Prospects for genetic technology in salmon breeding programmes

Selective breeding has been very successful in increasing production in Atlantic salmon. Gene technology opens new opportunities to comprehend the nature of the genetic variation underlying production traits. Two major areas in which gene technology may play an important role are (1) production of genetically modified fish and (2) development and utilization of genetic markers. Several studies of transgenic salmonids have shown substantially increased growth rates. However, many different issues are related to whether genetically modified fish should be used or not. Genetic markers can be used for aquaculture purposes and for monitoring wild populations. Construction of genetic maps based on markers enables the identification of quantitative trait loci (QTL) and/or markers linked to them. This will facilitate marker‐assisted selection, enabling improvement in economically important traits, in particular traits difficult to breed for, such as food conversion efficiency and disease resistance. Several experiments aimed at mapping QTL in salmonids using genetic markers are ongoing. DNA marker technologies can also be used for identification and monitoring of lines, families and individuals, and for genetic improvement through selection for favourable genes and gene combinations.     

近交及其对水产养殖的影响

因大多数野生物种的捕捞已接近甚至超过了可开发的限度，因此必须大量增加水产品的养殖以满足人们对水产品的需要。目前，许多水产养殖种类的苗种来源于野生亲体或野生种苗，但是当野生种群被过度捕捞或数量大量减少时，越来越多的苗种将来源于人工蓄养的亲体群体。     

Genetic improvement for important farmed aquaculture species with a reference to carp,tilapia and prawns in Asia: achievements,lessons and challenges

This study provides an overview of successful genetic improvement programmes for important farmed aquaculture species in Asia, with a focus on lessons and experiences gained as well as challenges remaining. In both fish and prawns (Macrobrachium rosenbergii), conventional selective breeding approaches have resulted in significant improvement in productivity, with genetic gains ranging from 8 to 12% per generation. Selection for high growth has also brought about beneficial changes in fillet weight of fish and edible meat in prawns without detrimental effects on flesh quality attributes and fitness‐related traits. Genetically improved animals show remarkable vigour and high adaptation to a range of culture environments/conditions in Asian countries. Despite these successes, however, the conduct and practical implementation of such breeding programmes still present several challenges. These include the expansion of breeding objectives, management of inbreeding in closed‐selection populations, controlling the effects of genotype by environment interactions, simultaneous production of large number of full‐ and half‐sib families for species with asynchronous spawning behaviour, maintaining pedigree records, dissemination of the improved strains for widespread production, as well as a reluctance by many to carry out systematically designed genetic improvement for aquatic animal species. There are also challenges with regard to the application of genomic information in genetic enhancement programmes and the development of genetically improved strains in response to climate and environmental changes. In this study, each of these challenges is discussed and solutions are proposed to increase efficiency of future genetic improvement programmes for economically important aquaculture species.     

遗传改良对世界水产养殖业发展的推动作用

随着全球水产品养殖产量快速增长，水产养殖业在近二十年间正快速替代捕捞业，成为满足人类对优质蛋白需求极具潜力的生产活动。世界水产品消费量近几十年来快速增长，水产品在人类食物系统中具有越来越重要的地位。遗传改良作为发展水产养殖业的关键环节而备受关注，长期以来，以选择育种和杂交育种为主要的育种方法，以生长速度、成活率等经济性状为主要改良的目标性状，对世界水产养殖业的发展发挥了基础性、先导性和战略性作用。随着人们对优质蛋白需求的不断增加以及“大食物观”概念的广泛普及，将水产品打造为更加高效的食物生产系统是大势所趋。但纵观全球，水产养殖业存在遗传改良种类不多、覆盖面不广、改良性状滞后于产业发展需求等问题，需要加强水产育种技术创新和品种培育，培育更多的遗传改良种，推进水产养殖业高质量发展。本文基于已有研究结果，结合渔业各类统计数据，对世界水产养殖业发展概况、重要养殖种遗传改良情况、水产育种技术应用、目标性状改良以及部分主要人工改良种产量数据进行整理概述，总结发展状况，分析存在问题，以期为水产种业研究以及产业高质量发展提供参考。     

