CURRENT AND CONTINUING PROJECTS
Project I. National Stock Assessment Program - Program Monitoring Office
Project II. Fisheries Resources and Ecological Study of Manila Bay
Project III. Fisheries Adaptation to Climate Change Tools (Fish ACT)
Projecr IV. FISHCODES: DNA BArcoding Services in Support of the Development and Implementation of Fisheries Management Plans
Project V. Bangus Fry: Status Assessment of the Bangus (Milkfish) Fry Resources and Fishery in the Philippines
COMPLETED PROJECTS
Project II: Genetic Stock Structure of Yellowfin (Thunnus albacares) and Bigeye (Thunnus obesus)Tunas in the Philippines
Team:
Noel C. Barut, Mudjekeewis Santos, Ph.D., Grace Lopez, Elsa Furio, November Romena, Roselyn Aguila and Sweedy Kay Perez
Funding Agency:
Department of Science and Technology–Philippine Council for Aquatic and Marine Research and Development (DOST-PCAMRD)
Duration:
January 2010 to December 2013
Collaborating Institutions (local/foreign):
- Department of Science and Technology–Philippine Council for Aquatic and Marine Research and Development (DOST-PCAMRD)
- Bureau of Fisheries and Aquatic Resources (BFAR) Regional Offices
- Private Sectors
Tunas constitute one, if not, the major fisheries commodity in the Philippines in terms of production, import and export (Barut et al., 2003). They contributed about 26% to the total marine production, an export share of about 37% (equivalent value of more than 6 million pesos), and import share of about 19% (equivalent value of more than 1 million pesos) in 2006 (BAS, 2007). Of the tuna species caught, yellowfin (Thunnus albacares) and bigeye (Thunnus obesus) comprise majority of the catch. Hence, it is important to sustain the tuna resources, particularly the yellowfins and bigeyes, in the country (Barut et al., 2003; Barut and Santos, 2000). Yellowfin and bigeye tunas are morphologically very similar in appearance, particularly the small sizes less than 40 cm, making them hard to separate. The difficulty in separating these two species (especially for the non-biologists like the statistical data enumerators) became an inherent problem in the generation of fisheries statistics by species for many years resulting in the aggregation of the Philippine statistical production record of yellowfin/bigeye to “yellowfin” only (OFP-SPC, 2004). There is therefore a question of accuracy in the data on tuna production that can lead to mismanagement. Moreover, the stock identity of yellowfin and bigeye tuna in the Western and Central Pacific Ocean is still unclear. Biochemical genetic markers such as MtDNA and microsatellites are powerful techniques to assess the level of gene flow between, and within populations or stocks. It is also very useful application in taxonomic studies by using a combination of genetic and classical taxonomic techniques (Grant & Leslie, 1984 as cited by Davies-Coleman et al., 2000). This technique will be employed to address these two abovementioned problems.
Project III: Gene Expression Profiling of Pathogenic Virus "Resistant" Shrimp
Team:
Mudjekeewis D. Santos, Ph.D., Benedict A. Maralit and Judith E. Ragaza
Funding Agency:
Department of Science and Technology–Philippine Council for Aquatic and Marine Research and Development (DOST-PCAMRD)
Duration:
January 2010 to December 2013
Collaborating Institutions (local/foreign):
- University of the Philippines in the Visayas (UPV)
- Tokyo University of Marine Science and Technology (TUMSAT)
- Research Center for the Natural Sciences
- Tomas Aquinas Research Center
- University of Santo Tomas
Shrimp viral pathogens such as the White Spot Syndrome Virus (WSSV), the Taura Syndrome Virus (TSV) and the Yellow Head Virus (YHV) have caused devastating losses in the shrimp culture industry worldwide. In the Philippines, WSSV has impacted the local shrimp aquaculture, in particular the major shrimp culture species - black tiger (Penaeus monodon) - such that the country is no longer one of the major shrimp exporting countries in the world. As a consequence, black tiger shrimp (Penaeus monodon) production in the country has remained stagnant at about 38,000 mt from a peak of 94,000 mt in the 1990’s. Although Pacific white shrimp (Penaeus vannamei) has recently been shown to be a very promising alternative to black tiger shrimp because it is relatively more resistant to WSSV and is actually on the rise now contributing to about 12.5% of total shrimp production at about 5,000 mt in 2007, this shrimp is still being limited by the virus where it can only be farmed during warm months when WSSV tend to be less of a problem (www.aquaphil.org). While there have been numerous advances in the study of shrimp-WSSV molecular interaction locally and internationally, the mechanisms for example of shrimp immunity is still unclear and largely debatable (Flegel, 2007).
