Random regression analysis for body weights and main morphological traits in genetically improved farmed tilapia (<Emphasis Type="Italic">Oreochromis niloticus</Emphasis>)

To genetically analyse growth traits in genetically improved farmed tilapia (GIFT), the body weight (BWE) and main morphological traits, including body length (BL), body depth (BD), body width (BWI), head length (HL) and length of the caudal peduncle (CPL), were measured six times in growth duration on 1451 fish from 45 mixed families of full and half sibs. A random regression model (RRM) was used to model genetic changes of the growth traits with days of age and estimate the heritability for any growth point and genetic correlations between pairwise growth points. Using the covariance function based on optimal RRMs, the heritabilities were estimated to be from 0.102 to 0.662 for BWE, 0.157 to 0.591 for BL, 0.047 to 0.621 for BD, 0.018 to 0.577 for BWI, 0.075 to 0.597 for HL and 0.032 to 0.610 for CPL between 60 and 140 days of age. All genetic correlations exceeded 0.5 between pairwise growth points. Moreover, the traits at initial days of age showed less correlation with those at later days of age. With phenotypes observed repeatedly, the model choice showed that the optimal RRMs could more precisely predict breeding values at a specific growth time than repeatability models or multiple trait animal models, which enhanced the efficiency of selection for the BWE and main morphological traits.     

Correlations between fitness and heterozygosity at allozyme and microsatellite loci in the Atlantic salmon, Salmo salar L

The relationship between heterozygosity at genetic markers (six allozyme and eight microsatellite loci), and fluctuating asymmetry (FA), length and weight was investigated in two samples of Atlantic salmon (Salmo salar L.) with different timings of first active feeding (early (EA) and late (LA) salmon). This trait had previously been related to fitness. EA fish show smaller values of FA, are longer, heavier and are more heterozygous at allozyme loci than are conspecific LA fish. Also within both samples, heterozygosity at allozyme loci was inversely related to FA and was positively related to weight and length. However, no significant differences in microsatellite diversity (heterozygosity and mean d2 measurements) were observed between samples (EA vs LA). Furthermore, no association was observed between the variability at microsatellite loci and FA, weight or length within each sample. These results suggest that allozyme loci, in themselves, influence fitness components, rather than associations arising from associative overdominance.     

胶州湾12种饵料鱼类耳石大小与体长的关系

根据2008年11月至2009年8月在胶州湾海域进行的逐月定点底拖网调查, 选择12种常见的饵料鱼类作为研究对象, 运用最小二乘法分析了每种饵料鱼类的体长与耳石形态大小(包括耳石的长度、宽度、长半径和短半径)的关系, 并建立回归方程, 旨在为深入研究高营养级鱼类的摄食生态和食物网营养动力学提供基础资料。研究表明, 12种饵料鱼类的体长与体重均呈显著的幂函数关系(P0.05), 回归系数b值在2.871-3.371, 平均值为3.1590.110 (95% CL), b值最小的鱼种是六丝钝尾虾虎鱼Amblychaeturichthys hexanema, 最大的是细条天竺鲷Apogon lineatus。经检验, Liza haematocheilus和箭鱼衔Callionymus sagitta的b值与3无显著差异(P0.05), 属等速生长; 李氏鱼衔Callionymus richardsonii和六丝钝尾虾虎鱼的b值显著小于3 (P0.05), 属负异速生长; 其余8种鱼类的b值均大于3 (P0.05), 为正异速生长。方差分析表明, 12种鱼类的体长与耳石各个形态参数的回归关系均极显著(P0.01)。在所有48个回归方程中, 有37个方程的决定系数R2值大于0.8, 拟合效果较好; 有9个回归方程的R2值在0.7-0.8; 其余2个回归方程的R2值小于0.7, 拟合效果略差。其中, 各方程拟合效果最好的是六丝钝尾虾虎鱼, 其R2值均接近于1。通过比较同种鱼类各个回归方程的R2值可知, 在这12种饵料鱼类中, 多数鱼种体长与耳石长度和宽度的拟合效果要略好于体长与耳石半径的拟合效果, 因此在实际应用中, 可以通过测量耳石的长度和宽度来推算饵料鱼类的体长等形态参数。另一方面, 由于多数鱼类的耳石比较脆, 尤其是耳石的两端更容易破损, 因此与耳石长度相比, 耳石宽度与体长的回归方程更加适合于实际应用。       

