Search

Background: The accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations., Results: The genetic distance between populations ranged from 0.03 to 0.07, while the genetic correlation ranged from 0.19 to 0.99. Nonetheless, compared to within-population prediction, there was limited or no impact of combining populations for multi-population prediction across the various models used or when using the selected subset of SNPs. The estimates of across-population prediction accuracy were low and to some extent proportional to the genetic correlation estimates. The persistency of LD phase between adjacent markers across populations using all SNP data ranged from 0.51 to 0.65, indicating that LD is poorly conserved across the studied populations., Conclusions: Our results show that a high genetic correlation and a high genetic relationship between populations do not guarantee a higher prediction accuracy from multi-population genomic prediction in Atlantic salmon., (© 2024. The Author(s).)

Consensus and sex-specific genetic linkage maps for large yellow croaker ( Larimichthys crocea ) were constructed using samples from an F 1 family produced by crossing a Daiqu female and a Mindong male. A total of 20,147 single nucleotide polymorphisms (SNPs) by restriction site associated DNA sequencing were assigned to 24 linkage groups (LGs). The total length of the consensus map was 1757.4 centimorgan (cM) with an average marker interval of 0.09 cM. The total length of female and male linkage map was 1533.1 cM and 1279.2 cM, respectively. The average female-to-male map length ratio was 1.2 ± 0.23. Collapsed markers in the genetic maps were re-ordered according to their relative positions in the ASM435267v1 genome assembly to produce integrated genetic linkage maps with 9885 SNPs distributed across the 24 LGs. The recombination pattern of most LGs showed sigmoidal patterns of recombination, with higher recombination in the middle and suppressed recombination at both ends, which corresponds with the presence of sub-telocentric and acrocentric chromosomes in the species. The average recombination rate in the integrated female and male maps was respectively 3.55 cM/Mb and 3.05 cM/Mb. In most LGs, higher recombination rates were found in the integrated female map, compared to the male map, except in LG12, LG16, LG21, LG22, and LG24. Recombination rate profiles within each LG differed between the male and the female, with distinct regions indicating potential recombination hotspots. Separate quantitative trait loci (QTL) and association analyses for growth related traits in 6 months fish were performed, however, no significant QTL was detected. The study indicates that there may be genetic differences between the two strains, which may have implications for the application of DNA-information in the further breeding schemes., Competing Interests: Author RJ is currently employed by GenoMar Genetics AS. The remaining authors also declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interests., (Copyright © 2022 Yu, Joshi, Gjøen, Lv and Kent.)

Bacillary necrosis is a problematic disease in farming of Mekong striped catfish (Pangasianodon hypophthalmus). The pathogenic bacterium is Edwardsiella ictaluri, causing numerous white spots in swelled liver, kidney and spleen. An alternative to antibiotic treatment and vaccine is to select for improved genetic resistance to the disease that requires to establish a proper challenge test. Here, four challenge tests of Mekong striped catfish against E. ictaluri are reported proposing 3 days of acclimatization of test fish prior to the challenge, with restricted water level in the test, keeping a temperature of 26°C. In the challenge, cohabitant shedders should be released directly into the test tank and make up around ⅓ of the fish, and bacteria should be added directly to water. The last two experiments, with the highest mortality, suggest that any factor involving the dead cohabitants should be removed and that additional experimentation should focus on bacteria (density) and timing for addition of bacteria to water. Genetic analyses revealed that resistance to bacillary necrosis tested in replicated tanks in the same experiment can be considered the same genetic trait., (© 2020 John Wiley & Sons Ltd.)

The aim was to carry out a joint genetic analysis of survival and harvest body weight, recorded in a growth performance test in Mekong striped catfish (Pangasianodon hypophthalmus), and susceptibility to bacillary necrosis (caused by Edwardsiella ictaluri), recorded in challenge tests. Data were from two challenge tested year-classes (~6,000 fish in both) that both had growth test data available for survival and body weight (~13,000 fish each year). Data were analysed with a linear tri-variate sire-dam model without the common environmental effect because otherwise genetic correlations were estimated with large standard errors. Susceptibility to bacillary necrosis was found weakly genetically correlated to both growth and survival in the growth test, while growth was found with moderate favourable genetic correlation to growth survival. To defend continued challenge testing of striped catfish in Vietnam, a strong genetic relationship needs to be established between bacillary necrosis and survival under a natural disease outbreak. This requires another field test (in addition to the growth test) with siblings, without antibiotic treatment and the cause of death continuously monitored. Meanwhile, the routine challenge testing with the aim to indirectly improve field survival through selection should continue., (© 2020 John Wiley & Sons Ltd.)

