The heritable landscape of near-infrared and Raman spectroscopic measurements to improve lipid content in Atlantic salmon fillets.

BACKGROUND: Product quality and production efficiency of Atlantic salmon are, to a large extent, influenced by the deposition and depletion of lipid reserves. Fillet lipid content is a heritable trait and is unfavourably correlated with growth, thus genetic management of fillet lipid content is needed for sustained genetic progress in these two traits. The laboratory-based reference method for recording fillet lipid content is highly accurate and precise but, at the same time, expensive, time-consuming, and destructive. Here, we test the use of rapid and cheaper vibrational spectroscopy methods, namely near-infrared (NIR) and Raman spectroscopy both as individual phenotypes and phenotypic predictors of lipid content in Atlantic salmon. RESULTS: Remarkably, 827 of the 1500 individual Raman variables (i.e. Raman shifts) of the Raman spectrum were significantly heritable (heritability (h2) ranging from 0.15 to 0.65). Similarly, 407 of the 2696 NIR spectral landscape variables (i.e. wavelengths) were significantly heritable (h2 = 0.27-0.40). Both Raman and NIR spectral landscapes had significantly heritable regions, which are also informative in spectroscopic predictions of lipid content. Partial least square predicted lipid content using Raman and NIR spectra were highly concordant and highly genetically correlated with the lipid content values ([Formula: see text] = 0.91-0.98) obtained with the reference method using Lin's concordance correlation coefficient (CCC = 0.63-0.90), and were significantly heritable ([Formula: see text] = 0.52-0.67). CONCLUSIONS: Both NIR and Raman spectral landscapes show substantial additive genetic variation and are highly genetically correlated with the reference method. These findings lay down the foundation for rapid spectroscopic measurement of lipid content in salmonid breeding programmes.

Management of Genetic Diversity in the Era of Genomics.

Management of genetic diversity aims to (i) maintain heterozygosity, which ameliorates inbreeding depression and loss of genetic variation at loci that may become of importance in the future; and (ii) avoid genetic drift, which prevents deleterious recessives (e.g., rare disease alleles) from drifting to high frequency, and prevents random drift of (functional) traits. In the genomics era, genomics data allow for many alternative measures of inbreeding and genomic relationships. Genomic relationships/inbreeding can be classified into (i) homozygosity/heterozygosity based (e.g., molecular kinship matrix); (ii) genetic drift-based, i.e., changes of allele frequencies; or (iii) IBD-based, i.e., SNPs are used in linkage analyses to identify IBD segments. Here, alternative measures of inbreeding/relationship were used to manage genetic diversity in genomic optimal contribution (GOC) selection schemes. Contrary to classic inbreeding theory, it was found that drift and homozygosity-based inbreeding could differ substantially in GOC schemes unless diversity management was based upon IBD. When using a homozygosity-based measure of relationship, the inbreeding management resulted in allele frequency changes toward 0.5 giving a low rate of increase in homozygosity for the panel used for management, but not for unmanaged neutral loci, at the expense of a high genetic drift. When genomic relationship matrices were based on drift, following VanRaden and as in GCTA, drift was low at the expense of a high rate of increase in homozygosity. The use of IBD-based relationship matrices for inbreeding management limited both drift and the homozygosity-based rate of inbreeding to their target values. Genetic improvement per percent of inbreeding was highest when GOC used IBD-based relationships irrespective of the inbreeding measure used. Genomic relationships based on runs of homozygosity resulted in very high initial improvement per percent of inbreeding, but also in substantial discrepancies between drift and homozygosity-based rates of inbreeding, and resulted in a drift that exceeded its target value. The discrepancy between drift and homozygosity-based rates of inbreeding was caused by a covariance between initial allele frequency and the subsequent change in frequency, which becomes stronger when using data from whole genome sequence.

Genomic selection strategies to improve maternal traits in Norwegian White Sheep.

