Family-based Selection Research Articles

Establishment and application of multiplex microsatellite genotyping for parentage assignment in Manila clam Ruditapes philippinarum

The manila clam Ruditapes philippinarum has become an important bivalve species in worldwide aquaculture due to its delicious taste and high commercial value. With the rapid expansion of clam farming, there is an urgent need to obtain genetic improvement by selective breeding, such as family-based selection of improved varieties. In this study, 10 microsatellite loci were selected to establish four multiplex PCR groups using four different fluorescences (FAM, ROX, HEX, TAM). The accuracy of these loci was verified by the 100% success rate of parentage assignment in a full-sib family. Parentage assignment was carried out in the mixed-mating parents and their offspring with unknown pedigree information. The genotyping of ten microsatellite loci generated 90 alleles, having the observed heterozygosity (Ho) ranging from 0.333 to 0.729. The expected heterozygosity (He) varied from 0.358 to 0.794. The PIC ranged from 0.342 to 0.763, with a mean value of 0.620. The theoretical combined parentage exclusion (cEP) power for all ten microsatellites was 97% with known genotypes of one parent (P1) and 99% for given the genotypes of both parents (P2). The actual successful assignment rate reached 98% by using all four sets of multiplex microsatellites, serving as the effective method for parentage assignment in the clams. The development and application of multiplex microsatellite genotyping methods provide a cost-effective method for pedigree reconstruction, population genetics and selective breeding of the commercially important clams.

The genetics and breeding of the Portuguese oyster, Crassostrea angulata: lessons, experiences, and challenges in Vietnam

Aquaculture mollusc production is predominantly from Asia, with more than 80% of the total biomass produced in China. Vietnam’s annual mollusc production is growing rapidly but is comparatively small given its coastal resources. A significant challenge for future mollusc production, and oysters in particular, is the supply of high-quality spat. Most mollusc spat in Vietnam comes from local wild sources or is imported from China. Particularly in the case of oysters, where wild collection is low and importation of oyster spat into Vietnam from other jurisdictions is not controlled, supply is unreliable and presents a biosecurity risk to the industry. Controlling the life cycle in hatcheries can increase the sustainability and reliability of spat supply with the advantages of genetic enhancement in the long term. Beyond well-established selection methods based on phenotypic data for pedigreed families, the rapid development of genomic technology has enabled innovation in hatchery production based on genetic programs. This technology allows greater insight into oyster genetics in intensive aquaculture production systems. Recent reviews of selection programs demonstrate that inbreeding control via mate selection is an effective strategy for oyster species. Genetic response through combinations of individual and family-based selection can enhance morphometric traits by 10% per generation and disease resistance by 15% per generation in many aquaculture species. Genomic techniques provide information for selecting candidates at an earlier stage and improve prediction accuracy. In this paper, we review the literature on popular genomic tools and breeding techniques used for molluscs, focusing on the Portuguese oyster, Crassostrea angulata. This is to better comprehend how modern quantitative and molecular genetic technologies are being applied in mollusc breeding programs. It considers opportunities for and the feasibility of using genomic-based selection as well as the challenges that are faced in breeding programs transitioning to these new methods.

What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?

Simple SummaryInfectious diseases place an economic burden on aquaculture and a limitation to its growth. This state-of-the-art review describes the application of genetics and genomics as novel tools to control infectious disease in aquaculture.Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.

Impact of family-based selection on growth performance and immune response of Japanese quail.

