IJA Volume 58, Issue 4, 2006

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Selective breeding of food size rainbow trout:Currentandfutureprospects
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) LaPatra, Scott E.; Towner, Richard H.
Rainbow trout (Oncorhynchus mykiss) are a valuable aquaculture production species in the USA where an average 25,000 tons per year of food size rainbow trout were produced during 1988- 2002. Clear Springs Foods, Inc., is one of the largest producers of aquacultured rainbow trout, producing 10,000 tons annually. Privately held by an employee owned trust, Clear Springs is a vertically integrated company from brood stock through egg production, feed manufacturing, farm operations, processing, and distribution. Clear Springs has a significant commitment to research and development. Selective breed- ing of rainbow trout is an important component of its R&D program. The current goals of the selective breeding program are to improve growth and disease resistance. To improve these traits, data are recorded on thousands of individuals each year. Growth data is collected at var- ious ages to determine which families and which individuals within each family have the best growth. To improve disease resistance, a portion of the progeny from each family are exposed to specific pathogens in a standardized challenge test. Currently, each family is tested for sur- vivability to infectious hematopoietic necrosis virus (IHNV) and Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease (CWD) and rainbow trout fry syndrome (RTFS). Selection to improve growth began when the breeding program was initiated. The average weight of the odd-year generation group increased from 660 g at 328 days of age in 1991 to 921 g at 301 days in 2003. The average weight of the even-year group increased from 620 g at 328 days in 1992 to 866 g at 301 days in 2004. Selection to improve IHN resistance started with the 1994 generation. Using a standardized challenge test, IHN mortality decreased 25.8% in the odd-year generation group and 29.7% in the even. Growth is a moderately heritable trait that can be changed rapidly and economically with traditional quantitative genetic techniques. Disease resistance has much lower heritability and is more difficult to change. Better knowledge of spe- cific and general disease resistance mechanisms in trout would aid the industry in improving future stocks.
Marker-assisted breeding for viral disease resistance in Japanese flounder (Paralichthys olivaceus)
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Sakamoto, Takashi; Fuji, Kanako; Kobayashi, Kazunobu; Hasegawa, Osamu; Ozaki, Akiyuki; Okamoto, Nobuaki
DNA marker technologies can be used for genetic improvement through selection of favorable traits such as disease resistance. These traits are generally modeled as being controlled by many genes of small additive effects, known as quantitative trait loci (QTL). Construction of a genetic linkage map based on DNA markers at a large number of sites in the fish genome is necessary to identify QTL controlling traits of disease resistance. By identifying markers associated with high per- formance QTL in different strains or species, it may be possible to improve the performance of such traits in other strains through intro- gression of the desired QTL. One of the goals of selective breeding programs is to integrate genetic marker information from pedigreed brood stock into successful management and culture. Such an approach, termed marker- assisted selection (MAS) and/or marker- assisted gene introgression (MAI), is expect- ed to increase genetic response by affecting efficiency and accuracy of selection.
Genetic perspective on stress response and disease resistance in aquaculture.
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Cnaani, Avner
Despite continuous progress and improvements in aquaculture technologies and husbandry techniques, fish diseases remain a major limiting factor in the fish culture industry. The aqua- culture environment exposes fish to repeated acute stress, which leads to physiological respons- es that have suppressive effects on growth, reproduction, and immune capacity. The strong link between stress and susceptibility to diseases in farm animals has long been acknowledged, and parameters of high and low stress response are associated with disease resistance in fish. Few studies on genetic aspects of immune response to stress have been conducted. The estimated heritability of several parameters of the innate immune response is mostly moderate. Quantitative trait loci have been found for different responses to stress conditions. Gene expres- sion studies show that hundreds of genes can be involved in fishes’ physiological and immuno- logical response to stress. This general response to stress is controlled by a few major genes at the top of the pathway, which activate a cascade of reactions, having a significant effect on the overall health of the fish. Selective breeding for disease resistant fish is an attractive strategy for disease prevention and several studies have reported progress in this field. However, the bio- logical pathways of stress response and disease resistance are not well characterized, and their genetic basis and control are still poorly understood. Extensive research is still needed for a bet- ter understanding of these pathways, and this should be a collaborative effort of researchers from different fields: genetics, immunology, pathology, physiology, and endocrinology.