Genotyping‐by‐sequencing for construction of a new genetic linkage map and QTL analysis of growth‐related traits in Pacific bluefin tuna

Pacific bluefin tuna (Thunnus orientalis) has high market value, but its wild populations have decreased in recent years. The broodstock of Pacific bluefin tuna that were hatched artificially and reared under aquaculture conditions is beginning to be used for production. The creation of broodstock with commercially valuable traits, such as rapid growth, is therefore of great interest. Genetic linkage map‐based identification of markers associated with quantitative trait loci (QTLs) facilitates marker‐assisted selection (MAS) breeding and allows efficient genetic improvement of broodstock. Single nucleotide polymorphism (SNP)‐based genetic linkage map construction using the genotyping‐by‐sequencing method can expand the number of mapped markers and help identify growth‐related QTLs. In this study, we constructed sex‐specific maps for 24 linkage groups consisting of 677 SNP and 651 microsatellite markers. The total lengths of 93 progenies in the mapping population followed normal distribution, with an average length of 9.4 mm. We performed composite interval mapping in the mapping population. QTL analysis revealed one significant QTL in LG10 on the female linkage map. The genetic linkage map—the second such map generated for Pacific bluefin tuna—and the growth‐related QTLs detected in this study will be useful for tuna aquaculture MAS programs.     

An Assessment of Hatchery Cohort Growth Rates of South African Abalone,Haliotis midae,Across Four Commercial Environments

The abalone, Haliotis midae (commonly referred to as “perlemoen”), is an important aquaculture species in South Africa, accounting for the highest percentage of total aquaculture production revenue. The industry largely makes use of wild, undomesticated broodstock and thus a consortium of top producers was formed to develop a genetic improvement program to increase efficiency and sustainability of the industry. As such, the current study aimed to evaluate growth trait performance (wet weight and shell length) of four hatchery‐derived cohorts of South African abalone, across four differing production environments. No significant cohort‐by‐location effects were found for weight and length traits; however, differences were detected between respective cohorts and locations. It is concluded that a single synthetic population comprised of all hatchery cohorts under a single breeding goal is suitable for production at all test locations. Furthermore, advances in artificial reproductive technologies, genetic markers, and individual identification hold promise for genetic improvement of the species.     

Genetic relationship between broodstocks of olive flounder, Paralichthys olivaceus (Temminck and Schlegel) using microsatellite markers

For the first generation of a selective breeding programme, it is important to minimize the possibility of inbreeding. This mostly occurs by mating between closely related individuals, while proper mating can provide an opportunity to establish the base families with wide genetic variation from which selection for subsequent generations can be more effective. Genotyping with microsatellite‐based DNA markers can help us determine the genetic distances between the base populations. The genetic markers further facilitate the identification of the correct parents of the offspring (parentage assignments) reared together with many other families after hatching. We established a genetic analysis system with microsatellite DNA markers and analysed the genetic distances of three farmed stocks and a group of fish collected from wild populations using eight microsatellite markers. The averaged heterozygosity of the farming stocks was 0.826 and that of the wild population was 0.868. The hatchery strains had an average of 8.6 alleles per marker, which was less than a wild population that carried an average of 14.3 alleles per marker. Significant Hardy–Weinberg disequilibrium (HWDE) was observed in two farming stocks (P<0.05). Despite relatively low inbreeding coefficiency of the hatchery populations, the frequency of a few alleles was highly represented over others. It suggests that the hatchery stocks to some extent have experienced inbreeding or they originated from closely related individuals. We will develop a selective program using the DNA markers and will widen the usage of the DNA‐based genetic analysis system to other fish species.     