Genetic parameters and response to selection for growth in tambaqui

Although the tambaqui (Colossoma macropomum) is the most cultivated native fish species in Brazil, estimated breeding values for growth traits are rarely used for selection of superior individuals in commercial fingerling production. This study aimed to estimate the (co)variance components of growth traits. Body weight, length and width of 2500 tambaqui were determined at tagging and at 6 and 12 months after tagging in a commercial breeding programme in Brazil. Heritability estimates were low for traits measured at tagging (0.10 to 0.19) and moderate to high for traits measured at 6 and 12 months (0.23 to 0.81). Common full-sib effects were high at tagging (>73%), low at 6 months and negligible at 12 months. Positive genetic correlations were found among growth traits at 12 months (0.84 to 0.99) and between growth traits at 6 and 12 months (0.80 to 0.92). These results show that animal selection can be performed at 6 months after tagging. Expected genetic gains for growth traits ranged from 8% to 31%. A simulation of the sex ratio was performed, as individuals did not reach sexual maturity during the experimental period. Because of the sexual dimorphism, more accurate heritability estimates were obtained when considering the female proportion to be 90% in the high-weight group. The findings indicate that it is possible to obtain considerable genetic gains in growth by selecting for growth traits. The development of a tool to determine the sex of animals at early stages can improve the response to selection in tambaqui.     

鱼类的重量-身体维数关系的研究

在运用一元数学公式:W=alb(或W=aLb)来描述鱼类的重量与身体维数关系时存在许多缺陷。作者从确立一条模式鱼的边界曲线方程出发,应用求旋转体体积的方法建立了鱼类重量与长度、体高的多元数学公式: W=alb1Hb2(或W=aLb1Hb2),并推演出鱼类重量与长度、体高、体周长之间的另外两种关系式: W=alb1Sb3(或W=aLb1Sb3) 和W=alb1Hb2Sb3(或W=aLb1Hb2Sb3)。上述几类多元数学公式在用来拟合白鲢、翘嘴红鲌和长春鳊种群及它们的不同生长阶段的观测数据时,都比一元数学公式更接近于实际情况,由多元数学公式进行预报的精度也比一元数学公式高。多元数学公式之所以优于一元数学公式是因为多元数学公式能够较全面地反映不同维数对鱼体重量的综合影响。对于不同体形的鱼类,不同维数对重量影响的程度是不同的,因此在应用时应有所选择。从多元数学公式的组成及应用情况看,真正有使用价值的是考虑了体周长的二元数学公式。由于体高易于测量,为此考虑了体高的二元数学公式更具有实用价值。作者建议,在鱼类生长的理论与应用研究中,可采用: W=alb1Hb2(或W=aLb1Hb2) 和W=alb1Sb3(或W=aLb1Sb3) 来描述鱼类的重量与身体维数之间的关系。       

Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax

Background

In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stress, is less studied. In this study, we have estimated heritabilities of two growth traits (body weight and length) and of cortisol response to confinement stress in the European sea bass.

Findings

The F1 progeny analysed (n = 922) belonged to a small effective breeding population with contributions from an unbalanced family structure of just 10 males and 2 females. Heritability values ranged from 0.54 (±0.21) for body weight to 0.65 (±0.22) for standard body length and were low for cortisol response i.e. 0.08 (±0.06). Genetic correlations were positive (0.94) between standard body length and body weight and negative between cortisol and body weight and between cortisol and standard body length (−0.60 and −0.55, respectively).

Conclusion

This study confirms that in European sea bass, heritability of growth-related traits is high and that selection on such traits has potential. However, heritability of cortisol response to stress is low in European sea bass and since it is known to vary greatly among species, further studies are necessary to understand the reasons for these differences.     