The present study was aimed to evaluate the growth performance and immune response of three genetic lines of Japanese quails. These lines i.e., selected for 4-week body-weight group (WBS), selected for egg number (EBS), and random-bred control (RBC), were selected for three consecutive generations from a base population of 1125 quails. In total, 2700 four-week-old quails from three selected groups were slaughtered in total of four generations (G0 to G3). Effects of selection and generations as well as their interactions were assessed for growth performance and immune response by applying a two-way analysis of variance. Significant means were compared with Duncan's Multiple Range Test. The statistical analysis showed a significant effect of selection and generations on most of the growth and immune response parameters. WBS in G3 presented significantly higher values of body weight, weight gain, and FCR than RBC and EBS. FCR was better in WBS during G3 than those of EBS and RBC. However, Livability% was highest in RBC while the lowest was noted in G3 of WBS line. Thymus% and spleen% were higher in EBS as compared to RBC and WBS. RBC presented a better B/S ratio and ND titer than those of EBS and WBS. The decreasing trend of ND titer in both lines of WBS and EBS as compared to RBC suggested a decrease in New Castle disease resistance in progressive generations of selection. It was concluded that selection for body weight and egg number has a positive impact on respective traits but negatively affects the immunity in later generations.

Heterosis for Biomass-Related Traits in Interspecific Triploid Hybrids of Willow (Salix spp.)

Species hybridization is key for the improvement of shrub willow (Salix spp.) bioenergy crops because hybrids often display heterosis for yield. The development of high-yielding genotypes requires numerous broad attempts at hybridization followed by field evaluation and selection for stable performance. Selection of improved shrub willow varieties for use as a bioenergy crop involves evaluation of full-sib progeny in family-based selection trials. Improving the accuracy of evaluation through the use of components of yield would greatly improve the efficiency of selection. Heterosis for biomass yield in intra- and interspecific F1 and F2 shrub willow crosses, made between Salix sections and ploidy, was examined by utilizing a suite of morphological, physiological, and chemical composition traits collected over the course of 12 weeks in the greenhouse and over 3 years in the field. Triploid families generated from diploid S. viminalis and tetraploid S. miyabeana displayed the greatest levels of heterosis for harvestable biomass and biomass-related growth traits in the greenhouse and in the field. While intraspecific S. purpurea diploids exhibited low levels of heterosis for these traits, interspecific diploids produced moderate levels of heterosis in greenhouse experiments. Differences between greenhouse and field trial results can largely be explained by pest damage, which negatively impacted interspecific diploids. Heterosis for the traits that form the basis for biomass yield, including stem growth, foliar, and physiological traits, was quantified, and family-level differences are discussed.

Genetic parameters for Crassostrea virginica and their application to family-based breeding in the mid-Atlantic, USA

A family-based breeding program was established at the Aquaculture Genetics and Breeding Technology Center (ABC) at the Virginia Institute of Marine Science beginning in 2004. Over the course of developing the program, data were acquired to determine the optimal way to structure the breeding population for the Eastern oyster, Crassostrea virginica, in the Chesapeake Bay estuary, and how best to implement our now-operational ‘industrial breeding’ program. Traits studied were survival, total weight, meat yield, and shell shape and decisions were based on estimates of heritability, genetic correlations, and genotype by environment interaction for these traits. Post-hoc, we examined the effect of genetic groups and genetic trends. Genetic variation was abundant and additive, with no evidence of large non-additive effects. Age: age correlations were high, allowing abbreviated field deployment to assess market qualities as early as possible. Survival at high and low salinity were poorly correlated, meaning the gene processes that control survival at each salinity zone are different, and therefore survival at high and low salinities were treated as separate traits. Total weight (indicator of growth rate) was moderately correlated between salinity zones and, while there was some commonality in genetic control across salinities (with 70% of genes in common), total weight was also treated as a separate trait at high and low salinities. Meat yield and shell shape were highly correlated among sites and can therefore be managed as a single trait across all site types. The mass selected lines from our previous work were used as a source of founders, which allowed genetic gains from those lines to be captured in the family program, thus making family-based selection a continuation of previous efforts rather than a restart. The ABC lines have found wide utility not only in the Chesapeake but also in the mid-Atlantic, defined as Rhode Island to South Carolina, USA. Family-based breeding, using the principles encapsulated in this strategy, would be appropriate as a common approach for contiguous breeding efforts for C. virginica along the east coast of the US from the Northeast to the Gulf coasts.

Effects of genomic selection for intramuscular fat content in breast muscle in Chinese local chickens.