Quantitative genetic properties of four measures of deformity in yellowtail kingfish Seriola lalandi Valenciennes, 1833

The main aim of this study was to estimate the heritability for four measures of deformity and their genetic associations with growth (body weight and length), carcass (fillet weight and yield) and flesh‐quality (fillet fat content) traits in yellowtail kingfish Seriola lalandi. The observed major deformities included lower jaw, nasal erosion, deformed operculum and skinny fish on 480 individuals from 22 families at Clean Seas Tuna Ltd. They were typically recorded as binary traits (presence or absence) and were analysed separately by both threshold generalized models and standard animal mixed models. Consistency of the models was evaluated by calculating simple Pearson correlation of breeding values of full‐sib families for jaw deformity. Genetic and phenotypic correlations among traits were estimated using a multitrait linear mixed model in ASReml. Both threshold and linear mixed model analysis showed that there is additive genetic variation in the four measures of deformity, with the estimates of heritability obtained from the former (threshold) models on liability scale ranging from 0.14 to 0.66 (SE 0.32–0.56) and from the latter (linear animal and sire) models on original (observed) scale, 0.01–0.23 (SE 0.03–0.16). When the estimates on the underlying liability were transformed to the observed scale (0, 1), they were generally consistent between threshold and linear mixed models. Phenotypic correlations among deformity traits were weak (close to zero). The genetic correlations among deformity traits were not significantly different from zero. Body weight and fillet carcass showed significant positive genetic correlations with jaw deformity (0.75 and 0.95, respectively). Genetic correlation between body weight and operculum was negative (?0.51, P < 0.05). The genetic correlations' estimates of body and carcass traits with other deformity were not significant due to their relatively high standard errors. Our results showed that there are prospects for genetic selection to improve deformity in yellowtail kingfish and that measures of deformity should be included in the recording scheme, breeding objectives and selection index in practical selective breeding programmes due to the antagonistic genetic correlations of deformed jaws with body and carcass performance.     

Recent advances of genome mapping and marker‐assisted selection in aquaculture

Aquaculture is the fastest growing sector in agriculture. Substantial genetic gains have been achieved in a few cultured species using conventional selective breeding approaches. However, the majority of fish and shellfish species remain in their wild state. Due to the recognition of the enormous potential of marker‐assisted selection (MAS) to speed up genetic gain through early selection, aquaculture scientists have constructed linkage maps in over 40 species and mapped quantitative trait loci (QTL) for important traits in over 20 species since the 1990s. Although MAS and genomic selection (GS) have not been widely used in aquaculture, their application in breeding programmes is expected to be a fertile area of research. In this paper, I summarized the recent advances of linkage and QTL mapping, as well as MAS in aquaculture species. I also discussed the potentials of genome‐wide association studies (GWAS) and GS in aquaculture species.     

A review on genome mapping of penaeid shrimps of commercial importance

Genome mapping of any organism has become vital and most essential to control the gene related functions and also for the production of new traits of the desired properties. Gene mapping has become a very powerful tool in agriculture sector as well as for terrestrial livestock and going to revolutionize both these sectors from the point of view of enhancing production. However, for aquatic organisms, the information pertaining to gene mapping research is limited and only in recent past few attempts have been made in this direction. The rationale behind genome mapping particularly for aquaculture species is to improve the quality of animals through selective breeding and produce genetically superior traits for commercial production. There is a great potential in this field since most of the aquaculture species have not been subjected to genetic improvement. The advantage of gene mapping tool for any organism is to identify and characterize quantitative trait loci associated with commercial important traits and to use these markers in marker‐assisted selection programmes. Now with advent of gene editing (CRIPSR‐Cas) technology one can modify/repair the gene structure and remove the adverse impact of the gene related characters without replacing the whole genome. Gene mapping of polygenic traits of aquaculture species is also gaining lot of importance because of dominant nature of such additional functional genes with unique predominant character in the species. In the present review, attempts have been made to collect details of information on gene mapping of cultivable penaeid shrimps. Furthermore, how these gene maps can be used to modify the gene structure at the targeted cites using gene editing techniques, has also been discussed.     