This study tested and compared different implementation strategies for genomic selection for Norwegian White Sheep, aiming to increase genetic gain for maternal traits. These strategies were evaluated for their genetic gain ingrowth, carcass and maternal traits, total genetic gain, a weighted sum of the gain in each trait and rates of inbreeding through a full-scale stochastic simulation. Results showed genomic selection schemes to increase genetic gain for maternal traits but reduced genetic gain for other traits. This could also be obtained by selecting rams for artificial selection at a higher age. Implementation of genomic selection in the current breeding structure increased genetic gain for maternal traits up to 57%, outcompeted by reducing the generation interval for artificial insemination rams from current 3 to 2 years. Then, total genetic gain for maternal traits increased by 65%-77% and total genetic gain by18%-20%, but at increased rates of inbreeding.

Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations.

BACKGROUND: Two distinct populations have been extensively studied in Atlantic cod (Gadus morhua L.): the Northeast Arctic cod (NEAC) population and the coastal cod (CC) population. The objectives of the current study were to identify genomic islands of divergence and to propose an approach to quantify the strength of selection pressures using whole-genome single nucleotide polymorphism (SNP) data. After applying filtering criteria, information on 93 animals (9 CC individuals, 50 NEAC animals and 34 CC × NEAC crossbred individuals) and 3,123,434 autosomal SNPs were used. RESULTS: Four genomic islands of divergence were identified on chromosomes 1, 2, 7 and 12, which were mapped accurately based on SNP data and which extended in size from 11 to 18 Mb. These regions differed considerably between the two populations although the differences in the rest of the genome were small due to considerable gene flow between the populations. The estimates of selection pressures showed that natural selection was substantially more important than genetic drift in shaping these genomic islands. Our data confirmed results from earlier publications that suggested that genomic islands are due to chromosomal rearrangements that are under strong selection and reduce recombination between rearranged and non-rearranged segments. CONCLUSIONS: Our findings further support the hypothesis that selection and reduced recombination in genomic islands may promote speciation between these two populations although their habitats overlap considerably and migrations occur between them.

Dietary Fish Oil Alters DNA Methylation of Genes Involved in Polyunsaturated Fatty Acid Biosynthesis in Muscle and Liver of Atlantic Salmon (Salmo salar).

Adequate dietary supply of eicosapentaenoic acid (20:5n-3) and docosahexaenoic acid (22:6n-3) is required to maintain health and growth of Atlantic salmon (Salmo salar). However, salmon can also convert α-linolenic acid (18:3n-3) into eicosapentaenoic acid (20:5n-3) and docosahexaenoic acid (22:6n-3) by sequential desaturation and elongation reactions, which can be modified by 20:5n-3 and 22:6n-3 intake. In mammals, dietary 20:5n-3 + 22:6n-3 intake can modify Fads2 expression (Δ6 desaturase) via altered DNA methylation of its promoter. Decreasing dietary fish oil (FO) has been shown to increase Δ5fad expression in salmon liver. However, it is not known whether this is associated with changes in the DNA methylation of genes involved in polyunsaturated fatty acid synthesis. To address this, we investigated whether changing the proportions of dietary FO and vegetable oil altered the DNA methylation of Δ6fad_b, Δ5fad, Elovl2, and Elovl5_b promoters in liver and muscle from Atlantic salmon and whether any changes were associated with mRNA expression. Higher dietary FO content increased the proportions of 20:5n-3 and 22:6n-3 and decreased Δ6fad_b mRNA expression in liver, but there was no effect on Δ5fad, Elovl2, and Elovl5_b expression. There were significant differences between liver and skeletal muscle in the methylation of individual CpG loci in all four genes studied. Methylation of individual Δ6fad_b CpG loci was negatively related to its expression and to proportions of 20:5n-3 and 22:6n-3 in the liver. These findings suggest variations in dietary FO can induce gene-, CpG locus-, and tissue-related changes in DNA methylation in salmon.

Individual differences in EPA and DHA content of Atlantic salmon are associated with gene expression of key metabolic processes.