Chromosome analysis in coregonid individuals in the interspecific hybridization zone

Artificial spawning (reproduction), a popular method in fisheries, has caused the unintentional hybridization between native European whitefish (Coregonus lavaretus) and introduced peled (Coregonus peled). The resultant hybrids are fertile and their morphological identification is impossible. The study shows the genetic characteristics of the hybrid coregonid fish specimens. Analyses of the number and morphology of chromosomes were based on conventional Giemsa staining. Nucleolar Organiser Regions (NOR) were analysed using CMA₃‐ and Ag‐NOR staining. Metaphases were also investigated by C‐banding methods. Hybrid specimens had a diploid chromosome number (2n) ranging from 76 to 80 and an arm chromosome number ranging from 96 to 100. NORs were observed on the subtelo‐acrocentric and submeta‐metacentric chromosomes. Results of the present study indicate a high level of chromosomal differentiation due to rearrangement taking place in the gene pool of whitefish/peled hybrids.     

Predictions of response to selection caused by angling in a wild population of Atlantic salmon (Salmo salar)

1. Recreational angling activities in wild populations of Atlantic salmon may induce a selection pressure towards a reduction in body size and length if the angling season coincides with the return of the largest sea age fish class. 2. Using estimates of heritability for growth traits and estimates of the selection pressure from angling operating on growth, we predicted the response to selection expected to occur in a wild population of Atlantic salmon. 3. The dataset used here comprised individuals from two consecutive generations (parents and offspring) from the River Bidasoa (NW Spain). Offspring were assigned to parents using six highly polymorphic microsatellite loci. Use of restricted maximum likelihood methodology and the animal model allowed us to estimate the heritability for body length and body weight as well as their genetic correlation. 4. Estimated heritabilities (0.32 ± 0.12 for length and 0.32 ± 0.11 for weight) and selection pressure caused by angling were used to obtain predictions of response to selection because of angling. Our results suggested a decline of 1.9 mm in body length and 103.3 g in body weight per generation because of angling pressure. 5. The results derived from this study suggest that the angling season should be annually delayed in order to avoid selective angling of the multi‐year class and further reductions in body weight and length.     

Heritability variations of body linearity and obesity indicators during growth

Longitudinal as well as cross-sectional studies have shown variations with age in heritability estimates for body dimensions from infancy to adulthood, even though the patterns of variation are not completely clear. Further study on this subject is of great interest and may help obesity interventions for preventing or treating obesity in children. Therefore, the aim of the present study is to analyse the changes in the genetic and environmental architecture of 8 body linearity and obesity-related phenotypes during the growth process in a cross-sectional sample of 1018 nuclear families from the province of Biscay (Basque Country, Spain). The contribution of additive genetic effects to the variation of the analysed traits was estimated by a variance component analysis using the SOLAR program. Moderate to high heritability estimates were obtained for all 8 anthropometric phenotypes (38.23–65.98%). The heritability values show an increasing trend with age and in the course of the entire ontogenetic development two age periods were remarkable. At 7⁺–8⁺ years of age a strong increase in heritability estimates was found for all the anthropometric phenotypes, except for the sum of skinfolds (SF6), reflecting the biological significance of genes during mid-childhood. During puberty, most of the obesity related phenotypes showed their highest heritability values while linear measurements and weight presented a decrease in the genetic contributions. In conclusion, this study confirms that additive genetic influences have a considerable effect on body linearity and obesity-related traits throughout the growth period and that mid-childhood and puberty are very sensitive periods in human life cycle.     

Body weight and growth rate in laboratory lines ofPoecilia reticulata reared on two different diets

Summary Body weight and growth rate of fish from three laboratory lines fed with two different diets have been analyzed. The differences in response to the diets seem to be related to the different degree of genetic homogeneity of the lines considered. The most homogeneous line shows the greatest variation under the two diets for average body weight at 30 and 70 days as well as for growth rate. An effect of the parents' diet on their offspring was also observed. The increase in growth rate observed when fish are fed with the live food diet is amplified when the progenies derive from parents fed with the dry food diet. Moreover, an effect due to the mother's size is also evident on the mean values of body weight at 30 days. The persistence of this maternal effect on the offspring phenotype during post-embryonic development seems to depend on the degree of genetic homogeneity of the line considered-being the greatest in the most homogeneous line.     

