding
Molecular Makers
Molecular Maker Development
Bioinformatics
Genomics
Researches:
Article title: Resistance Gene Analogs of Mango: Insights on Molecular Defenses and Evolutionary Dynamics
Authors: Darlon Vasquez Lantican, Anand Manohar, Fe M. Dela Cueva, Cris Q. Cortaga, et al.
Publication title: Philippine Journal of Science 149(3-a):915-934, October 2020
Abstract:
Mango is an economically important fruit crop largely cultivated in the tropics and, thus, is constantly challenged by a myriad of insect pests and diseases. However, no detailed analysis of its resistance gene analogs (RGAs) has been performed, which is a vital resource for plant breeding. Here, we analyzed the RGAs of mango via de novo assembly of transcriptomic sequences and mining of the recently published whole genome sequence (WGS). From the transcriptomic assembly, a core mango RGA database with 747 protein models was established. Meanwhile, 1,775 RGAs were identified in the mango WGS and classified based on conserved domains and motifs: 54 nucleotide binding site proteins (NBS), 107 NBS – leucine rich repeat proteins (NBS- LRR), 242 coiled-coil NBS-LRR (CNL), 79 toll/interleukin-1 receptor NBS-LRR (TNL), 78 coiled-coil NBS (CN), 30 toll/interleukin-1 receptor NBS (TN), 45 toll/interleukin-1 receptor with unknown domain (TX), 133 receptor-like proteins (RLP), 917 receptor-like kinases (RLK), 83 transmembrane coiled-coil domain protein (TM-CC), and seven NBS-encoding proteins with other domains. The transcriptome- and genome-wide RGAs have been functionally well- annotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also examined. Phylogenetic analyses of expressed and genome-wide RGAs suggest highly divergent functions of the RGAs, which were broadly clustered into 6 and 8 major clades, respectively, based on their domain classification. From the mango RGA transcripts, 134 unique EST-SSR (expressed sequence tags – simple sequence repeat) loci were identified and primers were designed targeting these potential markers. Moreover, comparative analysis of mango with other plant species revealed 65 species-specific RGA families (396 orthologous genes) and detected 1,005 RGA gene duplication events. To date, this is the most comprehensive analysis of mango RGAs, which also provide insights into the dynamic mango- pest co-evolutionary arms race and offer a trove of markers for utilization in resistance breeding.
Full text https://tinyurl.com/nfer72xa
Article title: Glandular Trichome Gene-Linked SSR Marker Development for Genetic Diversity Analysis and Trait Association in 'Tambulilid' Coconut (Cocos nucifera L.)
Authors: Angelica Kate G. Gumpal, Darlon V. Lantican, Roanne R. Gardoce, Melvin P. Dancel, Jomari C. Domingo, Ronilo M. Bajaro, and Hayde F. Galvez
Publication title: Philippine Agricultural Scientist 102(Special Issue):64-76, December 2019
Abstract:
Massive infestation of coconut scale insect (Aspidiotus sp.) in major coconut growing regions in the country has caused serious damage to the coconut industry. Coconut ‘Tambulilid’, a Javanica variety grown in Bicol, was reported to exhibit antibiosis form of host-resistance against Aspidiotus sp. To further elucidate the mechanism of resistance of this variety, linked microsatellite (SSR) marker was designed, screened, and optimized to target each of the 10 candidate plant glandular trichome genes (PPO, ALS, GL3, SESQ, ETC3, CPC, GSD, TDA, COI1, TTG1) based on the coconut genome. Out of the ten SSR markers designed, eight SSRs were used to determine the extent of genetic differentiation among 30 ‘Tambulilid’, 7 ‘Coco Niño’, and 16 ‘Laguna Tall’ representative individual palms. Four sub-populations could be differentiated at 0.17 similarity coefficient, validated by pairwise F-test (FST) statistics involving the heterozygosity of the 8 SSR markers. Sub-clusters containing ‘Laguna Tall’ individuals exhibit considerable genetic differentiation when compared with sub-clusters generally consisting of ‘Tambulilid’ coconut palms. Single-factor ANOVA of SSR marker genotype segregation with existing trichome density data revealed that the SSR markers linked to germacrene synthase D could be associated to the trichome density trait.