Background: The availability of both pedigree and genomic sources of information for animal breeding and genetics has created new challenges in understanding how they can be best used and interpreted. This study estimated genetic variance components based on genomic information and compared these to the variance components estimated from pedigree alone in a population generated to estimate non-additive genetic variance. Furthermore, the study examined the impact of the assumptions of Hardy-Weinberg equilibrium (HWE) on estimates of genetic variance components. For the first time, the magnitude of inbreeding depression for important commercial traits in Nile tilapia was estimated by using genomic data., Results: The study estimated the non-additive genetic variance in a Nile tilapia population of full-sib families and, when present, it was almost entirely represented by additive-by-additive epistatic variance, although in pedigree studies this non-additive variance is commonly assumed to arise from dominance. For body depth (BD) and body weight at harvest (BWH), the proportion of additive-by-additive epistatic to phenotypic variance was estimated to be 0.15 and 0.17 using genomic data (P < 0.05). In addition, with genomic data, the maternal variance (P < 0.05) for BD, BWH, body length (BL) and fillet weight (FW) explained approximately 10% of the phenotypic variances, which was comparable to pedigree-based estimates. The study also showed the detrimental effects of inbreeding on commercial traits of tilapia, which was estimated to reduce trait values by 1.1, 0.9, 0.4 and 0.3% per 1% increase in the individual homozygosity for FW, BWH, BD and BL, respectively. The presence of inbreeding depression but lack of dominance variance was consistent with an infinitesimal dominance model for the traits., Conclusions: The benefit of including non-additive genetic effects for genetic evaluations in tilapia breeding schemes is not evident from these findings, but the observed inbreeding depression points to a role for reciprocal recurrent selection. Commercially, this conclusion will depend on the scheme's operational costs and resources. The creation of maternal lines in Tilapia breeding schemes may be a possibility if the variation associated with maternal effects is heritable.

Despite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper, we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia ( Oreochromis niloticus ). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and were selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O&#95;niloticus&#95;UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups (LGs). Around one-third of the LGs showed a different recombination rate between sexes, with the female being greater than the male map by a factor of 1.2 (1632.9 to 1359.6 cM, respectively), with most LGs displaying a sigmoid recombination profile. Finally, the sex-determining locus was mapped to position 40.53 cM on LG23, in the vicinity of the anti-Müllerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasively measured traits in Nile tilapia.

Evolution has resulted in behavioural responses to threat which show extensive similarities between different animal species. The reaction to predator cues is one example of such prevailing responses, and functional homologies to mammalian limbic regions involved in threat-sensitive behaviour have been found in the teleost telencephalon. The dorsolateral (Dl) and dorsomedial (Dm) regions of the pallium are thought to perform hippocampus and amygdala-like functions respectively. To what degree these regions are involved in the neuroendocrine responses to stress and predator cues however remains largely unknown. In the present study the involvement of Dl and Dm in such responses was investigated by exposing Nile tilapia (Oreochromis niloticus) to a standardized confinement stress and to skin extract from conspecifics. Nile tilapia develops a characteristic anticipatory behaviour to hand feeding, and effects of skin extract on this behaviour and locomotor activity were studied to characterise threat sensitive behaviour. Nile tilapia responded behaviourally to conspecific alarm cues by reducing feeding anticipatory behaviour. This may reflect a general elevation of alertness, and further studies combining skin extract with other challenges are needed to reveal neuroendocrine effects associated with this predator cue. Confinement stress resulted in an elevation of cortisol and serotonin (5-hydroxytryptamine, 5-HT) metabolism in both Dl and Dm. A similar tendency was observed in fish exposed to chemical alarm cues, but this effect did not reach the level of statistical significance. Hence, limbic responses to stress and fear, akin to those seen in extant mammals, are also present in the teleost lineage., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Consistent individual variation in behaviour and physiology (i.e. animal personality or coping style) has emerged as a central topic in many biological disciplines. Yet, underlying mechanisms of crucial personality traits like feeding behaviour in novel environments remain unclear. Comparative studies, however, reveal a strong degree of evolutionary conservation of neural mechanisms controlling such behaviours throughout the vertebrate lineage. Previous studies have indicated duration of stress-induced anorexia as a consistent individual characteristic in teleost fishes. This study aims to determine to what degree brain 5-hydroxytryptamine (5-HT, serotonin) activity pertains to this aspect of animal personality, as a correlate to feed anticipatory behaviour and recovery of feed intake after transfer to a novel environment. Crucial to the definition of animal personality, a strong degree of individual consistency in different measures of feeding behaviour (feeding latency and feeding score), was demonstrated. Furthermore, low serotonergic activity in the hypothalamus was highly correlated with a personality characterized by high feeding motivation, with feeding motivation represented as an overall measure incorporating several behavioural parameters in a Principle Component Analyses (PCA). This study thus confirms individual variation in brain 5-HT neurotransmission as a correlate to complex behavioural syndromes related to feeding motivation.