This study, will achieve to provide new information on the molecular responses of 2 major cultured shrimp species, black tiger and Pacific white shrimp, that are “resistant” to WSSV using Expressed Sequence Tag (EST) analysis and use this, in addition to existing EST databases, to identify and develop genetic markers for SPR broodstock development. In particular, the study will a) determine the cause of “resistance” by showing and comparing the gene expression profiles of “resistant” and “susceptible” shrimps, b) identify genes specifically expressed in “resistant” strains, c) characterize and analyze the function of these genes using transcriptomic expression profiles and RNA silencing and d) identify and analyze these “resistance”-related genes, through their single nucleotide polymorphisms (SNPs) and identified microsatellites for SPR broodstock selection.
Project IV: FISHCODES-Genetic Barcoding of CITES listed and Regulated Aquatic Species Applied Biotech Research
Team:
Mudjekeewis D. Santos, Ph.D., Minerva Fatimae H. Ventolero and Joanne Krisha M. Lacsamana
Funding Agency:
Department of Agriculture-Bureau of Agricultural Research (DA-Biotech)
Duration:
August 2011 to July 2013
Collaborating Institutions (local/foreign):
- Bureau of Fisheries and Aquatic Resources (BFAR)
- RFO’s
- SUC’s
As the Philippines is now known to be the center of marine biodiversity in the world, preservation with regards to such resources is a must. With the growing anthropogenic (human) activities and environmental factors as well as the inevitable change in the global climate that threaten the university, the project offers an in-depth species profiling for conservation of aquatic species (especially those that are priority commodities for research and development) in the country. Genetic profiles generated from this project will serve as important baseline information for conservation, listing, monitoring, genetic development, stock enhancement and population studies needed for the sustainable management of the species being studied.
Project V: Intitutionalizing the Department of Agriculture (DA) DNA Library, DNA Barcoding of Philippine Crop, Livestock and Fishery
Team:
Mudjekeewis D. Santos, Ph.D., June Feliciano F. Ordoñez, Apollo Marco D. Lizano
Funding Agency:
Department of Agriculture-Bureau of Agricultural Research (DA-Biotech)
Duration:
October 2011 – September 2013
Collaborating Institutions (local/foreign):
- Philippine Rice Research Institute
- National Seed Industry Council
DNA barcodes, otherwise also known as DNA markers or DNA fingerprints, are essentially a short stretch of nucleotide sequences that aid in the specific identification of species strains or substrains. They are used to resolve taxonomy and phylogeny.DNA barcoding involves the collection and databasing of DNA sequence data from a single gene region. Ideally, one gene sequence would be used to identify species in all of the taxa (taxonomic groups) from viruses to plants and animals. However, that ideal gene has not yet been found, so different barcode DNA sequences are used for animals, plants, microbes. The Second International Barcode of Life Barcoding projects have already generated hundreds of thousands of reference barcodes for tens of thousands of species. These species have been selected because they are of special interest to users who need the ability to identify species of scientific, economic, or social importance. There are numerous examples of successful barcoding projects in agriculturally important animals and plants, many also with considerable application potential, e.g., DNA-based identifications of insect pests (Ball and Armstrong, 2006), pathogens of food crops (Kumar and Sharma, 2010) and fish of the ornamental fish trade (Steinke et al., 2009).
This work focuses on the creation of a national DNA library as a repository of sequence and marker data obtained from different agriculturally important species in the Philippines:(1) Philippine crops (specifically Oryza sativa);(2) fishery species, especially tilapia; and (3) livestock. The, carried out by the National Fisheries Research and Development Institute (NFRDI)focuses on determining the DNA barcodes of the different species of tilapia(Oreochromis sp.) using bioinformatics and data mining as well as generating trait-associated markers of the species. DNA sequences that would serve as barcodes for tilapia strains developed and bred in the Philippinesare also generated. On the other hand, the Philippine Rice Research Institute spearheads the analysis of DNA sequences of registered modern rice varieties.
