To support the growing demand for milkfish and improve the country’s food security, a team from the University of the Philippines Diliman (UPD) are utilizing advanced approaches to support improved broodstock selection and development protocols for one of the country’s most important fish. Using genomic tools to develop marker-assisted selection protocols, the project aims to help the aquaculture industry produce faster-growing and better-quality milkfish.
Milkfish or ‘bangus’ is vital to the Philippines as one of the major sources of animal protein. The milkfish aquaculture industry accounts for a majority of production in the Philippines and is a substantial sector, playing an important role in food security and livelihood. However, the nation’s milkfish fry supply has struggled to keep pace with the industry's increasing needs. One promising solution posed by the researchers is genetic improvement of broodstock, particularly in identifying and selecting traits linked to growth performance.
Using advanced DNA and RNA sequencing techniques, the UPD team analyzed the milkfish genome and transcriptome to identify genes and genetic markers associated with growth performance. These molecular markers are envisioned as tools to guide the selection of broodstock with desirable production traits to improve hatchery production and fish quality.
These efforts were conducted through the project, “Developing genomic resources for improved production traits in hatchery bred milkfish” under the program, “Enhancement of Milkfish Aquaculture Productivity through genomics.” Funded by the Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development of the Department of Science and Technology (DOST-PCAARRD), the team led by Dr. Rachel June Ravago-Gotanco of UPD examined the genetic basis underlying growth variation in milkfish early juvenile stages using high-throughput sequencing of transcriptome and genome regions.
During the project’s terminal review, Dr. Ravago-Gotanco shared that the primary motivation for the project was to address the aquaculture industry’s need for increased and more efficient production through genetic improvement of broodstock.
Consequently, the project’s main objective was to identify potential genetic markers that can aid in selecting and developing broodstock with desirable production traits such as superior growth performance. She highlighted that marker-assisted selection offers a path to accelerate broodstock selection and development, significantly reducing the time needed, which is a key advantage for milkfish which takes five years to reach sexual maturity.
As part of project activities, milkfish larvae from several broodstock populations were reared to fry (21 days post-hatch) and fingerling stage (80 days post-hatch), collected, and sorted by size (total length) into two phenotypes (small and large). Fry samples were processed for transcriptome sequencing (RNA-Seq) while fingerling samples were analyzed using two DNA sequencing approaches: reduced representation genome sequencing (RADseq) and low-coverage whole genome sequencing (lcWGS). The resulting RNA and DNA sequences represent valuable genomic resources for Philippine milkfish populations.
The team generated comprehensive transcriptome sequence data to map active genes potentially involved in growth performance and understand their function. Researchers identified a suite of genes that are differentially expressed between size phenotypes that also showed consistent patterns across two independent spawning populations. Notably, genes that were highly expressed in larger juveniles were linked to essential biological processes and molecular functions involved in metabolism, gas and oxygen transport, nutrient response and immune responses, indicating their potential role in accelerated growth.
Two genomic sequence datasets were also generated from RADseq and lcWGS sequencing approaches to identify genetic variants associated with growth performance. Integrating transcriptome and genome sequence data, one of the main achievements of the project was the identification of growth-related single nucleotide polymorphisms (SNPs), variations in DNA sequence that can influence specific traits such as the size and growth rate. The team has developed an initial SNP panel which will be validated in the next phase of the study to determine their utility in predicting growth performance.
The project team acknowledges the contribution of industry partners, Feedmix Specialist II and Finfish Hatcheries Inc. (FHI), who provided support for milkfish rearing experiments, and allowed access to broodstock for genotyping. While the identification of genetic markers is a significant achievement representing important tools that can support breeding improvements and stock management of Philippine milkfish populations, further validation and development is needed before they can be fully integrated into commercial breeding operations. Once validated, SNP genotyping is expected to assist hatchery operators and fish farmers in making more informed decisions for broodstock selection and management. The project results can pave the way towards employing marker-assisted or genomic selection in milkfish breeding. This enhances the accuracy and efficiency of selection, thus, accelerating genetic improvement for more productive and sustainable aquaculture practices.
The project supports the aquaculture industry’s goals of higher efficiency, improved fish quality, and a more secure and sustainable milkfish supply.