Heritability estimates for growth‐related traits in the Pacific oyster (Crassostrea gigas) using a molecular pedigree

Pacific oyster is one of the leading species in world aquaculture, but heritability estimation applying mixed‐family approach has not been actively pursued. In this study, heritability for growth‐related traits in the Pacific oyster was first estimated by creating a single cohort of 45 families in a full‐factorial mating design consisting of nine sires and five dams. A total of 270 offspring were analysed and parentage assignment inferred by six microsatellite markers achieved 100% success. All parents contributed to the spawn and a total of 42 full‐sib families were represented. Using an animal model, heritability estimates at 12 months of age were 0.49 ± 0.25 for shell height, 0.36 ± 0.19 for shell length, 0.45 ± 0.23 for shell width and 0.35 ± 0.17 for wet weight. Genetic correlation between shell height and wet weight was quite high (0.79 ± 0.25), suggesting that direct selection of shell height, which is an easily measurable trait, also improves wet weight. The results obtained in this study indicate that growth‐related traits could be improved by exploiting additive genetic effects through selective breeding.     

Testing options for the commercialization of abalone selective breeding using bioeconomic simulation modelling

The genetic response and economic benefit from alternative breeding programme designs for blacklip and greenlip abalone (Haliotis rubra and Haliotis laevigata, respectively) were evaluated using a computer simulation model. Two selection criteria were investigated, one used family breeding values for liability to disease challenge test infection and the other used a direct selection of the best performing individuals across families for growth rate. Five scales of breeding programme were tested and the model predicted that if growth rate is the only selection criterion, breeding programmes of a scale using 150 families of each species each generation would result in 12–13% genetic improvement in initial generations and have the greatest beneficial economic impact on the Australian abalone industry of the options tested. The model predicts an average discounted benefit–cost ratio of 48:1, total added discounted benefit of AU$4.90 for each kilogram of abalone produced and nominal economic effect on operating income of over AU$16 million per year after 10 years. If disease resistance is the only selective breeding criterion, 100 families of each species would result in the highest benefit–cost ratio of the options tested, although some genetic gain would need to be sacrificed to reduce inbreeding to acceptable levels in this scenario. A strategy for a stand‐alone abalone selective breeding cooperative was also modelled. For a farm of current tank area yielding 100 t year^?1, participation is expected to yield over AUThe genetic response and economic benefit from alternative breeding programme designs for blacklip and greenlip abalone (Haliotis rubra and Haliotis laevigata, respectively) were evaluated using a computer simulation model. Two selection criteria were investigated, one used family breeding values for liability to disease challenge test infection and the other used a direct selection of the best performing individuals across families for growth rate. Five scales of breeding programme were tested and the model predicted that if growth rate is the only selection criterion, breeding programmes of a scale using 150 families of each species each generation would result in 12–13% genetic improvement in initial generations and have the greatest beneficial economic impact on the Australian abalone industry of the options tested. The model predicts an average discounted benefit–cost ratio of 48:1, total added discounted benefit of AU$4.90 for each kilogram of abalone produced and nominal economic effect on operating income of over AU$16 million per year after 10 years. If disease resistance is the only selective breeding criterion, 100 families of each species would result in the highest benefit–cost ratio of the options tested, although some genetic gain would need to be sacrificed to reduce inbreeding to acceptable levels in this scenario. A strategy for a stand‐alone abalone selective breeding cooperative was also modelled. For a farm of current tank area yielding 100 t year^?1, participation is expected to yield over AU$0.7 million in discounted total added production value and annual discounted returns of over AU$0.4 million per annum by year 10.     

Mate selection in aquaculture breeding using differential evolution algorithm

An algorithm to perform mate selection in aquaculture breeding using a computational optimization procedure called “differential evolution” (DE) was applied under optimum contribution selection and mate selection scenarios, to assess its efficiency in maximizing the genetic merit while controlling inbreeding. Real aquaculture data sets with 8,782 Nile tilapias from five generations and 79,144 coho salmon from eight generations were used to optimize objective functions accounting for coancestry of parents and expected genetic merit and inbreeding of the future progeny. The mate selection results were compared with those from the realized scenario (real mates), truncation selection and optimum contribution selection method. Mate selection allowed reducing inbreeding up to 73% for Nile tilapia, compared with truncation selection, and up to 20% for coho salmon, compared with realized scenario. There was evidence that mate selection outperformed optimum contribution selection followed by minimum inbreeding mating in controlling inbreeding under the same expected genetic gain. The developed algorithm was computationally efficient in maximizing the objective functions and flexible for practical application in aquaculture breeding.     