Traditional and phylogenetic approaches in the diagnosis and identification of pathogens in mariculture.
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Colorni, Angelo; Diamant, Ariel; Kvitt, Hagit; Ucko, Mical
Traditionally, the most common approach to diagnosis of microbial fish pathogens has relied on in vitro isolation of the microorganism and the information provided by its phenotypic features. However, viruses are generally highly species-specific and established cell lines do not neces- sarily show cytopathic effect, many species of bacteria are difficult or impossible to culture in vitro, while parasitic microorganisms often have a complex life cycle that requires propagation in live hosts. An increasing number of microbial pathogens are identified today by molecular meth- ods, without the need for isolation. A PCR direct method for detection and identification of Mycobacterium marinum based on the 16S rRNA gene sequence was successfully developed already 13 years ago at NCM. Comparison of the 16S rRNA sequence of Streptococcus iniae isolates revealed that, despite phenotypic, biochemical and pathogenetic similarities, marine and freshwater isolates were different strains. With time, however, it has become clear that 16S rRNA gene sequences alone are often insufficient to detect variation within bacterial species, and today other specific loci are also being employed. More recently, on the basis of hsp65 gene in addition to 16S rRNA gene, Israeli M. marinum isolates in marine and freshwater fish were found to belong to two distinct strains, and both were different from Israeli M. marinum clinical (human) isolates. Specific 18S rDNA probes for detection of elusive life stages of two myx- osporean parasites, Kudoa iwatai and Enteromyxum leei, in sea bream and sea bass are being employed in studies conducted over the last few years at NCM. By using whole-genome struc- tures rather than single gene sequences, two fingerprinting techniques - Amplified Fragment Length Polymorphism (AFLP) and Randomly Amplified Polymorphic DNA (RAPD) - have pro- vided a generally higher level of precision in genotyping. However, while the AFLP method revealed broad polymorphism among S. iniae isolates, the RAPD method did not provide addi- tional information. These examples show that not all regions of the DNA are equally useful in diagnosis and genotyping and therefore there is no single “best” molecular method. Molecular strategies have provided a phylogenetic approach to determining identification and taxonomic position by grouping closely related organisms that share a relatively recent ancestry into clus- ters. Although the question remains of how much genetic diversity is permissible in a discrete cluster for its members to be regarded as a single taxon, the ability to place a microorganism in a given taxon on the basis of its evolutionary development is of importance: if known members of the same family do not have a “clean bill” concerning their pathogenicity, any related organ- ism may be justifiably regarded as a potential offender. Traditional methods and molecular meth- ods provide different levels of information: only their combination offers a comprehensive insight into the microorganism’s nature.
Genomic approaches to identifyingsex-determininggenesintilapia
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Kocher, Thomas D.; Lee, Bo-Young; Cnaani, Avner
Variation in sex determination mechanisms among the different tilapia species has been recog- nized for over 40 years. We have looked for associations between microsatellite DNA markers and sex in families from different species and strains of tilapia. We found that at least two dif- ferent linkage groups are involved in sex determination in this group of fishes. In two species, O. niloticus and T. zillii, we found evidence for male heterogamety with a major sex-determining locus on linkage group 1 (LG1). In two other species, O. aureus (Israeli strain) and O. karongae, we found evidence for female heterogamety with a major locus for sex determination on LG3. In O. aureus (Egyptian strain) and in O. mossambicus, loci associated with sex determination were found on both LG1 and LG3, and a complex mechanism of sex determination was detected. Physical mapping by fluorescence in situ hybridization (FISH) suggests that LG3 corresponds to the largest chromosome pair, and that there is recombination suppression in the sex determina- tion region. The sex-determining region in O. niloticus has been mapped to an 11cM region between markers GM201 and UNH995 on LG1. A BAC contig containing UNH995 was identi- fied and several BACs in the contig were end- or shotgun sequenced. BLAST analysis of these sequences identified Tetraodon chromosome 5 as the homolog of tilapia LG1. Additional SNP and microsatellite markers were developed from published cichlid ESTs and the order of these markers is consistent between tilapia and Tetraodon. We have narrowed the sex-determining region to a 2.6cM interval which corresponds to a 400 kb region of Tetraodon chr5. We are com- pleting genetic and physical maps across this region in order to identify the gene(s) responsible for sex determination in this species.
