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College of Food, Agricultural, and Environmental Sciences



Research Facility:

Aquaculture Genetics and Breeding Laboratory 

Aquaculture Research Breeding Center 

Research areas:

OCARD has established three dimensional programs of aquaculture through integration of fish genetics/breeding, fish nutrition, and fish health. We have used genetics/genomics to develop genetic tools (genetic markers and maps) to assist selective breeding and sex control for improvement of growth, soybean diet utilization, larval quality/survival of aquatic animals, and to develop biomarkers of environmental stressors for fish health and disease management.  Specifically, our research involved:

Genetics and Genomics


Selective Breeding

Nutrition and Feed

Stress and Disease

Sustainable Aquaponics

Genetics and Genomics:

Aquaculture researchers at the OCARD have completed whole genome sequencing of yellow perch and bluegill and developed SNPs and microsatellite markers for selective breeding and developing monosex populations of important aquaculture species. We are analyzing genetic diversity of different strains and genetically improved lines of yellow perch and largemouth bass using both SNPs and microsatellites. We are also conducting functional genomics research to identify genes associated with traits of interest such as growth, stress, spawning time, ω-3 fatty acids synthesis and compensatory growth for yellow perch. We have completed two projects on genotype by environment interaction in yellow perch. We have also been conducting studies to identify the sex determination mechanism of aquaculture species.


We conducted RNA-Seq and hormonal analysis of males, females and neo-males and results showed that steroid exposure during the critical period of sexual differentiation could epigenetically modulate subsequent hormonal responses and gene expression. In addition, we performed BS-seq of the males, females and neo-males to exam how epigenetically-modulated hormonal responses and gene expression regulates sexual size dimorphism (SSD)  throughout the lifespan. The female samples showed different methylation patterns with the other two groups, and the numbers of C methylated in CpG context in female are much lower than neomales and males. These results support our hypotheses: 1) Sex-biased or sex-specific gene expression is partially responsible for SSD; 2) The differences in sex-biased or sex-specific gene expression are associated with or the results from estrogen-mediated regulation; 3) Steroid exposure during the critical period of sexual differentiation can epigenetically modulate subsequent hormonal responses and gene expression; and 4) Epigenetically-modulated hormonal responses and gene expression in turn regulates SSD throughout the lifespan. Our research in this hot topic, including several years of investigating how animal behaviors and environment can cause changes that affect the way their genes work, resulted in publication of a book “Epigenetics in Aquaculture.” with Wiley.

Selective Breeding:

Multiple improved lines of yellow perch have been developed, and over two million genetically improved fish have been distributed to fish farms. Three-year on-farm tests on three sites in two states show that our improved fish exhibited 28-42% higher production, and 26-38% higher growth rates even while having 28% higher survival than local strains. We have selected yellow perch that better utilize soybean-based diets. Through selective breeding, we developed all-female yellow perch and all-male bluegill strains and related technologies and investigated their mechanisms. Growth tests funded by USDA-NCRAC showed weight gain and growth rate of all-male bluegill were twice that of regular stocks, and all-females perch grew 26% faster than a mixed group, and 66% faster than males. The research in this field has resulted a 2-volume book Sex Control in Aquaculture and more than 15 peer-reviewed publications. In addition, a project on the evaluation of hatchery stocks and wild populations of largemouth bass across North America and Asia has been completed. The results of this study provide a valuable base for developing a future selective breeding program for largemouth bass. 

Nutrition and Feed:

We are developing alternative protein sources for aquaculture diets. We have evaluated modified soybean protein concentrate as a fish meal replacer in the yellow perch diet, and found soy protein concentrate could replace 50% of the fish meal protein in the yellow perch diet without compromising the growth and health of the fish, and also exhibited better growth performance than soy bean meal fed groups. Meanwhile, We have been conducting studies on developing systems and diet strategies to increase survival of fry and larvae of aquaculture species including yellow perch and striped bass. In addition, we are also developing new biomarkers by using genomics (gene expression analysis), proteomics (protein expression analysis) and metabolomics (metabolite profiling) approaches to define a healthy phenotypic fish.

Stress and Disease:

We are investigating stress response to various husbandry and environmental stressors such handling and temperature in farmed fish, the relationship between stress and fish disease, gene expression patterns associated with various stressors, fish immune-relevant genes and their relation to stress, and probiotics, natural products, and bioactive substances and their effect to counteract and minimize the stress in fish. The major goal of our research is to reduce and minimize stress, uphold a healthy aquatic environment, decrease disease incidence, inhibit the spread of diseases and mortality related to handling and low and high temperature for yellow perch and bluegill.

Sustainable Aquaponics:

We are testing different fast-growing and stress/disease tolerant fish strains with various vegetables/plants for developing novel aquaponic production model systems. We are using metagenomics to determine major microbial players that optimize nutrient conversion and cycling in the aquaponic systems identified and we are manipulating the microbial consortia associated with the rhizosphere to enhance plant yield and nutrient cycling.