Genetic and genomic analyses for economically important traits and their applications in molecular breeding of cultured fish

TONG JinGou ) 1 SUN XiaoWen 0 0 Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences , Harbin 150070 , China 1 State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072 , China The traits of cultured fish must continually be genetically improved to supply high-quality animal protein for human consumption. Economically important fish traits are controlled by multiple gene quantitative trait loci (QTL), most of which have minor effects, but a few genes may have major effects useful for molecular breeding. In this review, we chose relevant studies on some of the most intensively cultured fish and concisely summarize progress on identifying and verifying QTLs for such traits as growth, disease and stress resistance and sex in recent decades. The potential applications of these major-effect genes and their associated markers in marker-assisted selection and molecular breeding, as well as future research directions are also discussed. These genetic and genomic analyses will be valuable for elucidating the mechanisms modulating economically important traits and to establish more effective molecular breeding techniques in fish. - Fish are produced to supply high-quality protein to the market through breeding of new fish strains with better traits, such as fast growth, high resistance to disease and stress, and a high feed conversion rate (FCR). Fish-breeding methodologies have developed rapidly in past decades, from traditional selection and hybridization to modern biotechnologies, such as marker-assisted selection and molecular breeding. Although selection is the basis for all breeding techniques, traditional family or population-based selection is usually less efficient and the breeding programs may take a long period of time to develop. Most economically important traits in fish, such as growth rate, disease resistance, and sex, are controlled by multiple genes, known as quantitative trait loci (QTL). Most of these genes have minor effects, but several may have major effects on traits. Theoretically, if genes and genetic markers associated with traits of interest are identified, the genetic variants could be used as tools in marker-assisted selection (MAS) analyses. The idea of using genetic markers during selective breeding has been proposed since the 1960s, but the genetic basis for economically important traits in animals including fish has not been analyzed effectively due to a shortage in high-resolution and powerful techniques. However, genetic mechanisms underlying the economically important traits in fish have been studied more effectively with the development of quantitative genetics, molecular genetics, structural and functional genomics, and molecular marker technologies. In particular, an understanding of QTL from zero to the present provides a solid basis for developing fish molecular breeding strategies. The tools to genetically analyze economic traits in fish The Author(s) 2015. This article is published with open access at link.springer.com include (i) developing a large number of molecular markers; (ii) constructing medium and high-density genetic linkage maps and conducting QTL/expression quantitative trait locus (eQTL) analyses throughout the whole genome; (iii) using a candidate gene approach or an association study; (iv) conducting a bulked segregant analysis (BSA); (v) linkage disequilibrium (LD), or LD associate mapping; and (vi) genome-wide association study (GWAS). Molecular markers are one of the most powerful tools for genetic analyses of fishs economically important traits. In the early stages of this field, genetic variations were represented by a limited number of less polymorphic allozyme loci. Then dominant markers, such as restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP), were developed one after another. In recent years, two types of DNA markersmicrosatellite or simple sequence repeat (SSR) and single nucleotide polymorphisms (SNPs)have been widely used in genetic analyses due to their wide genome distribution and high rate of polymorphisms [1]. Molecular breeding includes molecular marker-assisted selection, transgenic breeding, and computer-based molecular design breeding [2]. In the late 1990s, the United States, Japan, Norway, Canada, and Australia initiated genome projects in several aquatic animals. Chinese scientists also started genome sequencing projects for oyster, scallop, shrimp, half-smooth tongue sole, common carp, yellow croaker, grass carp, and grouper. Silver carp, bighead carp, bluntsnout bream, and gibeio carp will also be decoded one after another in the near future. The great advances in genomics, including structural, functional, and comparative genomics, have provided new insights into molecular breeding studies [35]. In this review, we will concisely summarize current genetic and genomic analyses for economically important traits and discuss future directions and prospects for fish molecular breeding. 1 Status of genetic and genomic studies on economically important traits in fish Genetic linkage maps Since the first genetic linkage map was published for tilapia in 1998 [6], genetic maps of various densities have been published on some important aquaculture species, and many of these maps used co-dominant genetic markers, such as microsatellites and SNPs. More high- density maps of aquatic species have been reported with the advances in molecular marker technology and increased financial input. Up to 2010, about 30 aquatic animals had publicly accessible genetic maps [7]. However, more aquaculture fish have been added in the past three years, including three of the four major Chinese carp, among them grass carp, silver carp, and bighead carp, and other important aquaculture fish (Table 1). QTL analysis for growth traits Growth is one of the most important economic traits of all aquaculture species. Up to 2012, QTL analyses have been conducted in more than 20 aquatic species [7], and growth is the most popular trait studied. Wang et al. [21] used 380 F1 Asian seabass to identify five major QTLs and 27 potential QTLs. Of them, three major QTLs for body weight, total length, and body length were located at a similar linkage group 2 (LG2) position with the nearby Lca287 microsatellite and accounted for 28.8%, 58.9%, and 59.7% of the phenotypic variations. The other two major QTLs for body weight were located at another LG2 position. These five major QTLs have been confirmed in two other Asian seabass populations [22]. Further QTL fine mapping of the Asian seabass growth trait identified three candidate growth genes (cathepsin D, KCTD15, and csmd2) affecting body weight, body length, and total length [10]. The Table 1 Medium and high-density genetic linkage maps for some economically important fish species Type of marker (...truncated)