Full text link https://tinyurl.com/mbtw33s
Article title: Isolation of a CEL 1 Homolog in Tomato (Solanum lycopersicum L.) Fruit as a Cost-effective Endonuclease Source for Targeting Induced Local Lesions IN the Genome (TILLING) Analysis
Authors: Rochelle E. Alcasid, Maria Elizabeth B. Naredo, Darlon V. Lantican and Hayde F. Galvez
Publication title: Philippine Journal of Science 148(3):465-472, September 2019
Abstract:
CEL 1, an endonuclease originally purified from celery, has been used in TILLING (Targeting Induced Local Lesions IN the Genome) analysis to cut the hairpin loop and single-strand DNA generated from heteroduplex of mutant and wild DNA molecules. However, one major limitation as with most mutation screening technologies and especially in a large-scale application is the availability of affordable sources of endonuclease. This study searched for CEL 1 gene homologs in tomato through Basic Local Alignment Search Tool for nucleotides (BLASTn) and relevant bioinformatics analysis in public genomic databases. Results showed that the SlENDO 1 gene (SGN Accession Number Solyc02g078910.1.1) of tomato (Solanum lycopersicum) has the highest homology of 78% to CEL 1 among all the Solanum species. As annotated, the SlENDO 1 gene has a genome sequence length of 2.182 Kb and consisting of eight and nine intron-exon sequences, respectively. For molecular confirmation, polymerase chain reaction (PCR) primers were designed to target the conserved gene region of SlENDO 1. The amplification and specificity of these primers were further verified first by in silico PCR prior to synthesis. The designed SlENDO 1-specific DNA marker has successfully amplified the target gene in five tomato varieties in actual wet-laboratory PCR experiments. Interestingly, the designed marker was able to cross-amplify orthologous regions (candidate regions of nuclease PA3, TIGR LOC_Os04g54390) in Nipponbare and IR64 rice varieties. Once validated using a wide-range of crop species, the developed SlENDO 1-specific DNA marker can be potentially used in rapid detection of gene homologs in other plants. The isolation of the SlENDO 1 enzyme was also done using a modified protocol for CEL 1 isolation in celery. Through preliminary EcoTILLING with rice positive control samples, the purified SlENDO 1 from unripe fruits of non-transgenic tomato was confirmed to have the same mutation cleavage specificity as that of the CEL 1 endonuclease. Unlike celery, tomato fruits are readily available in any vegetable market, shop, or store in the Philippines. Likewise, they can easily be grown in greenhouse and field production.
Full text link https://tinyurl.com/srdjwadm
Article title: De Novo Genome Sequence Assembly of Dwarf Coconut (Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species
Authors: Darlon V. Lantican, Susan R. Strickler, Alma O. Canama, Roanne R. Gardoce, Lukas A. Mueller, and Hayde F. Galvez
Publication title: G3-Genes Genomes Genetics 9(8), June 2019
Abstract:
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago® sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
Full text link https://tinyurl.com/yz45jha8
Article title: Genome-guided Molecular Characterization of Oil Genes in Coconut (Cocos nucifera L.)
Authors: Anand Noel C. Manohar, Darlon V. Lantican, Melvin P. Dancel, Don Emanuel M. Cardona, Alissa Carol M. Ibarra, et al.
Publication title:
Abstract:
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.
Full text link https://tinyurl.com/kkas2nyr
Papers Presented
Article title: Genomics in Coconut Towards Insect Resistance Breeding
Authors: Hayde Galvez, Darlon Vasquez Lantican, Maria Luz Josue Sison, Roanne Gardoce, et al.
Conference title: 14th Quadrennial Congress of the International Association for Plant Biotechnology (IAPB), August 2018
Abstract:
The Philippines is the topmost exporter of high-value coconut products. In partnership with industry and overseas collaborators, advancements in genomics were exploited to characterize coconut genes of interest. Insect pests are among the biotic factors that have threatened coconut production in the Philippines. By sequencing the whole genome of a representative dwarf variety of coconut, candidate genes and regulatory elements for host insect resistance were mined. Allelic variants were screened using a core set of germplasm conserved at the Philippine Coconut Authority (PCA). The genome sequence of the insect pest was also characterized. A speciesspecific DNA marker was developed to safeguard the purity of the insect population for resistance screening. Employing both ‘Choice’ and ‘No-Choice’ tests, the core coconut germplasm and on-farm outstanding selections were assayed for host resistance. RNA-sequence data from healthy and infested resistant/susceptible varieties were also analyzed; output of which could be mapped back to the coconut genome database to validate the candidate genes. The mechanisms of potential host insect resistance were elucidated in selected coconut varieties through correlation analysis of molecular, biochemical and phenotype data, and by employing relevant genomics/ bioinformatics tools.