Improvements in living standards have resulted in consumers having higher expectations for chicken meat quality. This is particularly true in Asia, where there is high consumer preference for local breeds. Nothing is presently known about the effectiveness of using genomic selection (GS) strategies in chickens to genetically improve meat quality traits that cannot be measured in living potential parents. In this study, 724 Beijing-You chickens were used as a training population; all were genotyped using Illumina 60K SNP chips, and intramuscular fat content in breast muscle (IMFbr ) was measured. Birds in the GS line were selected based on genomic estimated breeding values, IMFbr being the sole trait. Genetic progress in one generation was compared to that from conventional family-based selection, and both were evaluated against random-bred controls. Results showed that relative to the random-bred controls, IMF percentage was improved 9.62% using GS, comparable to the 10.38% improvement using family-based selection. We quantified the effectiveness of GS when applied to a meat quality trait with low heritability in chickens. We plan to introduce custom SNP chips, appropriate for native chicken breeds in China, to assist in applying GS in local breeding and accelerate genetic gain.

Retrospective Evaluation of Marker-Assisted Selection for Resistance to Bacterial Cold Water Disease in Three Generations of a Commercial Rainbow Trout Breeding Population.

Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is an endemic and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. Previously, we have identified SNPs (single nucleotide polymorphisms) associated with BCWD resistance in rainbow trout. The objectives of this study were (1) to validate the SNPs associated with BCWD resistance in a commercial breeding population; and (2) to evaluate retrospectively the accuracy of MAS (marker-assisted selection) for BCWD resistance in this commercial breeding program. Three consecutive generations of the Troutlodge May breeding population were evaluated for BCWD resistance. Based on our previous studies, a panel of 96 SNPs was selected and used to genotype the parents and ten offspring from each of the 138 full-sib families of the 2015 generation, and 37 SNPs associated with BCWD resistance were validated. Thirty-six of the validated SNPs were clustered on chromosomes Omy3, Omy8 and Omy25. Thus, at least three QTL (quantitative trait loci) for BCWD resistance were validated in the 2015 generation. Three SNPs from each QTL region were used for haplotype association analysis. Three haplotypes, Omy3TGG, Omy8GCG and Omy25CGG, were found to be associated with BCWD resistance in the 2015 generation. Retrospective analyses were then performed to evaluate the accuracy of MAS for BCWD resistance using these three favorable haplotypes. The accuracy of MAS was estimated with the Pearson correlation coefficient between the total number of favorable haplotypes in the two parents and the family BCWD survival rates. The Omy8 and Omy25 haplotypes were positively correlated with the family BCWD survival rates across all three generations. The accuracies of MAS using these two haplotypes together were consistently around 0.5, which was equal or greater than the accuracy of the conventional family-based selection in the same generation. In conclusion, we have demonstrated that MAS for BCWD resistance is feasible in this commercial rainbow trout breeding population.

Genomic Tools and Selective Breeding in Molluscs.

The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement. Here we review characteristics of the life history and genetics of molluscs including high fecundity, self-fertilization, high genetic diversity, genetic load, high incidence of deleterious mutations and segregation distortion, and critically assess their impact on the design and effectiveness of selective breeding strategies. A survey of the results of current breeding programs in the literature show that selective breeding with inbreeding control is likely the best strategy for genetic improvement of most molluscs, and on average growth rate can be improved by 10% per generation and disease resistance by 15% per generation across the major farmed species by implementing individual or family-based selection. Rapid advances in sequencing technology have resulted in a wealth of genomic resources for key species with the potential to greatly improve hatchery-based selective breeding of molluscs. In this review, we catalog the range of genomic resources currently available for molluscs of aquaculture interest and discuss the bottlenecks, including lack of high-quality reference genomes and the relatively high cost of genotyping, as well as opportunities for applying genomics-based selection.