Application of Genomics Tools to Animal Breeding

The main goal in animal breeding is to select individuals that have high breeding values for traits of interest as parents to produce the next generation and to do so as quickly as possible. To date, most programs rely on statistical analysis of large data bases with phenotypes on breeding populations by linear mixed model methodology to estimate breeding values on selection candidates. However, there is a long history of research on the use of genetic markers to identify quantitative trait loci and their use in marker-assisted selection but with limited implementation in practical breeding programs. The advent of high-density SNP genotyping, combined with novel statistical methods for the use of this data to estimate breeding values, has resulted in the recent extensive application of genomic or whole-genome selection in dairy cattle and research to implement genomic selection in other livestock species is underway. The high-density SNP data also provides opportunities to detect QTL and to encover the genetic architecture of quantitative traits, in terms of the distribution of the size of genetic effects that contribute to trait differences in a population. Results show that this genetic architecture differs between traits but that for most traits, over 50% of the genetic variation resides in genomic regions with small effects that are of the order of magnitude that is expected under a highly polygenic model of inheritance.     

Length–weight relationships of 55 fish species from the Three Gorges Reservoir in the Yangtze River,China

The paper reports the length–weight relationships of 55 species from the Three Gorges Reservoir (TGR) of the Yangtze River, China, and the largest reservoir in the world. A total of 24,176 specimens were collected from July 2012 to January 2015. Length–weight relationships for 33 fish species not recorded previously in FishBase, and the maximum total lengths computed for eight species are presented. The a values varied between 0.00054 and 0.01923, and the b values ranged from 2.729 to 3.583. The results will be useful for the application of sustainable management and conservation of these fishes in the TGR of the Yangtze River.     

Longitudinal analyses of correlated response efficiencies of fillet traits in Nile tilapia

Recent studies with Nile tilapia have shown divergent results regarding the possibility of selecting on morphometric measurements to promote indirect genetic gains in fillet yield (FY). The use of indirect selection for fillet traits is important as these traits are only measurable after harvesting. Random regression models are a powerful tool in association studies to identify the best time point to measure and select animals. Random regression models can also be applied in a multiple trait approach to analyze indirect response to selection, which would avoid the need to sacrifice candidate fish. Therefore, the aim of this study was to investigate the genetic relationships between several body measurements, weight and fillet traits throughout the growth period and to evaluate the possibility of indirect selection for fillet traits in Nile tilapia. Data were collected from 2042 fish and was divided into two subsets. The first subset was used to estimate genetic parameters, including the permanent environmental effect for BW and body measurements (8758 records for each body measurement, as each fish was individually weighed and measured a maximum of six times). The second subset (2042 records for each trait) was used to estimate genetic correlations and heritabilities, which enabled the calculation of correlated response efficiencies between body measurements and the fillet traits. Heritability estimates across ages ranged from 0.05 to 0.5 for height, 0.02 to 0.48 for corrected length (CL), 0.05 to 0.68 for width, 0.08 to 0.57 for fillet weight (FW) and 0.12 to 0.42 for FY. All genetic correlation estimates between body measurements and FW were positive and strong (0.64 to 0.98). The estimates of genetic correlation between body measurements and FY were positive (except for CL at some ages), but weak to moderate (−0.08 to 0.68). These estimates resulted in strong and favorable correlated response efficiencies for FW and positive, but moderate for FY. These results indicate the possibility of achieving indirect genetic gains for FW and by selecting for morphometric traits, but low efficiency for FY when compared with direct selection.     