Effects of genetic and environmental factors on sex differentiation in the Europeanseabass(Dicentrarchus labrax)
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Ron, Benny
One of the major problems in the mariculture of the commercially important European sea bass, Dicentrarchus labrax, is that females grow 20-50% more rapidly than males. For that reason, farmers are interested in developing female monosex populations. Studies on evolution, genet- ics, and physiology have been conducted during the last decade to solve this problem. This review summarizes the latest data related to the effects of evolution, genetics, physiology, and environment on sex determination and differentiation in the European sea bass.
Regulated sex control in commercially important fishes – a physiologicalperspective
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Shelton, William L.
The management of fish reproduction has resulted in major advancements in the commercial culture of fishes. Artificial propagation has stabilized seed-stock production, and reproductive manipulations in induced sex reversal and ploidy manipulations have provided mechanisms to improve yield. The design and effectiveness of these manipulations are regulated by various physiological factors. The effectiveness of protocols for the induction of gynogenesis, triploidy, and tetraploidy is improved through knowledge of physiological effects on important parameters. Application of the developmental rate based on the mitotic interval (τo) incorporates a standard- ization relative to temperature. Timing of shock with reference to the species-specific τo rela- tionship is effective in clarification and optimization of treatments. Such standardization is impor- tant to any late (endomitotic - Em) shock induction, and in polar-body (Pb) induction for many species. Hormonally induced sex reversal also must be applied relative to an efficacious treat- ment protocol, developed relative to a window of gonadal lability during the genetically directed chronology and physiologically influenced differentiation. Size and/or age are important modify- ing parameters that can be affected by various growth-altering environmental factors such as temperature and density-dependent effects. The consideration of influences that affect physio- logical rates relative to reproductive manipulations provides a more in-depth understanding of protocol effectiveness.
Genetic basis of sex determination in fishes: Searching for master key regulator genes in the sex determination pathway of tilapias
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Shirak, Andrey; Seroussi, Eyal; Zilberman, Noam; Hulata, Gideon; Ron, Micha; Cnaani, Avner; Kocher, Thomas D.
Recent results show a striking similarity in the dynamics of expression of gonad differentiation regulators in zebrafish and mammals. Candidates for the role of master key regulators (MKRs) in tilapia were selected, based on three concepts established in the literature for non-mammal species. These three concepts are: (a) MKRs are DM-proteins or their close downstream/ upstream partners in the sex determination pathway, (b) MKRs are genes working just upstream of aromatase in the sex determination pathway, or the aromatase itself, and (c) MKRs are homologs of mammal genes which are close partners of SRY (“missing” in non-mammal verte- brates), mostly belonging to the SOX family. Coding sequences of putative genes were searched in cichlid (TIGR) and general (NCBI) databases, and in the tilapia gonad EST library (RBEST). Primers in two adjacent exons were designed, based on predicted exon-intron boundaries for each of 11 selected genes. Amplified segments of the targeted genes in two purebred tilapia species were sequenced. Seven SSLP and four SNP-based markers were identified in the can- didate genes for MKRs of sex determination and mapped to the tilapia genetic map using geno- type data of 76-90 individuals of the F2 mapping family. The mapping positions of the selected genes relative to previously reported QTL regions for sex determination are discussed.