Project VI: Sustainable Fisheries in the Sulu-Celebes LME; Genetic Stock Structures of Some Commercially Important Small Pelagics in the Region.
Team:
Mudjekeewis D. Santos, Ph.D., Ivane Pedrosa-Gerasmio and Shy Anne G. Dela Peña
Funding Agency:
UNDP/Global Environment Facility
Duration:
June 2011 to May 2012
Project Description:
The project aims to determine whether the four pelagic stocks namely Frigate Tuna (Auxis thazard), Bali Sardines (Sardinella lemuru), Indian Mackerel (Rastrellinger kanagarta) and Bigeye Scad (Selar crumenopthalmus) in the Sulu-Celebes Large Marine Ecosystem are genetically a single stock or if they constitute multiple stocks. Information that will be generated will be used as a basis for recommendation in the management of these stocks, Sampling sites includes Philippines (Zamboanga City and Palawan), Indonesia (Manado) and Malaysia (Kota Kinabalu).
Project VII: Sustainability of the Sardine Fisheries in the Philippines: Genetic and Biological Analyses
Team:
Mudjekeewis D. Santos, Ph.D., Demain Willette, Ph. D., Rey Thomas, Jr.
Funding Agency:
National Fisheries Research and Development Institute
Duration:
January –December 2011
Project Description:
The Sardine fishery is one of the major fisheries of the country and one of the most important pelagic species as far as the management of the fishery resources of the country is concerned. The sardine industry contributes greatly to the country’s economy, and a/the majority of the commercial sardine catch are delivered directly to the different canneries. In 2008, sardines contributed 9.8% (commercial) and 5.5% (municipal) to the total marine fish production amounting to 2,377,513.61 metric tons. The Philippine statistics keep a production record for the different sardines as lumped into two species only, the fimbriated sardines and Indian Sardines. By combining the top ten marine species by family, sardines ranked 2nd next to Family Scombridae for both municipal and commercial production in 2008 (BFAR,2008). Just like the rest of the country’s marine fisheries, the sardine fishery is also faced with the problem of resource depletion maybe due to the expansion of the commercial and municipal fisheries parallel with the increasing population demand. Although there are already various management efforts by the national and local government, the private sectors, and NGO’s to help primarily in the rehabilitation of overexploited fishery resources (Barut & Santos, 2000), constraints in the management of marine capture fisheries are yet to be resolved. It is with this dilemma that the government and the sardine industry are taking the necessary actions to manage the sardine fishery for its sustainable utilization in the future. Knowledge on the stock structure of sardines in the country remains uncertain and there is not much literature on this subject. Stock delimitation in sardine has been mainly based on phenotypic data and little is known about the phylogenetic relationships among the commercially important Sardinella species (Family Clupeida) especially at the molecular level (Samonte et al., 2000). The commonly used method of identifying sardine species for stock assessment still cause confusion or doubt in spite of the established morphological characters since these species are closely similar with each other in appearance. Since sardines are often caught in mixed schools, all of the species of sardine will be treated as a single management unit. Mitochondrial DNA has become widely used for genetic studies for fish populations, as it is rapidly evolving marker that is anticipated to be more sensitive to gene flow (Ward et al., 2001). In this study, mtDNA analysis will be conducted to study the Stock Structure of Sardines in the Philippines to support in the proper management of the resource.
Project VIII: Ludong and other mullet fishes in Cagayan: Taxonomic Classification and Population using Morphomeristic, Meristic and Genetic Characterization
Team:
Mudjekeewis D. Santos, Ph.D., Angelli M. Asis and Billy Joel N. Catacutan
Funding Agency:
Bureau of Fisheries and Aquatic Resources Region II
Duration:
September 2011-August 2012
Project Description:
Ludong also known as the President’s fish is one of the most expensive edible fish in the Philippines. Made famous by its unique and captivating taste and high market value, demand for the fish has become one of the causes for its striking decrease in abundance. Thus, conservation of the Ludong has been the top priority for the species. Efforts to the study of the species have been conducted such as research projects but there is still little information on the fish. The lack of morphological facts/information further complicates the taxonomical identification of the fish. Therefore, this study seeks to be substantiate the taxonomical identification of the Ludong through morphological and meristic data and genetic profile of the fish through barcoding in order to help in the establishment of the facts on the species and aide in the development of plans that will help in the conservation of the so called President’s fish.