Tilapia Genomics and Applications

Thomas D. Kocher

Department of Zoology and Program in Genetics

University of New Hampshire

Durham, NH 03824

Tom.Kocher@unh.edu

ABSTRACT

Further development of the tilapia industry in the U.S. will depend on improvement of broodstock for key traits of commercial importance. Molecular markers and maps can contribute to the identification and selection of favorable alleles for these traits. Good progress has been made in developing marker maps, and the complete sequences of two model fish species (pufferfish and zebrafish) will accelerate the positional cloning of genes underlying growth. A commitment to a long-term program of selective breeding is needed to incorporate and maintain these genes in commercial populations

KEYWORDS: Tilapia, Oreochromis, genetics, selective breeding, linkage mapping, quantitative traits

INTRODUCTION

The prospects for genetic improvement of aquaculture species are good. Most species have large progenies, and short generation times compared to hooved livestock. These features allow strong selection to be imposed, accelerating progress in selective breeding programs (Gjedrem, 1983; 1985). Still, progress in genetic improvement of these species has been slow. One reason is that reliable culture of the complete life cycle in captivity has only recently been achieved in some species. Second is the difficulty of physically marking offspring, and obtaining accurate measures of performance of juveniles. Finally, practical difficulties of hatchery management and product marketing have left growers little time to focus on breeding programs (Gall, 1991).

Tilapia are a commercially important group of perch-like fishes (family Cichlidae) native to the freshwaters of tropical Africa (Trewavas 1983). The most important species in aquaculture are Oreochromis niloticus, O. aureus and O. mossambicus. These species have been introduced to dozens of tropical countries as a means to increase supplies of animal protein in the developing world. Tilapia are sturdy fish, well suited to aquaculture under a broad range of culture conditions. World-wide production of tilapia exceeds 1 million metric tons per year (FAO, 1997), making them one of the most important aquatic species in culture today. In 1999, the total U.S. consumption of tilapia was about 135 million pounds (USDA, 2000).

Commercial culture of tilapia is focussing on O. niloticus. The most important breeding goals for tilapia are to improve growth rate and feed conversion efficiency, which are the prime factors regulating profitability of the industry. Related to this is the need for a better understanding of sex-determination mechanisms, because genetically male tilapia have higher growth rates than even hormonally-reversed females (Mair et al. 1995). Disease resistance is an emerging problem as production systems intensify (Perera et al. 1997, Bowser et al. 1998), and will require prompt response from breeding programs. Finally, improvements to color and form would improve marketability and processing yield.

The haploid genome of O. niloticus is approximately 1 gigabase distributed over 22 chromosome pairs (Hinegardner and Rosen 1972; Majumdar and McAndrew, 1986). The average length of a chromosome is therefore 43 megabases. The tilapia genome is roughly twice as big as the pufferfish (Takifugu rubripes), and only half as large as zebrafish (Danio rerio). Recent research has developed molecular markers for tracking parentage and mapping traits of economic importance. These molecular markers provide tools for accelerating future breeding programs.

Hybridization and Gynogenesis

Early maturation and subsequent slow growth of females is a major obstacle to profitability of tilapia farming. For many years, interspecific hybridization was an important means for producing all-male populations of fingerlings. Today most growers use hormone-treated feed to masculinize fingerlings (Gale et al. 1999). While relatively efficient, this approach is not acceptable to all consumers, and may impact the health of hatchery workers.

An alternative approach is the use of YY-males (Mair et al. 1995). Such males can be produced by a breeding scheme which includes sex-reversal of XY-males to phenotypic females. Subsequent gynogenesis, or crossing of the XY females with normal XY males, will produce some YY 'supermales'. When mated to normal XX females, these YY males produce nearly 100% XY male progeny.

Gynogenesis can also be used to produce clonal lines of tilapia (Sarder et al. 1999). Hybrids among such inbred lines are expected to exhibit significant heterosis and uniform performance with respect to growth rate and body conformation.

Markers and Maps

My lab has characterized more than 300 microsatellite markers for tilapia (Lee and Kocher 1996, Carleton et al. in prep.). We published the first relatively complete genetic map for a tilapia (Kocher et al., 1997). Other investigators have published partial maps which largely confirm the original map (Agresti et al. 2000; McConnell et al. 2000). In collaboration with a private corporation (Genomar AS) we have genotyped more than 500 of these microsatellites in the F₂ progeny of a cross between O. niloticus x O. aureus. This linkage map has an estimated map length of ~2000cM.

We have analyzed this same family for genes controlling growth, color and sex. Six markers in two linkage groups were linked to sex. QTL for various aspects of color were found on 5 chromosomes. After controlling for sex differences QTL for length were found on two chromosomes.

Our current work is focused on developing a physical map of BAC clones. We plan to fingerprint ~30,000 clones to assemble ~1000 contigs spanning ~1Mb each. Microsatellite markers will be used to tie the contigs to the genetic map. Expressed sequences will be used to tie the contigs to the complete genome sequences of pufferfish and zebrafish.

RECOMMENDATIONS

The U.S. tilapia industry has reached a critical point. Small farms throughout the U.S. have found success in local markets for live fish, but they have not yet been able to compete against the low price of fresh and frozen fillets imported from overseas. Genetic improvements which accelerated growth rates could dramatically affect profitability of recirculating indoor culture of this species, which would then attract the capital needed to achieve economies of scale.

Short term (1-3 years)

1. Develop and implement methods to characterize tilapia germplasm resources.

ACKNOWLEDGEMENTS

My work on tilapia genomics is supported by the USDA-NRI Competitive Grants Program, the University of New Hampshire Agricultural Experiment Station, and Genomar AS. I am also grateful to numerous colleagues for providing materials, and a generation of students who performed the work in the lab.

REFERENCES