The aim of this study was to explore how individual differences in content of the omega-3 fatty acids EPA and DHA in skeletal muscle of slaughter-sized Atlantic salmon, are associated with expression of genes involved in key metabolic processes. All experimental fish were fed the same diet throughout life and fasted for 14 days prior to slaughter. Still, there were relatively large individual variations in EPA and DHA content of skeletal muscle. Higher DHA content was concurrent with increased expression of genes of the glycolytic pathway and the production of pyruvate and lactate, whereas EPA was associated with increased expression of pentose phosphate pathway and glycogen breakdown genes. Furthermore, EPA, but not DHA, was associated with expression of genes involved in insulin signaling. Expression of genes specific for skeletal muscle function were positively associated with both EPA and DHA. EPA and DHA were also associated with expression of genes related to eicosanoid and resolvin production. EPA was negatively associated with expression of genes involved in lipid catabolism. Thus, a possible reason why some individuals have a higher level of EPA in the skeletal muscle is that they deposit - rather than oxidize - EPA for energy.

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish.

Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.

Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing.

BACKGROUND: Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90-100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1-49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. RESULTS: The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28-16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19-24% increase when using genomic information. CONCLUSION: The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs.

Genetic effects of fatty acid composition in muscle of Atlantic salmon.

BACKGROUND: The replacement of fish oil (FO) and fishmeal with plant ingredients in the diet of farmed Atlantic salmon has resulted in reduced levels of the health-promoting long-chain polyunsaturated omega-3 fatty acids (n-3 LC-PUFA) eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) in their filets. Previous studies showed the potential of selective breeding to increase n-3 LC-PUFA levels in salmon tissues, but knowledge on the genetic parameters for individual muscle fatty acids (FA) and their relationships with other traits is still lacking. Thus, we estimated genetic parameters for muscle content of individual FA, and their relationships with lipid deposition traits, muscle pigmentation, sea lice and pancreas disease in slaughter-sized Atlantic salmon. Our aim was to evaluate the selection potential for increased n-3 LC-PUFA content and provide insight into FA metabolism in Atlantic salmon muscle. RESULTS: Among the n-3 PUFA, proportional contents of alpha-linolenic acid (ALA; 18:3n-3) and DHA had the highest heritability (0.26) and EPA the lowest (0.09). Genetic correlations of EPA and DHA proportions with muscle fat differed considerably, 0.60 and 0.01, respectively. The genetic correlation of DHA proportion with visceral fat was positive and high (0.61), whereas that of EPA proportion with lice density was negative. FA that are in close proximity along the bioconversion pathway showed positive correlations with each other, whereas the start (ALA) and end-point (DHA) of the pathway were negatively correlated (- 0.28), indicating active bioconversion of ALA to DHA in the muscle of fish fed high FO-diet. CONCLUSIONS: Since contents of individual FA in salmon muscle show additive genetic variation, changing FA composition by selective breeding is possible. Taken together, our results show that the heritabilities of individual n-3 LC-PUFA and their genetic correlations with other traits vary, which indicates that they play different roles in muscle lipid metabolism, and that proportional muscle contents of EPA and DHA are linked to body fat deposition. Thus, different selection strategies can be applied in order to increase the content of healthy omega-3 FAin the salmon muscle. We recommend selection for the proportion of EPA + DHA in the muscle because they are both essential FA and because such selection has no clear detrimental effects on other traits.

Mating structures for genomic selection breeding programs in aquaculture.

BACKGROUND: In traditional family-based aquaculture breeding, each sire is mated to two dams in order to separate the sire's genetic effect from other family effects. Factorial mating involves more mates per sire and/or dam and result in more but smaller full- and/or half-sib families. For traits measured on sibs of selection candidates, factorial mating increases intensity of selection between families when selection is on traditional best linear unbiased prediction (BLUP) estimated breeding values (TRAD-EBV). However, selection on genome-wide estimated breeding values (GW-EBV), uses both within- and between-family effects and the advantage of factorial mating is less obvious. Our aim was to compare by computer simulation the impact of various factorial mating strategies for truncation selection on TRAD-EBV versus GW-EBV on rates of inbreeding, accuracy of selection and genetic gain for two traits, i.e. one measured on selection candidates (CAND-TRAIT) and one on their sibs (SIB-TRAIT). RESULTS: Sire:dam mating ratios of 1:1, 2:2 or 10:10 were tested with 100, 200 or 1000 families produced from a constant number of parents (100 sires and 100 dams), and a mating ratio of 1:2 with 200 families produced from 100 sires and 200 dams. With GW-EBV, changing the mating ratio from 1:1 to 10:10 had a limited effect on genetic gain (less than 5 %) for both CAND-TRAIT and SIB-TRAIT, whereas with TRAD-EBV, selection intensity increased for SIB-TRAIT and genetic gain increased by 41 and 77 % for schemes with 3000 and 12,000 selection candidates, respectively. For both GW-EBV and TRAD-EBV, rates of inbreeding decreased by up to ~30 % when the mating ratio was changed from 1:1 to 10:10 for schemes with 3000 to 12,000 selection candidates. Similar results were found for alternative heritabilities of SIB-TRAIT and total number of tested sibs. CONCLUSIONS: Changing the sire:dam mating ratio from 1:1 to 10:10 increased genetic gain substantially with TRAD-EBV, mainly through increased selection intensity for the SIB-TRAIT, whereas with GW-EBV, it had a limited effect on genetic gain for both traits. Rates of inbreeding decreased for both selection methods.

