Development and application of biological technologies in fish genetic breeding

Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties.For the purpose of genetic improvement,researchers can select for desirable genetic traits,integrate a suite of traits from different donors,or alter the innate genetic traits of a species.These improved varieties have,in many cases,facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield.In this review,we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies(containing traditional selective breeding,molecular marker-assisted breeding,genome-wide selective breeding and breeding by controlling single-sex groups),integration breeding technologies(containing cross breeding,nuclear transplantation,germline stem cells and germ cells transplantation,artificial gynogenesis,artificial androgenesis and polyploid breeding)and modification breeding technologies(represented by transgenic breeding)in fish genetic breeding.Additionally,we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish,including distant hybridization,gynogenesis,and androgenesis.Finally,we systematically summarize the research status and known problems associated with each technology.     

Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture

Aquaculture production comprises a diverse range of species, geographies, and farming systems. The application of genetics and breeding technologies towards improved production is highly variable, ranging from the use of wild-sourced seed through to advanced family breeding programmes augmented by genomic techniques. This technical variation exists across some of the most highly produced species globally, with several of the top ten global species by volume generally lacking well-managed breeding programmes. Given the well-documented incremental and cumulative benefits of genetic improvement on production, this is a major missed opportunity. This short review focusses on (i) the status of application of selective breeding in the world’s most produced aquaculture species, (ii) the range of genetic technologies available and the opportunities they present, and (iii) a future outlook towards realising the potential contribution of genetic technologies to aquaculture sustainability and global food security.     

Progress and biotechnological prospects in fish transgenesis

The history of transgenesis is marked by milestones such as the development of cellular transdifferentiation, recombinant DNA, genetic modification of target cells, and finally, the generation of simpler genetically modified organisms (e.g. bacteria and mice). The first transgenic fish was developed in 1984, and since then, continuing technological advancements to improve gene transfer have led to more rapid, accurate, and efficient generation of transgenic animals. Among the established methods are microinjection, electroporation, lipofection, viral vectors, and gene targeting. Here, we review the history of animal transgenesis, with an emphasis on fish, in conjunction with major developments in genetic engineering over the past few decades. Importantly, spermatogonial stem cell modification and transplantation are two common techniques capable of revolutionizing the generation of transgenic fish. Furthermore, we discuss recent progress and future biotechnological prospects of fish transgenesis, which has strong applications for the aquaculture industry. Indeed, some transgenic fish are already available in the current market, validating continued efforts to improve economically important species with biotechnological advancements.     

A survey of state insurance commissioners concerning genetic testing and life insurance.

Rapid advances in genetic testing have stimulated growing concern about the potential for misuse of genetic data by insurance companies, employers, and other third parties. Thus far, reports of genetically based discrimination in life insurance have been anecdotal. Reasoning that state insurance commissioners were likely to be aware of (1) the extent of current use of and interest in genetic tests by life insurers and (2) consumer complaints about insurance being denied because of genetic condition or because of genetic test results, we conducted a survey of that group. We received responses from 42 of the 51 jurisdictions. Our results suggest (1) that those who regulate the life insurance industry do not yet perceive genetic testing to pose a significant problem in how insurers rate applicants, (2) that life insurers have much legal latitude to require genetic tests, and (3) that so far few consumers have formally complained to commissioners about the use of genetic data by life insurers.     

Genomics to accelerate genetic improvement in tilapia

Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth-, quality- and robustness-related traits. Novel phenotyping technologies (i.e. phenomics), lower-cost whole-genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.     

现代生物技术与饲用微生态制剂

近年来,使用抗生素的副作用越来越多地受到关注,世界上许多国家已出台相应政策来控制抗生素的使用。但是由于养殖行业的迅猛发展,养殖密度加大,养殖动物病害发病的风险提高,急需可替代抗生素的新型绿色饲料添加剂产品。微生态制剂作为一种新型绿色饲料添加剂,在养殖行业发挥了重要作用。随着饲用微生态制剂产品研发的深入,现代生物技术在提升微生态制剂的理论和应用研究方面发挥着重要作用。PCR、核酸分子杂交、基因工程以及组学等技术已应用于微生物菌种鉴定、基因改良、作用机理等研究中。本文对饲用微生态制剂的研发现状进行了阐述,并综述了现代生物技术在饲用微生态制剂研究中的应用。     

用模式生物青鳉概观硬骨鱼性别决定及性分化研究进展

鱼类性别决定和性分化呈多元性,既有雌雄同体也有雌雄异体。性腺的雌雄性分化过程受遗传和环境因素(如温度、光照、激素和pH值等)影响,具有可逆可塑性。随着生物技术和基因组学的迅速发展,近年来脊椎动物性别决定和性分化的研究有了重大进展和显著突破。本文通过聚焦青鳉及其他硬骨鱼纲保守存在的dmrt1、gsdf、amh等雄性因子,探讨硬骨鱼普遍存在的雌雄性别可塑可逆信号通路,并介绍了新的基因组编辑和性控育种技术,为单性选育等水产养殖技术的研发提供参考。     