Aspects of comparative genomics in the gilthead seabream, Sparusaurata
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Kotoulas, Georgios; Consortium, BRIDGEMAP
Genome projects for new fish species are found in a transitional period during which resource development and meaningful com- parative genomics analysis or use of any other comparative approach must be done in parallel. In new species, full sequencing is still prohibitive due to the high cost of vertebrate genome sequencing and the fact that present technology is time consuming. However, in the case of the few model species whose research is pioneering and where huge progress has been made on developmental, physiological, behavioral, and genomic levels, knowledge integration is in a process of rapid change. These reasons may explain why a general strategy to facilitate the choice of tar- get species and the kind of developments needed has not yet been adopted. In such an environment,BRIDGEMAP ,theEuropean gilthead seabream genome project, was com- pleted in December 2005. This was one of the first genome projects for a non-model fish of aquaculture interest.
Comparative gene and QTL mapping in aquaculture species
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Thorgaard, Gary H.; Nicholas, Krista M.; Phillips, Ruth B.
Mapping genes and quantitative trait loci (QTLs) is of fundamental and applied interest in aquaculture species. Such studies can pro- vide essential information about rates and patterns of evolutionary change and may pro- vide tools which can be used in marker-assist- ed selection (MAS; e.g., Groenen et al., 2000). Mapping typically involves producing divergent crosses and analyzing segregation patterns in the offspring of hybrids between the divergent crosses. The more divergent the cross is, the greater the potential for finding useful marker and trait differences that can be mapped. The basic goal of mapping is to understand the position of loci on chromo- somes and how the positions change during evolution. The applied goal of mapping is to understand the position of loci associated with phenotypic traits which could be important in breeding programs. Correspondingly, QTL mapping seeks to identify the number and location of loci associated with phenotypic traits (e.g., Mackay, 2001; Mauricio, 2001; Burt and Hocking, 2002; Erickson et al., 2004) while applied QTL studies seek to identify candidate genes or markers for use in MAS.
Transcriptome characterization through the generation and analysis of expressed sequence tags: Factors to consider for a successful EST project
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Liu, Zhanjiang
Sequencing of expressed sequence tags (ESTs) has been one of the primary techniques used for transcriptome analysis in a wide spectrum of species including those utilized for aquaculture. However, many researchers are still unfamiliar with the many genome applications and byprod- ucts of EST analysis, and they often regard ESTs as only short random sequences. Additionally, lack of cDNA library normalization, project planning, and quality control have often restricted the value of EST resources created in many laboratories. This review aims to address these issues by providing information on the construction of normalized cDNA libraries for efficient generation and analysis of ESTs and by highlighting the significance of EST analysis for the genome research of species lacking a sequenced genome. A successful EST project can provide the sequence tools needed for not only gene discovery, but also for physical, linkage and compara- tive mapping, analysis of alternative splicing and gene duplication, and microarray development.
Integration of molecular genetic information into the NCCCWA selective breeding program for rainbow trout
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Rexroad, Caird E. III; Palti, Yniv; Vallejo, Roger L.; Silverstein, Jeffery T.
The USDA/ARS National Center for Cool and Cold Water Aquaculture (NCCCWA) in Leetown, West Virginia, is working to integrate molecular genetic technologies into a selective breeding program aimed at the genetic improvement of rainbow trout for aquaculture production efficien- cy. Our multidisciplinary approach aims to incorporate genome information with respect to dis- ease resistance and stress, growth, and reproductive physiology into our selective breeding pro- gram. Selective breeding is based on the hypothesis that sufficient genetic variation exists in broodstock to realize genetic improvement through contributions of superior performing germplasm to future generations. Our associated goal is to develop and transfer improved germplasm and technologies to the aquaculture industry. Our approach to implementing molec- ular information into our breeding program is outlined under three objectives: (a) development of a genetic map to reveal chromosomal locations affecting traits associated with aquaculture pro- duction, (b) use of a candidate gene approach to identify and characterize genes affecting impor- tant aquaculture production traits through functional genomic technologies, and (c) development of bioinformatic strategies to implement genetic mapping and functional genomic information into a selective breeding program.
