最佳遗传贡献理论及其在水产动物选择育种中的应用前景

水产动物多性状复合育种技术已发展成为国内水产选择育种的重要技术体系。在限定的近交水平下,如何选种和配种实现遗传进展最大化是当前该体系亟待解决的一个突出问题。在动植物选择育种中,最佳遗传贡献理论(Optimum Contribution,OC)已成为平衡育种核心群长期遗传进展与近交水平的有效工具。本文论述了OC理论的提出背景和发展过程、不同优化算法的特点和该理论在动植物选择育种中的应用进展,并进一步综述了基于基因组信息的OC理论研究新进展。遗传贡献目标函数的优化算法主要包括拉格朗日乘数法、半正定规划法和差分进化算法等。基于拉格朗日乘数法,执行OC选择10代后获得的遗传进展要比最佳线性无偏预测法(Best Linear Unbiased Prediction,BLUP)育种值直接选择高21%-60%。针对水产动物等高繁殖力大群体,育种学家进一步改进了算法,利用候选亲本父母本群体的加性遗传相关矩阵来计算候选亲本群体的加性遗传相关矩阵和逆矩阵,降低了逆矩阵的维数,提高了最佳遗传贡献值的计算效率。但是拉格朗日乘数法并不能保证求解出的遗传贡献值为全局最大值,而半正定规划方法利用内点算法可以获得候选亲本的最佳遗传贡献值,与前者相比遗传进展可进一步提高1.5%-9%。差分进化算法可将遗传进展、遗传多样性、后代近交、场间遗传联系、多阶段选择、分子标记利用和成本等多种因素纳入目标函数进行优化,同时完成个体选择和交配方案制定两个关键任务。复合系谱和基因组信息,在限定的近交水平下,可以获得更为准确的遗传贡献值,遗传进展可进一步提高。OC选择已经应用在畜牧、林木育种研究中,育种群体的近交水平得到了有效控制,与BLUP直接选择相比,目标性状的遗传进展进一步提高(17%-30%)。针对水产动物多性状复合育种技术体系的特点,本文分析了OC理论应用的紧迫性和可行性,提出了亟待解决的关键技术问题和解决方案,为下一步在水产动物选择育种中应用OC理论提供借鉴和指导。     

Can timing of spawning explain the increase in egg size with female size in salmonid fish?

A common observation is that egg size increases with maternal size within populations. Several hypotheses have been proposed to explain this phenomenon. Most recently, it was suggested that the optimal egg size depends on female size due to correlations between (i) breeding time and egg size selection and (ii) female size and breeding time, and as such, the positive egg size–maternal size relationship represents an adaptive strategy. Here, we test the second of these two premises in two salmonid species, Atlantic salmon (Salmo salar) and coho salmon (Oncorhynchus kisutch) for which we have detailed breeding and egg size data. The body size of spawning females decreased throughout the season in coho salmon, but not in Atlantic salmon. Furthermore, we did not find a direct correlation between egg size and breeding time, which would also be expected if this premise was correct. Accordingly, breeding date does not appear to be as important as other factors in shaping among female differences in egg size.     

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.     

Integrating molecular genetic technology with traditional approaches for genetic improvement in aquaculture species

Genetic improvement of aquaculture species offers a substantial opportunity for increased production efficiency, health, product quality and, ultimately, profitability in aquacultural enterprises. Technolo‐gies exist that can be implemented immediately to improve multiple traits that have economic value, while simultaneously accounting for inbreeding effects. Genetic improvement techniques for delivering genetic gain include formal definition of the breeding objective, estimation of genetic parameters that describe populations and their differences, evaluation of additive and non‐additive genetic merit of individuals or families and defining the structure of a breeding programme in terms of mating plans. Novel genetic technologies involving the use of DNA‐based tools are also under development for a range of aquaculture species. These gene marker technologies can be used for identification and monitoring of lines, families and individuals, monitoring and control of inbreeding, diagnosis of simply inherited traits and genetic improvement through selection for favourable genes and gene combinations. The identification of quantitative trait loci (QTL), and direct or linked markers for them, will facilitate marker‐assisted selection in aquaculture species, enabling improvement in economically important traits, particularly those that are difficult to breed for, such as food conversion efficiency and disease resistance.     

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。     

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.     

Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations

Genetic diversity between three farmed and four wild populations of Atlantic salmon from Ireland and Norway were analysed using 15 microsatellite markers. High levels of polymorphism were observed over all populations with the average number of alleles and average heterozygosity at 17.8 and 0.70, respectively. Farmed salmon showed less genetic variability than wild salmon in terms of allelic diversity but not necessarily in terms of overall heterozygosity. Between farmed populations significant differences were observed in expected heterozygosity suggesting that more intensive breeding practices may have resulted in a further erosion of genetic variability. Phylogenetic analysis using either populations or individuals as nodes show a clustering of populations into two groups, farmed and wild. This suggests that founder effects and subsequent selection have had more effect on the genetic differentiation between these strains than geographical separation. This technology has great potential for use in aquaculture situation where levels of genetic variation could be monitored and inbreeding controlled in a commercial breeding progra.     

Reproductive strategies in small populations: using Atlantic salmon as a case study

Abstract –  Wild salmonid populations with only a few breeding adults may not exhibit a significant reduction in genetic variability compared with larger populations. Such an observation suggests that effective population sizes are larger than population size estimates based on direct adult counts and/or the mating strategy maximises outbreeding, contributing to increased heterozygosity. In the case of wild Atlantic salmon Salmo salar populations, stratification by age classes and sexes on the spawning grounds avoids inbreeding and increases genetic variability. We studied the breeding composition of four Spanish salmon populations. Over a 7-year period we concluded that the probability of within-cohort mating is very low: females generally reproduce after two sea-winters whereas males reproduce mostly as one sea-winter ( grilse ) and/or mature parr. Considering different levels of contribution of mature parr to spawning derived from field surveys, we developed a simple model for estimating effective population sizes and found that they doubled with 65% parr contribution expected for rivers at this latitude (43°N), and ranged from 100–800 individuals. The effect of between-cohort mating was modelled considering different ranges of differences in allele frequencies between cohorts and resulted in 28–50% increases in heterozygosity when considering a 65% parr contribution. The complex mating strategy of Atlantic salmon contributes to explain the high levels of genetic variability found for small populations of this species. This model can probably be extended to other animal species with mating strategies involving different cohorts.     

Genetic variation in farmed populations of the gilthead sea bream Sparus aurata in Greece using microsatellite DNA markers

Genetic variation in seven reared stocks of gilthead sea bream Sparus aurata, originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of two natural populations from the Ionian and the Adriatic Seas. The total number of alleles per marker ranged from 11 to 19 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic diversity and expected heterozygosity. The global genetic differentiation for the cultivated samples was significant as indicated by F_st analysis, which might indicate random genetic drift and inbreeding events operating in the hatcheries. On the contrary, no significant difference was found between the two wild populations. Population pairwise tests between farmed and wild stocks were also significant, with the exception of one hatchery sample, the Central Greece 1, which was not significantly different from the two wild samples perhaps due to its recent use in aquaculture from wild‐caught animals. The UPGMA tree topology grouped the wild samples together with the Central Greece 1 stock, and showed a clear division between wild and farmed sample sets for the six remaining hatchery samples. Knowledge of the genetic variation in S. aurata cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for the proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.     

Approaches for delaying sexual maturation in salmon and their possible ecological and ethical implications

ABSTRACT

The aquaculture industry is under pressure to satisfy global demand for marine foods. Atlantic salmon has been bred for more than 40 years, and substantial progress has been made within the culturing and breeding programs. The improved growth rate of Atlantic salmon has been accompanied by an earlier onset of maturation. Among the factors controlling maturation in salmon are photoperiod, temperature, and body composition. Early sexual maturation is detrimental to fish health and quality when viewed from an aquacultural viewpoint. There are several approaches for alleviating this problem: (1) traditional selection, (2) manipulation of external factors affecting puberty (e.g., light), (3) novel biotechnological methods for improving breeding methods, (4) induction of polyploidy, and (5) genetic modification controlling maturation. This article presents the ecological and ethical issues connected to these approaches and argues the importance of acknowledging and discussing such issues in order to ensure that all stakeholder concerns are considered.     