Genetic Modification of Herbaceous Plants for Feed and Fuel

Referee: Dr. E. Charles Brummer, Forage Breeding and Genetics, 1204 Agromonomy, Iowa State University, Ames, IA 50011 Much of the research on the genetic modification of herbaceous plant cell walls has been conducted to improve the utilization of forages by ruminant livestock. The rumen of these animals is basically an anaerobic fermentation vat in which the micro flora break down the complex polysaccharides of plant cell walls into simpler compounds that can be further digested and absorbed by the mammalian digestive system. Research on improving the forage digestibility of switchgrass, Panicum virgatum L., and other herbaceous species has demonstrated that genetic improvements can be made in forage quality that can have significant economic value. To meet future energy needs, herbaceous biomass will need to be converted into a liquid fuel, probably ethanol, via conversion technologies still under development. If feedstock quality can be genetically improved, the economics and efficiency of the conversion processes could be significantly enhanced. Improving an agricultural product for improved end product use via genetic modification requires knowledge of desired quality attributes, the relative economic value of the quality parameters in relation to yield, genetic variation for the desired traits, or for molecular breeding, knowledge of genes to suppress or add, and knowledge of any associated negative consequences of genetic manipulation. Because conversion technology is still under development, desirable plant feedstock characteristics have not been completely delineated. Some traits such as cellulose and lignin concentration will undoubtably be important. Once traits that affect biomass feedstock conversion are identified, it will be highly feasible to genetically modify the feedstock quality of herbaceous plants using both conventional and molecular breeding techniques. The use of molecular markers and transformation technology will greatly enhance the capability of breeders to modify the morphologic structure and cell walls of herbaceous species. It will be necessary to monitor gene flow to remnant wild populations of biomass plants and have strategies available to curtail gene flow if it becomes a potential problem. It will also be necessary to monitor plant survival and long-term productivity as affected by these genetic changes to herbaceous species.     

Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stock supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, particularly for traits practically impossible to measure on selection candidates, such as disease resistance and fillet characteristics. The aim of our study was to design a combined-species 60 K SNP array for European seabass and gilthead seabream, and to test its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole-genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the ‘MedFish’ SNP array. The array was then tested by genotyping a subset of the discovery populations, highlighting a high conversion rate to functioning polymorphic assays on the array (92% in seabass; 89% in seabream) and repeatability (99.4–99.7%). The platform interrogates ~30 K markers in each species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to have high functional effects on proteins. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean farmed fish populations. In conclusion, the new MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs for each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection.     

Fish genome manipulation and directional breeding

Aquaculture is one of the fastest developing agricultural industries worldwide.One of the most important factors for sustainable aquaculture is the development of high performing culture strains.Genome manipulation offers a powerful method to achieve rapid and directional breeding in fish.We review the history of fish breeding methods based on classical genome manipulation,including polyploidy breeding and nuclear transfer.Then,we discuss the advances and applications of fish directional breeding based on transgenic technology and recently developed genome editing technologies.These methods offer increased efficiency,precision and predictability in genetic improvement over traditional methods.     

Biotechnology and agricultural improvement

A range of emerging technologies are expected to play a significant role in agricultural improvement in the next 20 years. Some are only now being explored, but others have already produced significant results. Recent progress in the tissue culture and genetic engineering of crop plants has opened the door to: (1) large scale and rapid propagation of genetically uniform plants from elite materials; (2) the selection of novel and improved varieties using somaclonal variation technology; (3) the development of new hybrids between different cultivars and species by means of protoplast fusion and (4) the use of recombinant DNA to introduce new genetic material into plant cells. It is expected that, by the year 2000, a wide range of crops will be affected by these advances in biotechnology.     

Mechanisms of population differentiation in seabirds

Despite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population-specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year-round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel, Pterodroma phaeopygia, and Xantus's murrelet, Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder-induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain unanswered, results of the present review should aid conservation efforts by enabling managers to predict the extent of population differentiation in species that have not yet been studied using molecular markers, and, thus, enable the identification of management units and evolutionary significant units for conservation.     

Isolation and characterization of polymorphic microsatellite markers in Pagellus bogaraveo,and cross‐species amplification in Sparus aurata and Dicentrarchus labrax

Several new fish species are currently being included in breeding programmes. However, as specific molecular markers have not yet been developed, this represents a commercial handicap with respect to traditional aquaculture species such as gilthead sea bream or Atlantic salmon. In the present study, 12 new microsatellite loci were developed for blackspot sea bream (Pagellus bogaraveo) that show high levels of polymorphism, especially useful in parentage assignment and individual identification. In addition, cross‐amplification was obtained for two important species for Spanish aquaculture, gilthead sea bream and sea bass.     