Full text available upon request to the author
Article title: Genome-guided characterization of medium-chain fatty acid (MCFA) genes in coconut (Cocos nucifera L.) towards marker-assisted breeding
Authors: Anand Manohar, Darlon Vasquez Lantican, Melvin Dancel, Don Emanuel Mendoza Cardona ,et al.
Conference title: 48th CSSP Scientific ConferenceAt: La Piazza Hotel, Legazpi City, Philippines, July 2018
Article title: Coconut Genetics and Genomics for Host Insect Resistance
Authors: Hayde Galvez, Darlon Vasquez Lantican, Maria Luz Josue Sison, Roanne Gardoce, et al.
Conference title: Plant and Animal Genome Conference XXVIAt: Town and Country Hotel, San Diego, California
Abstract:
The Philippines is the second world supplier of coconut (Cocos nucifera L.) products. Used to be the topmost producer/supplier, the country however has been threatened with serious production constraints including the recent outbreak of coconut scale insect (CSI) in major coconut regions. To facilitate the development of insect resistant variety, advancements in genomics and related technologies are harnessed for their optimum integration in the coconut breeding program. Coconut NGS reads were generated by sequencing the whole gDNA of Catigan Green Dwarf (CATD) coconut variety using several sequencing platforms i.e. 50X Illumina Miseq, 15X PacBio SMRT, and Dovetail Chicago sequencing. Based on combined analysis, a total genome sequence length of 2.1 Gb consisting of 8,062 scaffolds with N50 value of 569 kb was assembled. The genome assembly and initial gene models were uploaded in a local genome database and utilized to develop DNA markers targeting candidate genes for insect resistance. The genome sequence of CSI was also characterized and a species-specific DNA marker system was developed. Employing both ’Choice’ and ‘No-Choice’ tests, 73 core coconut germplasm and on-farm outstanding selections were assayed for host resistance against CSI. The coconut materials were also mined for point-mutations at the candidate gene sequences, which are being associated to the differential CSI host response. RNA-sequence data from these differential gene expressions are also being analyzed; output of which will be mapped back to the coconut genome for a targeted functional annotation. Through forward/reverse genetics correlation studies coupled with relevant genome and bioinformatics data, the mechanism of host insect resistance will be elucidated in selected coconut varieties.
Full text available upon request to the author
Article title: The Coconut Genome: Providing a Reference Sequence Towards Coconut Varietal Improvement
Authors: Darlon Vasquez Lantican, Susan R Strickler, Alma O. Canama, Roanne Gardoce, et al.
Conference title: Plant and Animal Genome Conference XXVIAt: Town and Country Hotel, San Diego, California, January 2018
Abstract:
We present the whole genome sequencing (WGS) of Catigan Dwarf (CATD) coconut variety, chosen for its genome simplicity and low heterozygozity. PacBio SMRT sequence data was generated at 15X coverage and corrected with assembled 50X Illumina paired-end MiSeq reads. Through the hybrid assembly approach, the draft assembly of the dwarf coconut genome has N50 of 120 kb. The genome was further improved through Dovetail Chicago sequencing. The input de novo hybrid assembly, Miseq PE reads and Chicago library reads were used as input data in the HiRise pipeline in order to scaffold the genome assembly. As a result, the final assembly has now a total sequence length of 2.1 Gb consisting of 8,062 scaffolds with N50 value of 569 kb. This covers around 97.6% of the estimated CATD genome of 2.15 Gb based on the homozygous k-mer peak. Around 1.556 Gb is identified as interspersed repeat sequences or 73.93% of the total assembled genome. A total of 35,231 high-confidence gene models are identified using the MAKER annotation pipeline. Result of the BUSCO analysis has revealed a 83.1% completeness of the current genome annotation, and 7.4% fragmented single copy orthologs (USCO) based on 1440 genes in the plant specific OrthoDB database. The assembly statistics and quality evaluation results demonstrate that our current draft scaffold assembly has covered most of the dwarf coconut and gene units. Such provides a good reference coconut genome for various applications such as re-sequencing projects, gene mining and DNA marker development, and functional annotation/genomics approaches.