Strain evaluation of striped bass (Morone saxatilis) cultured at different salinities

Striped bass (Morone saxatilis) and their hybrids have been well studied and are widely cultured in freshwater ponds as food and gamefish. Recent industry expansion has generated an interest in strain-specific broodstock development for marine netpen and pond culture. In this effort, Atlantic and Gulf coast striped bass strains were cultured in recirculating aquaculture systems (RAS) at different salinities for up to two years and production and morphometric parameters (specific growth, feed conversion, fillet yield, condition factor and stripe patterns) were compared. Striped bass juveniles produced from wild-caught broodstock from rivers in Nova Scotia, Delaware, Virginia, North and South Carolina, Florida, Texas and a selected, domesticated strain were reared in triplicate fresh (0 ppt), brackish (5 ppt) and saltwater recirculating (30 ppt) systems. After one year of age, a subset of fish were implanted with passive integrated transponder (PIT) tags, combined into a larger, “common-garden”, saltwater, recirculating system and monitored over an additional year. Parental broodstock and cultured offspring were fin-clipped and genotyped to identify juvenile family origin. Final weights of fish after one and two years averaged approximately 0.5 and 2.5 kg, respectively and did not differ by water salinity. Growth rates and condition factors differed by strain, but condition factor was not correlated with fillet yield. Consistent with other studies, juvenile fish from South Carolina and Nova Scotia were found to be slow growing compared to migratory Atlantic and Gulf strains. Mixed model analyses showed that family, and family by strain interactions were significant, but accounted for less growth variance than strain alone. These results indicate that family-based selection by strain may be useful in striped bass broodstock development programs.

Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture

BackgroundPreviously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation.MethodsWe compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model. We also assessed the impact of sampling design on the accuracy of GEBV predictions. For these comparisons, we used BCWD survival phenotypes recorded on 7893 fish from 102 families, of which 1473 fish from 50 families had genotypes [57 K single nucleotide polymorphism (SNP) array]. Naïve siblings of the training fish (n = 930 testing fish) were genotyped to predict their GEBV and mated to produce 138 progeny testing families. In the following generation, 9968 progeny were phenotyped to empirically assess the accuracy of GEBV predictions made on their non-phenotyped parents.ResultsThe accuracy of GEBV from all tested GS models were substantially higher than the P-BLUP model EBV. The highest increase in accuracy relative to the P-BLUP model was achieved with BayesB (97.2 to 108.8%), followed by wssGBLUP at iteration 2 (94.4 to 97.1%) and 3 (88.9 to 91.2%) and ssGBLUP (83.3 to 85.3%). Reducing the training sample size to n = ~1000 had no negative impact on the accuracy (0.67 to 0.72), but with n = ~500 the accuracy dropped to 0.53 to 0.61 if the training and testing fish were full-sibs, and even substantially lower, to 0.22 to 0.25, when they were not full-sibs.ConclusionsUsing progeny performance data, we showed that the accuracy of genomic predictions is substantially higher than estimates obtained from the traditional pedigree-based BLUP model for BCWD resistance. Overall, we found that using a much smaller training sample size compared to similar studies in livestock, GS can substantially improve the selection accuracy and genetic gains for this trait in a commercial rainbow trout breeding population.

Mass selection for survival and resistance to OsHV-1 infection in Crassostrea gigas spat in field conditions: response to selection after four generations