A novel breeding design to produce genetically protected homogenous fish populations for on‐growing

We present a novel KING breeding design to produce genetically protected homogeneous fish material for commercial producers from a breeding nucleus. KING F2‐production population is established from the nucleus, first through full‐sib mating within two unrelated high‐quality families to produce inbred F1‐progeny and then resolving the inbreeding in F2 through mating of the unrelated F1‐individuals. Owing to a small number of founders and the inbred F1‐parents, the remaining additive genetic variance is 37.5% of the original. This restricts the use of F2‐progeny to establish new breeding programmes, thereby protecting the genetic material of the nucleus. The theoretical calculations show that a concomitant decrease of phenotypic variance is possible. However, the reduction is considerable only for traits with high heritability (h² > 0.50). The method was tested with rainbow trout. The results revealed that the mean body weight of the KING‐progeny was similar, but, surprisingly, phenotypic variation (especially due to residual variance) was higher compared with either their outbred control group or the nucleus breeding population. Although further evaluation of this breeding design is needed, the results suggest that while genetic protection is achieved, the efficiency of the method to reduce phenotypic variation is limited for economically important traits with low‐to‐moderate heritability.     

Estimation of genetic parameters for growth traits in cultured clam Meretrix meretrix (Bivalvia: Veneridae) using the Bayesian method based on Gibbs sampling

The aim of this study was to estimate the genetic parameters of the growth performance of clam Meretrix meretrix. As part of the breeding programme, 25 full‐sib families nested within eight half‐sib families were produced, planted out and tested to assess the heritability of the total body weight (TW), shell length (SL), shell height (SH) and shell width (SW) at different growth stages. Method of analysis was implemented using the Bayesian method based on the Multiple Trait using Gibbs Sampling under Animal Model program, which was used to estimate the (co)variance components of the traits and conduct genetic analysis. A total of 25 full‐sib families, each with 30–35 individuals within family, were used for the analysis. Significant positive genetic and phenotypic correlations between SL, SW, SH and TW with each other were observed. The growth traits showed high‐magnitude heritabilities, with values ranging from 0.64 to 0.85, which indicates that these traits should respond to selection and therefore should be included in genetic improvement programmes.     

Breeding Programs for Sustainable Aquaculture

ABSTRACT

Definition of breeding goals for sustainable fish production is considered, with emphasis on non-market (e.g., ethical) as well as market values. The need for long-term biologically, ecologically, and sociologically sound breeding goals is emphasized, because animal breeding determined only by short-term market forces has lead to unwanted side effects. Farmed fish is at an early stage of domestication and breeding, but rapid selection responses for growth have already been documented for several species. Reports of selection responses for fish and shellfish in both temperate and tropical environments are reviewed. Growth-rate responses of 4-20% have been obtained per generation. Broad breeding goals, including health and functional traits, in addition to production traits, are required. More basic knowledge of, e.g., animal welfare and behavioral disorders of fish is also needed.

Less than 1% of the aquaculture fish material in 1993 originated from selection programs. For most species under improvement, only one or very few programs are running, and the effective population sizes are often limited. Such populations may however easily gain sufficient advantage above non-improved populations to capture much of the market.

This will also discourage further genetic introductions into the breeding nucleus. Long-term inbreeding and loss of genetic variability because of genetic drift may then affect performance and further genetic progress. A sufficiently large and genetically diverse breeding population with appropriate family structure is therefore fundamental when establishing and running a selection program.