The aim of this study was to investigate whether observed time-until-death of Atlantic cod (Gadus morhua L.) juveniles in separate challenge tests with Vibrio anguillarum (causes vibriosis) and nodavirus [causes viral nervous necrosis (VNN)] are due to differences in susceptibility (whether at risk or not) or increased endurance (individual hazard, given that the animal is susceptible) using a cure mixture (CURE) model with Gibbs sampling. Observed time-until-death, prepared as sequential binary records, were analyzed with the CURE model and results were compared with cross-sectional threshold (SIMPLE) and an ordinary longitudinal survival score (NAÏVE) model (i.e., assuming that all animals are susceptible). Overall mortality at the end of the test was 86 and 71% for vibriosis and VNN, respectively. But the CURE model estimated 92 and 82% of the population to be susceptible to vibriosis and VNN, respectively. Hence, a substantial fraction among the survivors were considered to be susceptible but with high endurance. The underlying heritability of susceptibility was moderate for vibriosis (0.33) and extremely high for VNN (0.91), somewhat greater compared with classical SIMPLE model (0.19 and 0.76 for vibriosis and VNN, respectively), analyzing end survival as a cross-sectional binary trait. Estimates of the underlying heritability were low for single test-day scores of both endurance (0.02 and 0.15 for vibriosis and VNN, respectively) in the CURE model and for the NAÏVE model (0.02 and 0.18 for vibriosis and VNN, respectively). Based on the CURE model, the genetic correlation between susceptibility and endurance was low to moderately positive and significantly different from unity (P < 0.01) for both vibriosis (0.13) and VNN (0.47). Estimated breeding values from the SIMPLE and NAÏVE models showed moderate to high correlations (0.41 to 0.96) with EBV for susceptibility and endurance in the CURE model. The analyses indicate that susceptibility and endurance are apparently distinct genetic traits. Still, the genetic variation estimated in the SIMPLE and NAÏVE models seems to a large extent to be controlled by susceptibility and an efficient genetic selection for reduced susceptibility to vibriosis and VNN is therefore likely feasible even when using classical (noncure) models. Earlier termination of the challenge test or back truncation of survival data is not recommended as this likely shifts the focus of selection towards endurance rather than susceptibility.

Correlations between behavioral and physiological traits, often referred to as stress coping styles, have been demonstrated in numerous animal groups. Such trait variations often cluster in two contrasting styles, with animals characterized as either proactive or reactive. In natural populations of salmonid fishes, emergence from spawning nests, when fry establish a territory and shifts from exogenous to endogenous feeding, is a crucial niche shift with a high selection pressure. The timing of this event is correlated to behavioral and physiological traits such as aggression, boldness/shyness, dominance, and metabolic rate; resembling those of proactive and reactive stress coping styles. In farmed fish populations, however the relation between emergence and stress coping styles seems to be absent, an effect which has been related to lack of selection pressure during emergence. In the present study two rainbow trout strains genetically selected as LR (low-responsive) and HR (high-responsive) trout, characterized with proactive (LR) and reactive (HR) stress coping traits, was used to further investigate the relationship between the time of emergence and stress coping style in salmonid fishes. For this task LR and HR larvae were hatched in mixed batches, and thirty individuals from the earliest and latest 25% of emerging larvae were randomly collected. Thereafter, a line specific genetic marker was used to distinguish the proportion of LR and HR occurring in early and late fractions. The result demonstrates a higher proportion of LR fry in the early fraction in comparison to the HR fry, which emerged at a higher proportion during the late period. Early emerging individuals had larger yolk reserves at emergence, lending further support to a relationship between emergence times, yolk reserves at emergence and stress coping styles in salmonids. Smaller larval bodies in early compared to late emerging individuals suggest that this difference in yolk size reflects differences in developmental stages at emergence. These data suggests that a genetic link between emergence time and stress coping style persists in captive salmonid fishes., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Individual variation in the way animals cope with stressors has been documented in a number of animal groups. In general, two distinct sets of behavioural and physiological responses to stress have been described: the proactive and the reactive coping styles. Some characteristics of stress coping style seem to be coupled to the time to emerge of fry from spawning redds in natural populations of salmonid fishes. In the present study, behavioural and physiological traits of stress coping styles were compared two and five months after emergence in farmed Atlantic salmon (Salmo salar), using individuals with an early or late time to emerge. Initially, compared to late emerging individuals, early emerging individuals showed a shorter time to resume feeding after transfer to rearing in isolation. Resumption of feeding after isolation was suggested to be related to boldness behaviour, rather than hunger, in the present study. This observation was repeated five months after emergence, demonstrating behavioural consistency over time in this trait. However, in other traits of proactive and reactive stress coping styles, such as social status, resting metabolism or post stress cortisol concentrations, early and late emerging individuals did not differ. Therefore, this study demonstrates that boldness in a novel environment is uncoupled from other traits of the proactive and reactive stress coping styles in farmed salmonids. It is possible that this decoupling is caused by the low competitive environment in which fish were reared. In natural populations of salmonids, however, the higher selection pressure at emergence could select for early emerging individuals with a proactive coping style., (Copyright © 2011. Published by Elsevier Inc.)