Age, growth and reproduction of Sarcocheilichthys nigripinnis from the Qingyi Stream in the Huangshan Mountains

Identifying the life-history strategies of fish and their associations with the surrounding environment is the basic foundation in the conservation and sustainable utilization of fish species.We examined the age,growth,and reproduction of Sarcocheilichthys nigripinnis using 352 specimens collected monthly from May 2009 to April 2010 in the Qingyi Stream.We found the sex ratio of this study population was 0.58:1(female:male),significantly different from expected 1:1.Females and males both comprised four age groups.The annuli on the scales were formed during February and March.No obvious between-sex difference was observed in length-weight and length-scale-radius relationships.The total length in back-calculation significantly increased with age for both sexes,but did not differ significantly at each age between the two sexes.An inflection point was observed in the growth curves given by the von Bertalanffy growth function for total weight.At this inflection point,fish were 3.95 years.Both sexes reach their 50% sex maturity at age 2,when females and males were 94.7 mm and 103.0 mm total length.The temporal pattern of the gonado-somatic index corresponded to a spawning period that occurred from April through July.The non-synchronicity of egg diameter in each mature ovary during the breeding period suggested these fish may be batch spawners.The absolute fecundity increased significantly with total length and weight,whereas no significant correlation was observed between the relative fecundity and body size.     

Survival,growth and sexual maturation in Atlantic salmon exposed to infectious pancreatic necrosis: a multi-variate mixture model approach

Background

Outbreaks of infectious pancreatic necrosis (IPN) in Atlantic salmon can result in reduced growth rates in a fraction of the surviving fish (runts). Genetic and environmental variation also affects growth rates within different categories of healthy animals and runts, which complicates identification of runts. Mixture models are commonly used to identify the underlying structures in such data, and the aim of this study was to develop Bayesian mixture models for the genetic analysis of health status (runt/healthy) of surviving fish from an IPN outbreak.

Methods

Five statistical models were tested on data consisting of 10 972 fish that died and 3959 survivors with recorded growth data. The most complex models (4 and 5) were multivariate normal-binary mixture models including growth, sexual maturity and field survival traits. Growth rate and liability of sexual maturation were treated as two-component normal mixtures, assuming phenotypes originated from two potentially overlapping distributions, (runt/normal). Runt status was an unobserved binary trait. These models were compared to mixture models with fewer traits (Models 2 and 3) and a classical linear animal model for growth (Model 1).

Results

Assuming growth as a mixture trait improved the predictive ability of the statistical model considerably (Model 2 vs. 1). The final models (4 and 5) yielded the following results: estimated (underlying) heritabilities were moderate for growth in healthy fish (0.32 ± 0.04 and 0.35 ± 0.05), runt status (0.39 ± 0.07 and 0.36 ± 0.08) and sexual maturation (0.33 ± 0.05), and high for field survival (0.47 ± 0.03 and 0.48 ± 0.03). Growth in healthy animals, runt status and survival showed consistent favourable genetic associations. Sexual maturation showed an unfavourable non-significant genetic correlation with runt status, but favourable genetic correlations with other traits. The estimated fraction of healthy fish was 81-85%. The estimated breeding values for runt status and (normal) growth were consistent for the most complex models (4 and 5), but showed imperfect correlations with estimated breeding values from the simpler models.

Conclusions

Modelling growth in IPN survivors as a mixture trait improved the predictive ability of the model compared with a classical linear model. The results indicated considerable genetic variation in health status among survivors. Mixture modelling may be useful for the genetic analysis of diseases detected mainly through indicator traits.     

3×3完全双列杂交F1不同阶段生长特点的分析

为了了解鲤杂交F1不同组合、不同阶段生长性状的变化情况,研究以建鲤、黄河鲤和黑龙江野鲤3个鲤品种双列杂交F1为试验材料,通过组合、组合内性别间、性别、不同时期体重、体增重以及协方差分量的分析,来确定完全双列杂交F1生长性状的变化特点,以及在此过程中起重要作用的影响因素。结果表明:不同时期各个组合体重不同,不同时期组合内性别间体重差异不同;不同时期不同性别间体重差异不同;不同协方差分量,同一组合PIT标记17个月时的体重的最小二乘估计值不同,同一个协方差分量,9个组合中极值估计值出现的组合也不同;除PIT标记17个月后的体厚作为协方差分量外,性别之间体重没有差异,其余分量均是雌鱼体重显著高于雄鱼体重。这些说明选取合适的协方差分量对组合的选择和育种的结果有重要影响。     