Genetic diversity and population structure of a giant freshwater prawn (Macrobrachium rosenbergii) breeding nucleus in China

The giant freshwater prawn breeding programme in China has been carried out as a closed nucleus from 2006. The programme aimed to improve the harvest body weight and pond survival and has achieved remarkable progress. In this study, the genetic diversity and population structure of the giant freshwater prawn breeding nucleus was analysed. Pedigree completeness, the status of genetic diversity, inbreeding accumulation and effective population size of the breeding nucleus were analysed according to the pedigree record. From 2006 to 2014, a total of 107,941 individuals with 555 males and 967 females in nine generations were included in the analyses. Pedigree completeness index in six generations was at least 0.92. After performing eight selections, the genetic diversity decreased by 3%, 67% of which was caused by random genetic drift. After performing 2 years’ selection, the inbreeding level began to show a marked upward trend. The regression of the average rate of inbreeding and the average rate of co‐ancestry was 0.0041 and 0.0051 from 2006 to 2014. The effective population size calculated from the above two parameters was 122 and 98 respectively. The effective population size is still within the recommended level for a population to continue the genetic improvement programme, but below the level required (500) for retaining the evolutionary potential. To restrain the increasing level of inbreeding and maintain effective population size, measures are required to develop a breeding programme which integrates management of genetic variability and selection.     

Genetic parameters and response to selection for harvest body weight of pacific white shrimp,Litopenaeus vannamei

Genetic parameters and response to selection were estimated for the harvest body weight of Litopenaeus vannamei. The data consisted of 24 072 progeny from 178 sires and 171 dams in two generations (G₀ and G₁) with a nested mating structure. All families were randomly divided into two groups and then cultured in two farms at different locations (Huanghua and Qingdao). The heritability estimates from G₀ and G₁ were 0.278 ± 0.136 and 0.423 ± 0.065 respectively. Over two generations, the heritability estimate was 0.335 ± 0.087, and the common environmental effect was 0.084 ± 0.031. A bivariate animal model was used to estimate variance and covariance components, whereby the body weight in the two farms was treated as a genetically distinct trait. Genetic correlation was close to unity (0.943 ± 0.066), indicating that a genotype by environmental interaction for harvest body weight was small. The response to selection in harvest body weight was estimated using two methods (the realized and predicted responses). The realized response was estimated from the difference in the least squares means of body weight for the selection and control populations. The predicted response was obtained from the difference in the mean estimated breeding values between generations. The realized response was 2.30%, while the predicted responses were 2.00% and 1.37% for within‐ and across‐generation datasets using two sets of genetic parameters respectively. The results would provide crucial information in pacific white shrimp breeding programs in China.     

Evaluation of non‐traditional modelling techniques for forecasting salmon returns

Forecasting adult salmon abundance is problematic when the number of observations is small relative to the number of potential explanatory variables. Machine learning and other non‐traditional techniques employ algorithms designed to prevent model overfitting. Data from 18 coho salmon, Oncorhynchus kisutch (Walbaum), and seven Chinook salmon, Oncorhynchus tschawytscha (Walbaum), populations on the Oregon coast were used to evaluate the forecast performance of artificial neural networks, elastic net, least absolute shrinkage and selection operator, principal component regression (PCR) and ridge regression (RR) compared to several more traditional techniques. In general, the non‐traditional modelling techniques evaluated in this study performed similarly to the traditional techniques with the exception of sibling regression. This suggests that they have merit for improving actual predictions. Among the non‐traditional techniques, PCR resulted in the lowest prediction error for the coho salmon populations, and RR predicted Chinook salmon returns most accurately. The techniques explored are not an easy solution to a difficult problem. Spurious conclusions about the processes that generate salmon returns still may result as evidenced by the inclusion of an unrelated variable in many of the non‐traditional models.     

Genetic effects of selection on polygenic traits with examples from Atlantic salmon, Salmo salar L.

Abstract. Recent attempts to apply selective breeding strategies in fish populations have focused on the genetic effects of selection. The basic mechanisms of long-term response to selection are discussed with reference to experience from laboratory and farm animal populations. A simplified polygenic model is presented, and it is shown that considerable response may be obtained for polygenic traits without essential changes in allele frequencies and genetic variability, and that the probability of fixation of alleles or genotypes because of selection will be low when the trait is affected by a larger number of loci. The span between the extreme fixed genotypes for such traits may easily become wider than that which may be realized under normal biological conditions. This is illustrated with some examples from Atlantic salmon. Salmo salar L. The effects of divergent fitness selection of populations on genetic differentiation and allele frequencies are also considered, and some examples from experiments with Norwegian river strains of Atlantic salmon are discussed. It is shown that the river strains are not expected to differ much in frequencies of fitness alleles if the number of loci affecting the fitness trait is large, and that considerable overlapping of genetic values for fitness between strains may be expected.     