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Genetic heterogeneity of within-family variance of body weight in Atlantic salmon (Salmo salar).

BACKGROUND: Canalization is defined as the stability of a genotype against minor variations in both environment and genetics. Genetic variation in degree of canalization causes heterogeneity of within-family variance. The aims of this study are twofold: (1) quantify genetic heterogeneity of (within-family) residual variance in Atlantic salmon and (2) test whether the observed heterogeneity of (within-family) residual variance can be explained by simple scaling effects. RESULTS: Analysis of body weight in Atlantic salmon using a double hierarchical generalized linear model (DHGLM) revealed substantial heterogeneity of within-family variance. The 95% prediction interval for within-family variance ranged from ~0.4 to 1.2 kg2, implying that the within-family variance of the most extreme high families is expected to be approximately three times larger than the extreme low families. For cross-sectional data, DHGLM with an animal mean sub-model resulted in severe bias, while a corresponding sire-dam model was appropriate. Heterogeneity of variance was not sensitive to Box-Cox transformations of phenotypes, which implies that heterogeneity of variance exists beyond what would be expected from simple scaling effects. CONCLUSIONS: Substantial heterogeneity of within-family variance was found for body weight in Atlantic salmon. A tendency towards higher variance with higher means (scaling effects) was observed, but heterogeneity of within-family variance existed beyond what could be explained by simple scaling effects. For cross-sectional data, using the animal mean sub-model in the DHGLM resulted in biased estimates of variance components, which differed substantially both from a standard linear mean animal model and a sire-dam DHGLM model. Although genetic differences in canalization were observed, selection for increased canalization is difficult, because there is limited individual information for the variance sub-model, especially when based on cross-sectional data. Furthermore, potential macro-environmental changes (diet, climatic region, etc.) may make genetic heterogeneity of variance a less stable trait over time and space.

A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values.

BACKGROUND: Genomic selection can increase genetic gain within aquaculture breeding programs, but the high costs related to high-density genotyping of a large number of individuals would make the breeding program expensive. In this study, a low-cost method using low-density genotyping of pre-selected candidates and their sibs was evaluated by stochastic simulation. METHODS: A breeding scheme with selection for two traits, one measured on candidates and one on sibs was simulated. Genomic breeding values were estimated within families and combined with conventional family breeding values for candidates that were pre-selected based on conventional BLUP breeding values. This strategy was compared with a conventional breeding scheme and a full genomic selection program for which genomic breeding values were estimated across the whole population. The effects of marker density, level of pre-selection and number of sibs tested and genotyped for the sib-trait were studied. RESULTS: Within-family genomic breeding values increased genetic gain by 15% and reduced rate of inbreeding by 15%. Genetic gain was robust to a reduction in marker density, with only moderate reductions, even for very low densities. Pre-selection of candidates down to approximately 10% of the candidates before genotyping also had minor effects on genetic gain, but depended somewhat on marker density. The number of test-individuals, i.e. individuals tested for the sib-trait, affected genetic gain, but the fraction of the test-individuals genotyped only affected the relative contribution of each trait to genetic gain. CONCLUSIONS: A combination of genomic within-family breeding values, based on low-density genotyping, and conventional BLUP family breeding values was shown to be a possible low marker density implementation of genomic selection for species with large full-sib families for which the costs of genotyping must be kept low without compromising the effect of genomic selection on genetic gain.