Rhode Island Red (RIR) and Fayoumi chickens were evaluated on-station in a college farm and on-farm in village farms, whereas local chickens were only tested under on-farm condition. Traits recorded are egg production and egg quality, body weight and feed efficiency at 4, 8 and 12 months of age. Significant age effect was found for most traits except for shell thickness, albumen height and egg length. Also, significant breed by management system interactions were found for all traits measured in both systems. Fayoumi chickens were higher in egg production in both management systems. Moreover, they were higher than RIR in feed efficiency. RIR were higher in most egg quality traits and had higher weight gain. Local chickens performed below the two exotic breeds in most of the traits, but had higher weight gain than Fayoumi. Chickens kept on-farm had poorer performance than those kept on-station in all traits except for yolk colour.

Summary: High fecundity in fish allows for testing of large full-sib groups and testing of sub-samples of each group for different traits in different environments, and this benefit is especially useful when traits cannot be measured on the breeding candidate itself. A MIVQUE-method that compresses the information in such data, by estimating variance components based on full-sib mean data, is presented for a two-trait model. The efficiency of this method is compared in a simulation study with a model using an individual observation vector when estimating additive genetic and residual (co)variances. The effect on efficiency of continuous versus binary traits, of varied average number of full-sibs, of varied frequencies in the binary traits, of different combinations of frequencies in the two binary traits, of different heritabilities, of different genetic correlations, and of two different design sizes were studied. Generally, all parameters influenced the efficiency, and this influence was larger on the residual, than on the additive genetic variance component. The proposed methodology will be especially well-suited for analysing binary traits because the residual variance component can be calculated via the phenotypic variance, which can be estimated on basis of the frequency of the trait. ZUSAMMENFASSUNG: Effizienz der Schaetzung von Varianz- und Kovarianzkomponenten aus Vollgeschwistergruppen-Mitelwerten bei kontinuierlichen und dichotomen Merkmalen Die hohe Vermehrungsrate von Fischen erlaubt es, große Vollgeschwistergruppen zu pruefen und auch Stichproben aus diesen für verschiedene Merkmale in verschiedenen Umwelten zu testen. Dies ist besonders hilfreich, wenn die interessierenden Merkmale nicht an den zu selektierenden Individuen erhoben werden können. Es wird ein MIVQUE-Ansatz zur Varianz- und Kovarianzkomponentenschätzung fuer ein Zwei-Merkmalsmodell vorgestellt, der auf der Beruecksichtigung von Vollgeschwistergruppen-Mittelwerten beruht. Die Effizienz dieses Ansatzes wird in einer Simulationsstudie untersucht, indem dieser mit einem auf individuellen Leistungen basierenden Ansatz verglichen wird. Dabei wird untersucht, welche Unterschiede sich bei kontinuierlichen und dichotomen Variablen ergeben sowie der Einfluß verschiedener Gruppengroessen, verschiedener Frequenzen der dichotomen Variablen, unterschiedlicher Heritabilitaeten und genetischer Korrelationen sowie zweier unterschiedlicher Designs. Im Allgemeinen waren die Einfluesse auf die geschaetzte Restvarianz immer groesser als die auf die genetischen Varianzkomponenten. Die vorgeschlagene Methode erwies sich als besonders geeignet fuer die Auswertung dichotomer Merkmale, weil dort die Groesse der Restvarianz sehr einfach aus der phaenotypischen Varianz approximiert werden kann, welche wiederum aus der beobachteten Frequenz des Merkmals gut zu schaetzen ist., (1997 Blackwell Verlag GmbH.)