Genotyping on the ark: A synthesis of genetic resources available for species in zoos

Using molecular genetic information to guide population management can improve the sustainability of species in captivity. However, empirical population genetics has not been commonly applied to species management programs in zoos. One limitation may be the availability of genetic resources (e.g., markers, primers, etc.) for species held in zoos. To assess the extent to which species held in zoos have been studied using population genetics in the wild, we conducted a systematic literature review of close to 8,000 papers. We synthesized information on the availability and scale of population genetics studies across amphibian, bird, mammal, and reptile species held in zoos, and discussed their potential for informing ex situ management. We found that more than half of the species in zoos (52%) already have some genetic markers described in the literature specific for them, or a congeneric species, that could be further developed to aid the management of zoo populations, and the accumulation of these resources has been steady over the past decades. Furthermore, the proportion of species with genetic resources is even higher (62%) for species that are being managed through a formal breeding program in zoos. Our study provides encouraging results for captive program managers interested in integrating population genetics into ex situ management strategies.     

Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.     

Insect transgenesis and its potential role in agriculture and human health

The ability to genetically engineer insects other than Drosophila melanogaster has further extended modern genetic techniques into important insect pest species ranging from fruit fly pests of horticulture to mosquito vectors of human disease. In only a relatively short period of time, a range of transgenes have been inserted into more than 10 insect pest species. Genetic transformation of these pest species has proven to be a very important laboratory tool in analyzing gene function and effects on phenotype however the full extension of this technology into the field is yet to be realized. Here we briefly review the development of transgenic technology in pest insect species and discuss the challenges that remain in this applied area of insect genetics and entomology.     

The history of tomato: From domestication to biopharming

Imported from the Andean region to Europe in the 16th century, today tomato is widespread throughout the world and represents the most economically important vegetable crop worldwide. Tomato is not only traded in the fresh market but is also used in the processing industry in soups, as paste, concentrate, juice, and ketchup. It is an incredible source of important nutrients such as lycopene, β-carotene and vitamin C, which all have positive impacts on human health. Its production and consumption is increasing with population growth. In this review, we report how tomato was already domesticated by the ancient Incan and Aztec civilizations, and how it came to Europe, where its breeding history started. The development of genetic, molecular biology and plant biotechnology have opened the doors towards the modern genetic engineering of tomato. The different goals of tomato genetic engineering are presented, as well as examples of successfully engineered tomatoes in terms of resistance to biotic and abiotic stresses, and fruit quality. The development of GM tomato for biopharming is also described.     

Technological advances in temperate hardwood tree improvement including breeding and molecular marker applications

Hardwood forests and plantations are an important economic resource for the forest products industry worldwide and to the international trade of lumber and logs. Hardwood trees are also planted for ecological reasons, for example, wildlife habitat, native woodland restoration, and riparian buffers. The demand for quality hardwood from tree plantations will continue to rise as the worldwide consumption of forest products increases. Tree improvement of temperate hardwoods has lagged behind that of coniferous species and hardwoods of the genera Populus and Eucalyptus. The development of marker systems has become an almost necessary complement to the classical breeding and improvement of hardwood tree populations for superior growth, form, and timber characteristics. Molecular markers are especially valuable for determining the reproductive biology and population structure of natural forests and plantations, and the identity of genes affecting quantitative traits. Clonal reproduction of commercially important hardwood tree species provides improved planting stock for use in progeny testing and production forestry. Development of in vitro and conventional vegetative propagation methods allows mass production of clones of mature, elite genotypes or genetically improved genotypes. Genetic modification of hardwood tree species could potentially produce trees with herbicide tolerance, disease and pest resistance, improved wood quality, and reproductive manipulations for commercial plantations. This review concentrates on recent advances in conventional breeding and selection, molecular marker application, in vitro culture, and genetic transformation, and discusses the future challenges and opportunities for valuable temperate (or “fine”) hardwood tree improvement.     

Genetic modification in floriculture

Micro-propagation, embryo rescue, mutagenesis via chemical or irradiation means and in vitro inter-specific hybridisation methods have been used by breeders in the floriculture industry for many years. In the past 20 years these enabling technologies have been supplemented by genetic modification methods. Though many genes of potential utility to the floricultural industry have been identified, and much has been learnt of the genetic factors and molecular mechanisms underlying phenotypes of great importance to the industry, there are only flower colour modified varieties of carnation and rose in the marketplace. To a large extent this is due to unique financial barriers to market entry for genetically modified varieties of flower crops, including use of technology fees and costs of regulatory approval.