Genomic growth curves of an outbred pig population

In the current post-genomic era, the genetic basis of pig growth can be understood by assessing SNP marker effects and genomic breeding values (GEBV) based on estimates of these growth curve parameters as phenotypes. Although various statistical methods, such as random regression (RR-BLUP) and Bayesian LASSO (BL), have been applied to genomic selection (GS), none of these has yet been used in a growth curve approach. In this work, we compared the accuracies of RR-BLUP and BL using empirical weight-age data from an outbred F2 (Brazilian Piau X commercial) population. The phenotypes were determined by parameter estimates using a nonlinear logistic regression model and the halothane gene was considered as a marker for evaluating the assumptions of the GS methods in relation to the genetic variation explained by each locus. BL yielded more accurate values for all of the phenotypes evaluated and was used to estimate SNP effects and GEBV vectors. The latter allowed the construction of genomic growth curves, which showed substantial genetic discrimination among animals in the final growth phase. The SNP effect estimates allowed identification of the most relevant markers for each phenotype, the positions of which were coincident with reported QTL regions for growth traits.     

EVOLUTION OF INTRINSIC GROWTH AND ENERGY ACQUISITION RATES. I. TRADE-OFFS WITH SWIMMING PERFORMANCE IN MENIDIA MENIDIA

Abstract Latitudinal populations of the Atlantic silverside, Menidia menidia , show substantial genetic variation in rates of energy acquistion and allocation. Reared in common environments, silversides from northern latitudes consume more food, grow faster and more efficiently, store more energy, and produce greater quantities of eggs than their southern conspecifics. The persistence of seemingly inferior southern genotypes in the face of ostensibly superior northern genotypes suggest that there are hidden evolutionary trade-offs associated with these elevated acquisition and allocation rates. We tested the hypothesis that rapid growth and high levels of food consumption trade-off against locomotory performance in M. menidia . We compared both aerobic (prolonged and endurance) and anaerobic (burst) swimming capacities between intrinsically fast-growing fish from the north (Nova Scotia, NS) and intrinsically slow-growing fish from the south (South Carolina, SC) and between growth-manipulated phenotypes within each population. We also compared swimming speeds and endurance between fasted and recently fed fish within populations. Maximum prolonged and burst swimming speeds of NS fish were significantly lower than those of SC fish, and swimming speeds of fast-growing phenotypes were lower than those of slow-growing phenotypes within populations. Fed fish had lower burst speeds and less endurance than fasted fish from the same population. Thus, high rates of growth and the consumption of large meals clearly diminish swimming performance, which likely increases vulnerability to predation and decreases survival and relative fitness. The submaximal growth rate of southern M. menidia appears to be adaptive, resulting from balancing selection on rates of somatic growth.     

Enhanced individual selection for selecting fast growing fish: the "PROSPER" method,with application on brown trout (Salmo trutta fario)

Growth rate is the main breeding goal of fish breeders, but individual selection has often shown poor responses in fish species. The PROSPER method was developed to overcome possible factors that may contribute to this low success, using (1) a variable base population and high number of breeders (Ne > 100), (2) selection within groups with low non-genetic effects and (3) repeated growth challenges. Using calculations, we show that individual selection within groups, with appropriate management of maternal effects, can be superior to mass selection as soon as the maternal effect ratio exceeds 0.15, when heritability is 0.25. Practically, brown trout were selected on length at the age of one year with the PROSPER method. The genetic gain was evaluated against an unselected control line. After four generations, the mean response per generation in length at one year was 6.2% of the control mean, while the mean correlated response in weight was 21.5% of the control mean per generation. At the 4th generation, selected fish also appeared to be leaner than control fish when compared at the same size, and the response on weight was maximal (≈130% of the control mean) between 386 and 470 days post fertilisation. This high response is promising, however, the key points of the method have to be investigated in more detail.