Production of recombinant hormones and growth factors for use in aquaculture
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Funkenstein, Bruria
Progress in recombinant DNA technology and development of new expression systems has provided valuable means to produce large quantities of hormones and growth factors from various fish species that otherwise required sacrifice of enormous numbers of fish to obtain only small amounts of the native protein. The motivation to produce recombinant hormones and growth factors for application to fish culture can be attributed to (a) the low amounts of pep- tides in producing tissues available for purifica- tion and characterization by classical methods, i.e., follicle stimulating hormone (FSH = GtH-I) in the pituitary or insulin-like growth factor-I (IGF-I) and IGF-II in the liver, (b) the similarity in chemical structure between two hormones that does not permit efficient separation (FSH and LH = GtH-II), (c) the need for large quanti- ties of hormones for growth enhancement by growth hormone (GH), and (d) interest in studying structure/function relationships, i.e., single or multiple amino acid deletion, amino acid substitution, etc.
Transgenic fish – where we are and where do we go?
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Dunham, Rex A.; Liu, Zhanjiang
Transgenic fish have been developed that have improved growth, color, disease resistance, sur- vival in cold, and body composition, and produce pharmaceutical proteins. Transgenes elicit pleiotropic effects, some positive and some negative. In general, transgenic fish appear to have lower fitness than controls and pose little environmental risk, but this research is not fully con- clusive. Transgenic zebrafish with altered coloration have been commercialized and growth hor- mone transgenic salmon, carp, and tilapia are near commercialization. To enhance commer- cialization and minimize environmental risk, additional technologies such as transgenic steriliza- tion need to be developed. Genomic research has produced an abundance of molecular genet- ic information including many genes for consideration for gene transfer, highly regulated gene promoters, and knowledge about their expression and function. Functional genomics analysis should be applied in the future to enhance the capacity and versatility of transgenic technology.
Use of molecular tools for research and improvement of aquaculture stocks
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Hallerman, Eric M.
Development of molecular genetic markers provides aquaculture with tools for a number of research and practical applications. Genetic marking of experimental groups allows their evalu- ation in the same rearing units, increasing statistical power within limited research infrastructure. Parentage can be inferred for individuals in mixed-progeny groups, quantifying the contributions of individual parents and supporting the estimation of sire and dam effects. Building upon parent- age assignment, walk-back selection entails retention of the best members of each family as broodstock for the next generation. Molecular markers can be used to detect the segregation of quantitative trait loci (QTL) and knowledge of such linkages can be used for marker-assisted selection. Gene expression profiling can identify genes affecting traits of interest, providing can- didates for QTL or functional analysis. Purposeful genetic marking can be used to identify pro- prietary stocks, marketed products, and fish out-planted or escaping into natural ecosystems. Although each application has been demonstrated, genetic markers are not routinely used in commercial aquaculture. The limited practical application can be explained by the limited devel- opment of broodstocks for most aquaculture species, the small size and limited scope of most aquaculture operations, and the costs of genetic screening.
Practical use of cytogenetics in fish biology and aquaculture
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Gorshkov, Galina
The reviewed information was accumulated from our current and earlier cytogenetic studies on various commercially important fish species. The major emphasis of the review is to show in which way classical cytogenetics can be practically used for basic and applied research in fish biology and aquaculture.
