The Catfish Genome Project

Justification

   Aquaculture must grow rapidly to become an alternative seafood source to the collapsing natural fisheries.  Marine fisheries are currently harvested at or above maximum sustainable levels, and are in global decline because of over-harvesting and habitat degradation. The world’s capture fisheries reached their peak harvest in the mid-1980s, and a rapid growth in aquaculture production was demanded by the growing human population. The experience of the last twenty years indicates that aquaculture has the potential to compensate for dwindling natural fisheries, producing a highly desired source of protein and trace nutrients for the human diet.  Aquaculture production has drastically increased in the last 20 years, and currently accounts for over 43% of fish consumption.

     Channel catfish fingerlings

 

 

   The catfish industry is the major aquaculture industry in the U.S. accounting for over 60% of the US aquaculture production. Several important production and performance traits such as growth rate, feed conversion efficiency, disease resistance, body conformation and fillet yield must be improved in order to make the catfish industry profitable in the face of stiff global competition. Genome research holds great promise because it deciphers all the genetic material into a road map that shows genes important for growth, disease resistance, etc. Through the development of genome technologies, we hope to provide the catfish industry with tools to identify broodstocks based on genetics, and make breeding decisions using genome selection. Such information would allow selection of fish with the combination of “good” genomic regions. The catfish genome project is conducted in the Molecular Genetics and Biotechnology Laboratory (http://www.auburn.edu/genomics).

Objectives

1. Understanding the road map of the catfish genome through mapping of thousands of DNA markers to the genome
2. Understanding of architecture of the catfish genome
3. Discovery and identification of all catfish genes (believed to be 25,000 to 30,000);
4. Production of a physical map for the catfish genome that places the long catfish genome into orderly overlapping DNA segments;
5. Locate the genes controlling performance traits such as growth, feed conversion efficiency, and disease resistance
6. Understanding the relationship of gene expression with performance of catfish.                                     

                                                Ph.D candidates ( left to right ) Shaolin Wang, Puttharat

                                       Baoprasertkul and Jason Abernathy work on catfish genomics

Research

Genome mapping

  The first step to genome mapping is to develop DNA markers, the same way as the landmarks for the development of a road map. Auburn researchers have developed thousands of DNA markers using various technologies. These markers are being used to construct the catfish genome map. The first framework linkage map constructed using the channel x blue hybrid system was published in 2003.        

Gene Discovery

  Humans have approximately 25,000 genes. How many genes catfish have is of interest for the understanding of its genome. Auburn Researchers have devoted a large effort for gene discovery in catfish. Many gene libraries have been constructed from various catfish tissues and cells. To date, over 50,000 gene sequences have been generated and deposited in the National Center for Biotechnology Information (NCBI) databases (http://www.ncbi.nih.gov). A large effort of sequencing 300,000 more clones is underway with the Joint Genome Institute of the Department of Energy (http://www.jgi.doe.gov/).

Physical Mapping

  Catfish genome is approximately 1 billion base pairs. In order to routinely handle the genome in the laboratory, it must be cut into many small pieces. To construct a physical map means to put many such small pieces together in an orderly fashion to represent the entire genome. Accordingly, Auburn researchers have analyzed almost 40,000 segments of DNA with each having an average size of 160,000 base pairs.

QTL mapping

  Performance traits are controlled by many genes, and therefore, understanding exactly which genes are contributing to a single trait such as disease resistance is difficult. In addition, their relative contribution and mode of action is also difficult to reveal. Auburn researchers have used DNA markers to make gene associations so that the genes controlling performance traits such as growth, feed conversion efficiency, and disease resistance can be located.

Anticipated Benefits

  The difficult part of fixing problems is the lack of understanding about exactly where the problem is.  Once we understand the genome and the genes controlling performance traits, technologies can be developed based on the information to combine all “good genes” together, and reduce or eliminate the “bad genes”. Superior catfish breeds can be developed that will help farmers increase profits.

Principal Investigators

Zhanjiang (John) Liu Alumni Professor Auburn University, Department of Fisheries and Allied Aquacultures liuzhan@auburn.edu	Rex Dunham Alumni Professor Auburn University, Department of Fisheries and Allied Aquacultures dunhara@auburn.edu
Huseyin Kucuktas Research Fellow III Auburn University, Department of Fisheries and Allied Aquacultures kucukhu@auburn.edu	John Grizzle Professor Auburn University, Department of Fisheries and Allied Aquacultures grizzjm@auburn.edu
Yolanda Brady Associate Professor Auburn University, Department of Fisheries and Allied Aquacultures bradyyj@auburn.edu

Affiliated Departments and Institutions

Dr. Lei Liu, W.M. Keck Center for Comparative and Functional Genomics,
University of Illinois at Urbana-Champaign

Dr. Bill Muir, Department of Animal Sciences, Purdue University