Abstract The ostreid herpesvirus 1 (OsHV-1) is one of the major pathogens affecting the Pacific oyster Crassostrea gigas , and numerous mortality outbreaks have been observed worldwide. We report the first results of our experimental breeding program using mass selection focused on survival and resistance to OsHV-1 after four generations of selection for two lines. These lines originated from two stocks of adult wild oysters sampled from the Marennes-Oleron Bay in 2008. Each line was spawned in February 2009 to produce the base populations. Both lines were then either protected from OsHV-1 or tested in the field in 2009 where they were exposed to OsHV-1. For each line during 2010 to 2013, one generation per year was produced using either the survivors of the previous generation for the selected group or the oysters protected from OsHV-1 for the control group. After one generation of selection (G 1 ) for both lines, the mean survival of the selected group was 34.5% compared with 12.3% in the control group. For the fourth generation of selection (G 4 ), the survival of the selected group reached 69.0% and the survival of the control group was 7.3%. The gain in survival of the selected C. gigas spat over the control increased by 22.2%, 43.9%, 50.2% and 61.8% for the G 1 , G 2 , G 3 and G 4 generations, respectively. Our study demonstrates that mass selection for survival and OsHV-1 resistance was successful after four generations of selection, thus indicating a significant genetic improvement for the selected trait. A genotype × size interaction was observed with 55.1% of survival in G 4 when selected spat were transferred at 1 g versus 89.9% of survival when they were transferred at 3 g. Our study is the first to provide some estimates of the realized heritability for disease resistance using a mass selection scheme in an oyster species with values ranging from 0.34 to 0.63 depending on the size of the oysters exposed to OsHV-1. Oysters selected for their higher resistance to OsHV-1 infection in G 4 showed higher growth (58.4 mm – 19.4 g) than controls (51.4 mm – 15.2 g), and mass selection had significantly improved the yield for the selected oysters (13.3 kg) over the controls (1.2 kg). Mass selection could be easily implemented by a commercial hatchery that cannot afford family-based selection that requires the production of numerous families for the base population. Statement of relevance Strong impact on breeding program working on OsHV-1 resistance in C. gigas.

Genomics in aquaculture to better understand species biology and accelerate genetic progress.

Genomics in aquaculture to better understand species biology and accelerate genetic progress.

Detection of QTL in Rainbow Trout Affecting Survival When Challenged with Flavobacterium psychrophilum

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation in survival following challenge with Flavobacterium psychrophilum (Fp), the causative agent of BCWD in rainbow trout (Oncorhynchus mykiss). A family-based selection program to improve resistance was initiated in 2005 at the USDA National Center for Cool and Cold Water Aquaculture. Select crosses were made in 2007 and 2009 to evaluate family-based disease survival using Fp injection challenges. From each putative F₂/BC₁ family generated in 2009, 200-260 fish were challenged in 4-7 replicates per family. Whole genome QTL scans of three F₂/BC₁ families were conducted with about 270 informative microsatellite loci per family spaced at an average interval size of 6 cM throughout the rainbow trout genome. Markers on chromosomes containing QTL were further evaluated in three additional F₂/BC₁ families. The additional F₂/BC₁ families were sire or dam half-sibs (HS) of the initially genome scanned families. Overall, we identified nine major QTL on seven chromosomes that were significant or highly significant with moderate to large effects of at least 13 % of the total phenotypic variance. The largest effect QTL for BCWD resistance explaining up to 40 % of the phenotypic variance was detected on chromosome OMY8 in family 2009070 and in the combined dam HS family 2009069-070. The nine major QTL identified in this study are candidates for fine mapping to identify new markers that are tightly linked to disease resistance loci for using in marker assisted selection strategies.

Development of in vivo haploid inducers for tropical maize breeding programs

Lack of adapted haploid inducers currently impedes adoption of the doubled haploid technology in tropical maize breeding programs. Our objective was to generate inducers with improved adaptation to tropical conditions. We developed segregating generations from crosses between temperate inducers having haploid induction rates (HIR) of 8–10 % and tropical CIMMYT maize lines (CML; HIR = 0 %) and evaluated these for HIR and agronomic performance under tropical lowland field conditions. The applied pedigree breeding scheme comprising mass selection on individual F2 plants for highly heritable and visually scorable traits, followed by family-based selection for HIR and other agronomic characteristics in advanced selfing and backcross (BC) generations seems highly suitable for breeding improved haploid inducers with adaptation to different agroecologies. The most advanced tropical inducer candidates (TIC) combine HIR of up to 10 % with improved pollen production, disease resistance, and plant vigor compared to temperate inducers under tropical conditions. Agronomic characteristics were significantly improved in the BC to CML compared to BC to inducers, while mean HIR of both populations were similar, indicating that backcrossing to the adapted parent was suitable to improve adaptation of new inducers without sacrificing high HIR. When screening random open-pollinated maize accessions, HIR of up to 3 % were observed, suggesting that novel genetic variation may be present in maize accessions that could be exploited to improve HIR in maize. In conclusion, tropical inducer development proceeds well, but evaluation of TIC in multi-environment trials needs to be completed before large-scale dissemination can commence.