Strategies for implementing genomic selection in family-based aquaculture breeding schemes: double haploid sib test populations.

BACKGROUND: Simulation studies have shown that accuracy and genetic gain are increased in genomic selection schemes compared to traditional aquaculture sib-based schemes. In genomic selection, accuracy of selection can be maximized by increasing the precision of the estimation of SNP effects and by maximizing the relationships between test sibs and candidate sibs. Another means of increasing the accuracy of the estimation of SNP effects is to create individuals in the test population with extreme genotypes. The latter approach was studied here with creation of double haploids and use of non-random mating designs. METHODS: Six alternative breeding schemes were simulated in which the design of the test population was varied: test sibs inherited maternal (Mat), paternal (Pat) or a mixture of maternal and paternal (MatPat) double haploid genomes or test sibs were obtained by maximum coancestry mating (MaxC), minimum coancestry mating (MinC), or random (RAND) mating. Three thousand test sibs and 3000 candidate sibs were genotyped. The test sibs were recorded for a trait that could not be measured on the candidates and were used to estimate SNP effects. Selection was done by truncation on genome-wide estimated breeding values and 100 individuals were selected as parents each generation, equally divided between both sexes. RESULTS: Results showed a 7 to 19% increase in selection accuracy and a 6 to 22% increase in genetic gain in the MatPat scheme compared to the RAND scheme. These increases were greater with lower heritabilities. Among all other scenarios, i.e. Mat, Pat, MaxC, and MinC, no substantial differences in selection accuracy and genetic gain were observed. CONCLUSIONS: In conclusion, a test population designed with a mixture of paternal and maternal double haploids, i.e. the MatPat scheme, increases substantially the accuracy of selection and genetic gain. This will be particularly interesting for traits that cannot be recorded on the selection candidates and require the use of sib tests, such as disease resistance and meat quality.

Genomic selection requires genomic control of inbreeding.

BACKGROUND: In the past, pedigree relationships were used to control and monitor inbreeding because genomic relationships among selection candidates were not available until recently. The aim of this study was to understand the consequences for genetic variability across the genome when genomic information is used to estimate breeding values and in managing the inbreeding generated in the course of selection on genome-enhanced estimated breeding values. METHODS: These consequences were measured by genetic gain, pedigree- and genome-based rates of inbreeding, and local inbreeding across the genome. Breeding schemes were compared by simulating truncation selection or optimum contribution selection with a restriction on pedigree- or genome-based inbreeding, and with selection using estimated breeding values based on genome- or pedigree-based BLUP. Trait information was recorded on full-sibs of the candidates. RESULTS: When the information used to estimate breeding values and to constrain rates of inbreeding were either both pedigree-based or both genome-based, rates of genomic inbreeding were close to the desired values and the identical-by-descent profiles were reasonably uniform across the genome. However, with a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding were much higher than expected. With pedigree-instead of genome-based estimated breeding values, the impact of the largest QTL on the breeding values was much smaller, resulting in a more uniform genome-wide identical-by-descent profile but genomic rates of inbreeding were still higher than expected based on pedigree relationships, because they measure the inbreeding at a neutral locus not linked to any QTL. Neutral loci did not exist here, where there were 100 QTL on each chromosome. With a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding substantially exceeded the value of its constraint. In contrast, with a genome-based inbreeding constraint and genome-based estimated breeding values, marker frequencies changed, but this change was limited by the inbreeding constraint at the marker position. CONCLUSIONS: To control inbreeding, it is necessary to account for it on the same basis as what is used to estimate breeding values, i.e. pedigree-based inbreeding control with traditional pedigree-based BLUP estimated breeding values and genome-based inbreeding control with genome-based estimated breeding values.

Effect of non-random mating on genomic and BLUP selection schemes.