Comparison of immune responses and antioxidant status of different generations of growth‐selected Portunus trituberculatus families

The purpose of this study was to investigate the effects of inbreeding on the immune responses and antioxidant status of Portunus trituberculatus juveniles. Results showed that inbreeding affected the total haemocyte count, and phagocytic, pro‐phenoloxidase (propo), phenoloxidase and antibacterial activities decreased after the seventh generation. Antioxidant status showed a similar pattern: total antioxidant capacity, superoxide dismutase (SOD) activity and GSH/GSSG in the cell‐free haemolymph and hepatopancreas decreased, while catalase activity in the cell‐free haemolymph increased (P < 0.05). There were no significant differences in α₂‐macroglobulin and bacteriolytic activities in the cell‐free haemolymph and glutathione peroxidase activity in the cell‐free haemolymph and hepatopancreas among nine inbreeding generations. Gene expression levels of proPO and crustin in haemocytes and SOD in haemocytes and hepatopancreas also decreased significantly as the inbreeding generations increased. The results suggest that a high level of inbreeding could severely reduce the physiological health of P. trituberculatus. Our obtained data would be particularly useful for P. trituberculatus breeding programmes.     

Genetic improvement of cold-water fish species

Carnivorous fish are two to three times as efficient as pigs and broilers in converting energy and protein to edible food for humans. As the domestication of fish continues, they will become more and more efficient and competitive with these industries. In the future, this will be very important, as more efficient utilization of available food resources is required to supply the growing human population with enough food. Today, about 1% of aquaculture production is based on genetically improved fish and shellfish. For salmonid fishes, we have the necessary knowledge to establish efficient breeding programmes. Large genetic variation has been associated with important economic traits. For growth rate, heritability ranges from 0.2 to 0.3, with a coefficient of variation of 20–30%. This implies that it is possible to obtain large responses from selection for growth rate. In several large‐scale experiments and in breeding programmes, 10–15% genetic change has been obtained per generation, which is much higher than that reported for other farm animals. In Norway, extensive breeding experiments with Atlantic salmon and rainbow trout were started in 1971. For the first two generations of selection, the breeding goal was growth rate. Age at sexual maturation (measured as frequency of grilse) was then included. From the fifth generation, disease resistance (measured by challenge test for furunculosis and the virus ISA) and meat quality (measured as fat percentage, fat distribution and flesh colour) were included. Today, Norsk Lakseavl AS (Norwegian Salmon Breeding Company Ltd) or NLA runs the National Breeding Programme and has two breeding stations where 400 full‐sib and half‐sib families of Atlantic salmon are tested in each of four year classes. For rainbow trout, the number of families totals 120 in each of three year classes. In 1997, the Norwegian production was 310 000 tons of Atlantic salmon and 33 000 tons of rainbow trout. At present, about 65% of the salmon and trout produced in Norway use genetically improved fish from NLA and multipliers. The cost–benefit ratio for the National Breeding Programme in Norway is estimated to be 1:15.     

Riparian defoliation by the invasive green alder sawfly influences terrestrial prey subsidies to salmon streams