Sexual antagonism for testosterone maintains multiple mating behaviour

1. The persistence of multiple mating remains one of the fundamental questions in evolutionary biology. In theory, multiple mating is predicted to improve female fitness cumulatively through direct and/or genetic benefits. However, intra-locus sexual conflicts may potentially constrain or even eliminate these benefits owing to the gender load imposed by sexually antagonistic selection. 2. Here, we tested whether sexually antagonistic selection can maintain the variance in multiple mating behaviour of bank voles (Myodes glareolus) by manipulating the hormone testosterone through artificial selection in the laboratory. Among mammals, testosterone is a sexually dimorphic fitness-related trait under selection and is known to affect mating behaviour. We conducted mating trials in which females derived from family-based selection of testosterone were sequentially paired with four males of different testosterone profiles. 3. We show that artificial selection for high testosterone increased the mating rate of males, but clearly decreased the number of partners that females mated with (and vice versa). Because multiple mating was beneficial for the reproductive success of both sexes, as evidenced by the positive Bateman gradients, the divergent evolutionary interests of testosterone between the sexes can maintain this polygynandrous mating system. 4. Our results highlight how mating rate is concordantly selected in both sexes; however, it is largely influenced by testosterone, which is under sexually antagonistic selection. 5. This study is the first one to emphasise the direct and indirect effects of the endocrine system not only on reproductive physiology and behaviour but also for the evolution of genetic mating strategies in mammals.

Rib and vertebral deformities in rainbow trout ( Oncorhynchus mykiss) explained by a dominant-mutation mechanism

We suggest and investigate a hypothesis of a dominant-mutation mechanism as a possible cause for rib and vertebral deformities found in farmed rainbow trout. We report on an X-ray characterization and a genetic study of a sample of 45 individuals from a rainbow trout broodstock population in the Faroe Islands, which was found to be affected by externally visible rib deformities. 41 fish were from 36 progeny families of 23 sires and 33 dams and 4 fish were of unknown family origin. These fish were from a family-based selection program, year-class 2005, produced from 144 females and 72 males, and the total number of families was 252. In the X-ray characterization both rib deformities and vertebral deformities were found. Only 8 fish were found to be unaffected: 15 fish had both rib and vertebral deformities, 20 fish had only rib deformities and 2 fish had only vertebral deformities. The abnormal ribs were observed as anomalously short and thin bones located inside the abdominal wall. Some had their ends pointing towards the skin, and in the most serious cases, they were perforating the skin. The numbers of rib and vertebral deformities in each individual were assigned rib and vertebral deformity scores. We estimate the proportions in year-class 2005 of deformed fish, of fish with rib deformities and of fish with vertebral deformities, to be 0.82 ± 0.11, 0.78 ± 0.12 and 0.38 ± 0.14, respectively. The 45 individuals were genotyped at nine microsatellite marker loci to investigate potential inbreeding problems. The actual and effective numbers of alleles, n a = 5.8 and n e = 4.2, the heterozygosity, H o = 0.718, and the inbreeding coefficient, F is = 0.034, are similar to the corresponding quantities for Danish strains. The heterozygosity and the inbreeding coefficient indicate a low inbreeding level. A phylogenetic tree and pairwise-relatedness estimates were also constructed from the genotype information and compared with the information from the family-based selection program for rainbow trout. We investigate the dominant-mutation hypothesis and show that genotype counts inferred from the deformity scores are consistent with Hardy–Weinberg equilibrium. From this model, we predict phenotypic segregation ratios of the deformity traits, which are in close agreement with the experimental observations. Finally, we discuss both environmental and genetic causes and conclude in favor of the dominant-mutation mechanism as the most likely cause of the observed deformities.

Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis1

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation for BCWD resistance in our rainbow trout population, and a family-based selection program to improve resistance was initiated at the National Center for Cool and Cold Water Aquaculture (NCCCWA). This study investigated evidence of major trait loci affecting BCWD resistance using only phenotypic data (without using genetic markers) and Bayesian methods of segregation analysis (BMSA). A total of 10,603 juvenile fish from 101 full-sib families corresponding to 3 generations (2005, 2007, and 2009 hatch years) of the NCCCWA population were challenged by intraperitoneal injection with Flavobacterium psychrophilum, the bacterium that causes BCWD. The results from single- and multiple-QTL models of BMSA suggest that 6 to 10 QTL explaining 83 to 89% of phenotypic variance with either codominant or dominant disease-resistant alleles plus polygenic effects may underlie the genetic architecture of BCWD resistance. This study also highlights the importance of polygenic background effects in the genetic variation of BCWD resistance. The polygenic heritability on the observed scale of survival status is slightly larger than that previously reported for rainbow trout BCWD resistance. These findings provide the basis for designing informative crosses for QTL mapping and carrying out genome scans for QTL affecting BCWD resistance in rainbow trout.

Response to selection for bacterial cold water disease resistance in rainbow trout1,2

A family-based selection program was initiated at the National Center for Cool and Cold Water Aquaculture in 2005 to improve resistance to bacterial cold water disease (BCWD) in rainbow trout. The objective of this study was to estimate response to 2 generations of selection. A total of 14,841 juvenile fish (BW = 3.1 g; SD = 1.1 g) from 230 full-sib families and 3 randomly mated control lines were challenged intraperitoneally with Flavobacterium psychrophilum, the bacterium that causes BCWD, and mortalities were observed for 21 d. Selection was applied to family EBV derived from a proportional-hazards frailty (animal) model while constraining rate of inbreeding to <or=1% per generation. After adjusting for nongenetic effects, survival rate of select-line families increased by 24.6 +/- 6.8 and 44.7 +/- 6.7 (cumulative) percentage points after 1 and 2 generations of selection, respectively (P < 0.01). Genetic trend, estimated from a linear animal model that fit genetic group effects, was 19.0 +/- 4.1 percentage points per generation and approached significance (P = 0.07). Heritability estimates from the proportional-hazards frailty model and linear animal model were similar (0.22 and 0.23, respectively), and family EBV from both models were highly correlated (-0.92). Accuracy of selection, estimated as the correlation between mid-parent EBV and progeny survival rate, was 0.20 (P < 0.01) for the proportional-hazards frailty model and 0.18 (P = 0.01) for the linear animal model. Accuracy estimates were not different (P = 0.81) between the models. This study demonstrates that selective breeding can be effective for improving resistance to experimental BCWD challenge in rainbow trout.

Body weight, sexual maturity, and spinal deformity in strains and families of Atlantic cod (Gadus morhua) at two years of age at different locations along the Norwegian coast

Abstract Body weight, occurrence of spinal deformity, and sexual maturity were recorded in 51 full-sib families of the strains coastal and Arctic cod at two years of age. The family groups were located at three sites along the Norwegian coast including Hordaland, Møre and Romsdal (M&amp;R), and Nordland County to detect genetic variation in important production traits and to investigate interactions between genetic composition and production environment. Body weight varied among locations partly owing to different production conditions. There were also large differences among the locations with respect to spinal deformity. M&amp;R had the highest occurrence of spinal deformity (p &lt; 0.001). Comparison of sexual maturity among the locations was made difficult owing to the different ways the trait was recorded. Only small differences were found between coastal and Arctic cod in spinal deformity (p &lt; 0.05 in Hordaland) and sexual maturity (p = 0.06 in M&amp;R), while no differences were found for body weight. Heritability estimates for body weight (0.51), spinal deformity (0.27), and sexual maturity (0.21) indicate the potential for improvement of all three traits by selective breeding using a family-based selection programme. Final recordings at the end of the growing period will provide further information. Genetic correlations estimated between weight and occurrence of spinal deformity (rg = 0.50) suggest that caution be used when selecting for growth, and that a need exists for including spinal deformity in the selection index. No significant correlations were found between these two traits and the incidence of sexual maturity.