The University of the Philippines Diliman (UPD) is working on improving tiger shrimp (Penaeus monodon) production through DNA study. The goal is to help shrimp farmers raise bigger and healthier shrimp through genomics.
P. monodon is one of the most valuable aquaculture products in the Philippines due to its high market demand. Because of this, researchers are prioritizing ways to improve its growth and production. Just like in farming animals or crops, some shrimps grow faster or bigger than the others. These differences are often caused by genetics, which is why researchers are focusing on identifying specific genes or genetic markers that are linked to better growth.
Use of genetic markers in farming is a widely accepted method to enhance productivity in agriculture and aquaculture. These markers act like signs in the DNA that help scientists spot which individuals carry traits that are good for breeding.
The current project under the Genomic technologies for improved production of Penaeus monodon program, “Validation of Genetic Markers Associated with Body Weight in the Tiger Shrimp (Penaeus monodon),” was built from an initiative, “Application of genomics in the development of genome-wide markers linked to production traits in Penaeus monodon.” This initiative led by Dr. Arturo O. Lluisma is part of the Tiger Shrimp Genomics Program. The earlier project successfully assembled a reference genome representative of the local P. monodon population in the Philippines and identified genetic markers by analyzing small variations known as Single Nucleotide Polymorphisms (SNPs).
Both projects are 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 aims to improve the quality of the reference genome assembly using circular consensus long-read sequencing and nanopore sequencing, which are two leading third-generation sequencing technologies. The project also seeks to identify SNPs with shrimp growth, and to validate previously identified genetic markers.
During the project’s second year, the team successfully generated genomic data from the third generation sequencing technologies. Efforts are also underway to improve the initial genome assemblies by applying multiple strategies to enhance their completeness and accuracy. Using the initial genome assembly of the P. monodon and extreme-phenotype genome-wide association studies (XP-GWAS) from the previous project, the team identified a set of growth-associated SNPs. In total, 19 SNPs were found to be significantly associated with growth. In addition to these, the team also identified SNPs associated with resistance to White Spot Syndrome Virus (WSSV) and a consumer-valued morphological trait (carapace length-to-abdomen length ratio).
To study these genetic traits, the project team employs the XP-GWAS approach. The process begins with phenotyping, which involves measuring the body weight of around 1000 individuals. These measurements are taken in several batches or cohorts to ensure consistency and to factor in environmental variation. The weight data typically follows a normal distribution, where most shrimps cluster around the average, while a smaller number fall into the lower and upper extremes. These individuals at both ends of the distribution are valuable for genetic studies.
Shrimp with lower weights may be slow growers, possibly due to developmental challenges or poor adaptability to their surroundings. On the other hand, the heavier shrimp may possess genetic variants that enhance growth rate or feed efficiency.
To pinpoint the genetic differences, the team grouped individuals from both extremes and pooled their DNA. Using second-generation sequencing technologies, they analyzed the pooled samples and performed genome-wide association analysis. This enabled them to identify genetic variants that constantly appear in fast or slow-growing shrimp. During the monitoring and evaluation, Dr. Lluisma mentioned that for the next steps of the project, the team will analyze sequence data from pools of extreme phenotypes and continue developing the reference genome using nanopore sequence data, a modern DNA sequencing technology.
The discovery and development of genetic markers that can be used to select for superior broodstock is significant towards enabling a more efficient shrimp farming in the country. Through the identification and utilization of best genetic traits, farmers can raise shrimp that grow faster, use feed more efficiently, and are disease resistant.