Underwater Genomics: Exploiting Fishes'€™ Unique Biology to Meet the Needs of the Aquaculture Industry

Rapid progress has been made in genomics and genetics research with aquaculture species. Fish live in aquatic environments, where labeling of individuals and observation of their performance is difficult. In spite of these and many other challenges, the unique biology of fish also offers some advantages. In this lecture, I will summarize our research progress in genomics toward aquaculture applications, share our experience with fish, and contrast the situations with those of mammals. For instance, gynogenesis was used to produce doubled haploid fish for whole genome sequencing; scale regeneration is used to figure out genes accounting for the evolutionary loss of scales in channel catfish; sex reversal was used to produce YY males that can be used for sequencing the Y chromosome without any confusion of the homologous sequences of the X chromosome. Comparative analysis of the X and Y chromosome sequences should generate information about sex determination. Fish have very high fecundity and fertility. Production of full-sib families with tens of thousands of progenies is routinely possible with fish. Taking the advantage of the large families, we have developed highly efficient 690K SNP arrays for genotyping analysis, and have used them for analysis of various traits through QTL mapping and GWAS. QTL have been identified for various traits including growth, disease resistance, tolerance to low oxygen, tolerance to high temperature, head size, and body conformation. Analysis of the genes involved in several traits suggested evolutionarily conserved mechanisms for disease resistance, for control of head size, and for body conformation.