Important prerequisites for breeding programs for sustainable production are appropriate governmental policies and awareness of our way of thinking about aquaculture, nature and society. A more communal worldview informed by a subjective epistemology (how we learn about/ analyze nature) and a holistic ontology (belief about what/how nature is) is also required.     

Phenotypic and genetic parameter estimation of morphological traits related to axial body growth in Japanese flounder

A quantitative genetic analysis was undertaken to estimate the genetic parameters for morphological traits associated with axial growth in Japanese flounder. Three year classes (2009, 2010, 2011) that included a total of 47 full-sib families were produced. At 180 and 360 days of age, six morphological traits that included total length, body length, head length, trunk length, caudal peduncle length and caudal fin length were measured on 1,185–1,981 individuals per year class. Based on these traits observed, fifteen length ratio traits were constructed as well. The phenotypic analysis showed that coefficients of variation for the caudal peduncle length and the ratio of it to other length traits had large variation relative to the other traits analyzed. Genetic variations in axial growth of Japanese flounder were revealed by using a single-trait animal model with the fixed, additive genetic and full-sib family effects. All analyzed traits exhibited moderate to high heritabilities, ranging from 0.33 to 0.80. Heritability was higher at 180 days of age than at 360. The current results for estimating genetic parameters demonstrated that these traits related to axial growth could be improved with family breeding in Japanese flounder.     

鞍带石斑鱼繁育群体遗传多样性分析

鞍带石斑鱼作为最大型的石斑鱼,生长速度快,有明显的生长优势,在石斑鱼的产业发展中起到举足轻重的作用。为了解人工养殖和选育活动对鞍带石斑鱼遗传多样性的影响,本文采用微卫星分子标记技术,对广东、海南和福建三个省份共五个代表性采集点的鞍带石斑鱼繁育群体的遗传变异信息进行了研究。群体内遗传多样性分析显示,5个群体等位基因(Na)的平均数目为7.326(6.375-8.380),观测杂合度(Ho)平均值为0.711(0.625-0.775),期望杂合度(He)平均值为0.705(0.684-0.734),多态信息含量(PIC)平均值为0.659(0.633-0.693)。其中,来自福建厦门翔安区的鞍带石斑鱼繁育群体遗传多样性最高。分子方差分析(AMOVA)结果显示,5.36%的遗传变异来自群体间,95.45%来自所有个体间。群体间遗传分化指数(Fst)及遗传距离结果显示,GC和CP群体聚为一支,再与AT群体聚为一支,再与XA群体距为一支,HL群体为独立一支。通过系统进化树分析显示,鞍带石斑鱼繁育群体交叉在一起,没有形成明显的地理格局分布。总而言之,这三省五地的鞍带石斑鱼繁育群体遗传多样性较高,没有明显的驯化迹象。整体研究表明,鞍带石斑鱼繁育群体仍具有较高的遗传多样性,品种受亲本近交影响而出现衰退的可能性不高,人工繁育技术的不完善及养殖管理不规范可能是导致品种病害频发及养殖成活率低的原因。本研究为鞍带石斑鱼种质评价和人工选育提供理论依据。     

斑点叉尾鮰基因组的研究

作为重要的水产养殖种类之一,斑点叉尾(IctalurusPunctatus)的基因组学研究已经取得了较大进展。其众多遗传连锁图以及与表型性状有关的DNA分子标记和基因组资源已经建立;基因组中一些重要的重复片段,已经得到鉴定和辨别,这更有利于对斑点叉尾鮰基因组进行物理学分析;通过基因组学方法,获得了大量基因或全长cDNA序列、以及基因进化和与功能相关基因表达方面的信息。利用细菌人工染色体叠连群技术,创建斑点叉尾鮰基因组物理图谱,开发特定片段分子标记,进行数量性状基因位点(QTLs)分析和高密度基因组绘图。通过比较图谱,可以更有效地进行大范围EST分析和I型分子标记绘图。cDNA微阵列或基因芯片技术的利用,加快新基因发现和鉴定的步伐,为分子标记辅助育种和病害诊断与防治研究奠定了坚实基础。