A review of ploidy manipulations in aquaculture: The Israeli experience
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Rothbard, Shmuel
Ploidy manipulation was introduced to Israel at the beginning of the 1980s. To improve existing methods, Israeli fish centers conducted intensive research in this field for more than two decades. Chromosome-set technology was adapted for ten fish species and varieties, including two marine fish. Presently, though methodology achievements are remarkable, practical imple- mentation is applicable only for the common carp. The aim was to integrate gynogenesis and androgenic sex-reversal to generate neomales with special genetic traits in this economically important species that is extensively cultured in Israel. Carp neomales can serve as parents for production of fast-growing all-female populations. This paper describes ploidy manipulation progress and activities carried out in four Israeli fish centers. Future objectives include (a) imple- mentation of the existing know-how to produce tilapia YY-males as broodfish for producing male- monosex populations, (b) dissemination and promotion of export to foreign markets of the advantageous female triploid grass carp and black carp, (c) continuation of genetic work with marine fish to develop breeds that could be advantageous for mariculture, and (d) reconsidera- tion of the ploidy-manipulated koi as a genetic tool to be utilized to facilitate gene-mapping in carps.
Lessons for aquaculture breeding from livestock
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Weller, Joel Ira
Investment in breeding is unique because genetic gains are eternal and cumulative. They are never “used up”, and never “wear out”. However, nearly all of the gain is transferred to the national economy. Very little stays with farmers or commercial breeders. Unlike genetic gains, costs are not cumulative. With a profit horizon of 20 years and a discount rate of 0.08, total dis- counted costs will equal total discounted gains if the value of the nominal annual genetic gains is 0.3 of the nominal annual costs. The rate of genetic gain for milk production in dairy cattle has been about 1% per year for the last 20 years. Since the 1950s, rates of genetic gain have increased due to better pedigree information, more traits recorded, more accurate recording, and better statistical methods. From the beginning of modern breeding programs, selection in dairy cattle focused on milk production. From 1985, breeding goals moved towards improving protein yield. In recent years, selection objectives were broadened to include “functional herdlife”, fertil- ity, and health traits. The main reasons behind this shift were quotas and/or price constraints, and increasing concerns associated with the deterioration of the health and fertility of dairy cows. Modern technology complements traditional breeding but does not replace it. To date, nearly all progress in animal breeding has been obtained by traditional trait-based methodology. There is no substitute for accurate data and pedigree recording.
History of catfish breeding and its application in the United States: Lessonstobelearned?
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Dunham, Rex A.
The history of selective breeding in the US catfish industry is reviewed. The failures and suc- cesses of technology and germplasm transfer for catfish genetic enhancement are discussed.
Practical genetics in Israeli mariculture: History and present status
(Israeli Journal of Aquaculture - BAMIGDEH, 2006) Gorshkov, Sergei
The aim of this review is to show the progress and achievements made to date in the selective breeding of cultured marine fish in Israel. The National Center for Mariculture (NCM) in Eilat was the first scientific organization to determine that a long-term selective breeding program is the key strategy for genetic improvement of commercially important marine fish. The main objective of the program is the development of genetically improved strains. The immediate practical goal is to improve the profitability of national mariculture through growth improvement in the gilthead sea bream (Sparus aurata). In this species, due to reproductive constraints that limit the prospects for family selection, mass selection was found to be the most practical tool for growth improvement. Currently, the selective breeding program for sea bream consists of several selected lines. Four cycles of mass selection for growth have been completed in commercial pro- duction environments. Mass selection and crossbreeding are integrated in the program. In the Eilat hatchery sea bream strain, a recessive deleterious Mendelian mutation (named “ebony”) was isolated by classical crossing experiments. A method was developed to use ebony for genetic protection of selected sea bream strains from unlicensed reproduction and propagation. Interspecific hybridization, chromosome set manipulation, and cytogenetic and sex control tech- niques were also applied; some were shown to be promising tools for short-term genetic improvement. In general, the NCM selective breeding program for sea bream showed that genetic gain for growth and faster economic return can be achieved within a “reasonable” time span of 10-12 years. The program is supervised by the Genetics and Physiology Department of the NCM. Presently, most Israeli commercial mariculture is using genetically improved strains of sea bream and newly domesticated strains of sea bass (Dicentrarchus labrax).

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