Full text link https://tinyurl.com/y84788bu
Article title: The Coconut Genome: Providing a Reference Sequence Towards Coconut Varietal Improvement
Authors: Darlon Vasquez Lantican, Noe Fernandez Pozo, Alma O. Canama, Susan R Strickler, et al.
Conference title: 26th International Plant and Animal Genome Conference (PAGXXVI)At: San Diego, CA USA, January 2018
Abstract:
Full text available upon request to the author
Article title: Host resistance screening in coconut against the invasive coconut scale insect, Aspidiotus rigidus Reyne (Hemiptera: Diaspididae)
Authors: Maria Luz Josue Sison, Don Serville Reynoso, Cris Q. Cortaga, Joseph P. Lagman, et al.
Conference title: 49th Pest Management Council of the Philippines, Inc. (PMCP) Scientific ConferenceAt: Crown Regency Resort and Convention Center, Boracay Island, Malay, Aklan, Philippines, October 2017
Abstract:
The devastation of millions of coconut palms caused by invasive Coconut Scale Insect (CSI), Aspidiotus rigidus, has posed a serious threat to the coconut industry in the Philippines. To help address this problem, host plant resistance (HPR) studies were conducted to provide a very economical and effective approach to mitigate the infestation through utilization of the innate resistance of coconut. This study aimed at identifying potential resistant variety/ies and mine putative resistance genes for coconut breeding. Host resistance screenings (natural infestation) were separately done at UPLB and two (2) sites in Basilan. Varieties used were 23 Tall, 25 Dwarf, 16 Synthetic, eight Orgullo for a total of 72, and a susceptible Laguna Tall (LAGT) as the control. Results showed that Dwarf, Synthetic, and Orgullo varieties were preferred by A. rigidus, but some Tall varieties during this duration were not infested or less preferred. These include Vanuatu (VTT), West African Tall (WAT), and Salambuyan (SALT). In Basilan, higher rate of progression of CSI infestation was observed at Lanote compared to East Side. Under no-choice test (controlled infestation), the least preferred variety was Tupi dwarf. Additional coconut varieties from Albay Research Center were also studied using no-choice test, namely: Coconiño, Tambulilid, and LAGT, and CALABARZON collection which were the putative progenies of the selected coconut trees resistant to CSI during the outbreak. Initially, LAGT was the least preferred variety based on the number of newly settled and developed CSI, while among CALABARZON selection, the least preferred was M11 having the fewest CSI.
Full text available upon request to the author
Article title: Development of Tomato Non-Host to Tomato Virus through Targeted Mutagenomics and Bioinformatics Approaches
Authors: Hayde Galvez, Alma O. Canama, Reynaldo B. Quilloy, Roland Schafleitner, et al.
Conference title:
Abstract:
Tomato (Solanum lycopersicum L.) is economically one of the most important vegetable crops grown worldwide. Tomato fruit makes important contributions to diet and livelihood, as an everyday ingredient in many dishes, and a rich source of nutrients and natural anti-oxidants. Yield and fruit quality losses caused by persistent virus diseases are among the major constraints in tomato production. Breeding for resistant varieties and search for genetic materials have always been a race with the fast virulence evolution of the pathogen. Mutational approaches such as Targeting Induced Local Lesions In Genome (TILLING) are carried out to generate and screen for vast germplasm resource. Large families of M2:3 tomato mutants are generated for mutational and subsequent phenotypic analysis. DNA markers are designed using computational biology tools, and SGN and other public genome databases targeting candidate virus-host factors and Rgene regulatory sequences. Bulk and individual DNA samples are processed from each M2 plant, and currently being analyzed for point-mutation/s at target loci, employing both high throughput DNA sequencing and TILLING/HRM mutation screening. M3 progenies are being generated from each M2 plant and will be used to validate the induced host resistance against target tomato viruses.
Full text link https://tinyurl.com/texm4d5x