Invasive species in riparian forests are unique as their effects can transcend ecosystem boundaries via stream‐riparian linkages. The green alder sawfly (Monsoma pulveratum) is an invasive wasp whose larvae are defoliating riparian thin‐leaf alder (Alnus tenuifolia) stands across southcentral Alaska. To test the hypothesis that riparian defoliation by this invasive sawfly negatively affects the flow of terrestrial prey resources to stream fishes, we sampled terrestrial invertebrates on riparian alder foliage, their subsidies to streams and their consumption by juvenile coho salmon (Oncorhynchus kisutch). Invasive sawflies altered the composition of terrestrial invertebrates on riparian alder foliage and as terrestrial prey subsidies to streams. Community analyses supported these findings revealing that invasive sawflies shifted the community structure of terrestrial invertebrates between seasons and levels of energy flow (riparian foliage, streams and fish). Invasive sawfly biomass peaked mid‐summer, altering the timing and magnitude of terrestrial prey subsidies to streams. Contrary to our hypothesis, invasive sawflies had no effect on the biomass of native taxa on riparian alder foliage, as terrestrial prey subsidies, or in juvenile coho salmon diets. Juvenile coho salmon consumed invasive sawflies when most abundant, but relied more on other prey types selecting against sawflies relative to their availability. Although we did not find effects of invasive sawflies extending to juvenile coho salmon in this study, these results could change as the distribution of invasive sawflies expands or as defoliation intensifies. Nevertheless, riparian defoliation by these invasive sawflies is likely having other ecological effects that merits further investigation.     

缢蛏选育系F5的生长优势比较及育种效应分析

以6个缢蛏(Sinonovacula constricta)自然群体(浙江象山群体、浙江乐清群体、福建霞浦群体、福建长乐群体、江苏射阳群体和上海崇明群体)为材料,构建基础群体F_0,采用群体选育方法进行多代连续选育(选择强度2.063),比较了选育系F_5与对照群体的生长差异,并估计F_5的选择反应、现实遗传力和遗传获得。结果表明,F_5的卵径及受精率与对照组无显著差异(P0.05),但F_5的变态率、存活率及后期壳长生长明显优于对照组(P0.05);7~360日龄F_5壳长的选择反应、现实遗传力与遗传获得的变化范围分别为0.30~0.78,0.14~0.37和4.83%~42.18%,平均为(0.49±0.06),(0.23±0.08)和(26.49±11.73)%。研究结果表明,对缢蛏的连续多代选育是有效的,可以明显提高其存活能力和主要经济性状。     

Microsatellites markers to depict the reproductive and genetic patterns of farmed gilthead seabream (Sparus aurata): illustration by a case study on mass spawning

In the absence of breeding strategy, natural spawning constitutes the breeding ground for fish farmers to empirically manage their commercial broodstock. In this context, we used six microsatellite markers to characterize the genetic pattern of six commercial seabream broodfish tanks having a common history spanning four generations. The progeny of one tank single‐day mass‐spawning event, reared in two different environments, was used to estimate the genetic parameters for body weight. Limited genetic differentiation was observed among broodfish groups. A panel of nine loci allowed us to unambiguously assign 95.4% of the offspring (1692) and identify 37 parents (65% of the total broodfish). The limited effective population size (N_e = 15.3) was due to the elevated variance of parental contributions and to broodfish failing to contribute to the progeny. The fluctuation of the allele frequency highlighted the risks of genetic drift and reduction in the heterozygosity in the next generations. Heritability for body weight was moderate at commercial size (0.40 ± 0.10) and the high genetic correlation at later stages laid the groundwork for precocious selection criteria for growth. The discussion opens on the opportunity to use mass spawning for selective breeding.     

熊本牡蛎多嵴和无嵴品系F3生长性状的连续选择效应

为进一步检测熊本牡蛎(Crassostrea sikamea)多嵴和无嵴品系F3的连续选择反应,以2个品系F2上选组为材料,开展2个品系F3混合上选研究,评估2个品系F3生长性状的选择反应、现实遗传力及遗传改进量,解析选育过程中选择效应、品系效应及二者交互作用对生产性状的影响。结果表明:多嵴品系F3生长性状具有较高的现实遗传力,表现出较好的遗传改良效果;无嵴品系F3表现出中等现实遗传力水平,但仍具有一定程度的遗传改良潜能。养成期360日龄时,多嵴品系子代壳高、鲜重的选择反应分别为0.70、0.76;现实遗传力分别为0.40、0.43;遗传改进量分别为7.02%、12.29%;无嵴品系的选择反应分别为0.36、0.33;现实遗传力分别为0.20、0.19;遗传改进量分别为3.74%、5.72%。经过双因子分析模型检测发现:品系来源是影响F3生长性状的主要因子,选择效应是次要因子,二者间不存在明显的交互作用。由此可见,随着连续选择的进行,选择反应逐渐降低,品系来源作用增强,本研究为熊本牡蛎遗传改良和新品系培育奠定了基础。