BACKGROUND: The risk of long-term unequal contribution of mating pairs to the gene pool is that deleterious recessive genes can be expressed. Such consequences could be alleviated by appropriately designing and optimizing breeding schemes i.e. by improving selection and mating procedures. METHODS: We studied the effect of mating designs, random, minimum coancestry and minimum covariance of ancestral contributions on rate of inbreeding and genetic gain for schemes with different information sources, i.e. sib test or own performance records, different genetic evaluation methods, i.e. BLUP or genomic selection, and different family structures, i.e. factorial or pair-wise. RESULTS: Results showed that substantial differences in rates of inbreeding due to mating design were present under schemes with a pair-wise family structure, for which minimum coancestry turned out to be more effective to generate lower rates of inbreeding. Specifically, substantial reductions in rates of inbreeding were observed in schemes using sib test records and BLUP evaluation. However, with a factorial family structure, differences in rates of inbreeding due mating designs were minor. Moreover, non-random mating had only a small effect in breeding schemes that used genomic evaluation, regardless of the information source. CONCLUSIONS: It was concluded that minimum coancestry remains an efficient mating design when BLUP is used for genetic evaluation or when the size of the population is small, whereas the effect of non-random mating is smaller in schemes using genomic evaluation.

The use of communal rearing of families and DNA pooling in aquaculture genomic selection schemes.

BACKGROUND: Traditional family-based aquaculture breeding programs, in which families are kept separately until individual tagging and most traits are measured on the sibs of the candidates, are costly and require a high level of reproductive control. The most widely used alternative is a selection scheme, where families are reared communally and the candidates are selected based on their own individual measurements of the traits under selection. However, in the latter selection schemes, inclusion of new traits depends on the availability of non-invasive techniques to measure the traits on selection candidates. This is a severe limitation of these schemes, especially for disease resistance and fillet quality traits. METHODS: Here, we present a new selection scheme, which was validated using computer simulations comprising 100 families, among which 1, 10 or 100 were reared communally in groups. Pooling of the DNA from 2000, 20000 or 50000 test individuals with the highest and lowest phenotypes was used to estimate 500, 5000 or 10000 marker effects. One thousand or 2000 out of 20000 candidates were preselected for a growth-like trait. These pre-selected candidates were genotyped, and they were selected on their genome-wide breeding values for a trait that could not be measured on the candidates. RESULTS: A high accuracy of selection, i.e. 0.60-0.88 was obtained with 20000-50000 test individuals but it was reduced when only 2000 test individuals were used. This shows the importance of having large numbers of phenotypic records to accurately estimate marker effects. The accuracy of selection decreased with increasing numbers of families per group. CONCLUSIONS: This new selection scheme combines communal rearing of families, pre-selection of candidates, DNA pooling and genomic selection and makes multi-trait selection possible in aquaculture selection schemes without keeping families separately until individual tagging is possible. The new scheme can also be used for other farmed species, for which the cost of genotyping test individuals may be high, e.g. if trait heritability is low.

Combined detection and introgression of QTL in outbred populations.

BACKGROUND: Detecting a QTL is only the first step in genetic improvement programs. When a QTL with desirable characteristics is found, e.g. in a wild or unimproved population, it may be interesting to introgress the detected QTL into the commercial population. One approach to shorten the time needed for introgression is to combine both QTL identification and introgression, into a single step. This combines the strengths of fine mapping and backcrossing and paves the way for introgression of desirable but unknown QTL into recipient animal and plant lines. METHODS: The method consisting in combining QTL mapping and gene introgression has been extended from inbred to outbred populations in which QTL allele frequencies vary both in recipient and donor lines in different scenarios and for which polygenic effects are included in order to model background genes. The effectiveness of the combined QTL detection and introgression procedure was evaluated by simulation through four backcross generations. RESULTS: The allele substitution effect is underestimated when the favourable QTL allele is not fixed in the donor line. This underestimation is proportional to the frequency differences of the favourable QTL allele between the lines. In most scenarios, the estimates of the QTL location are unbiased and accurate. The retained donor chromosome segment and linkage drag are similar to expected values from other published studies. CONCLUSIONS: In general, our results show that it is possible to combine QTL detection and introgression even in outbred species. Separating QTL mapping and introgression processes is often thought to be longer and more costly. However, using a combined process saves at least one generation. With respect to the linkage drag and obligatory drag, the results of the combined detection and introgression scheme are very similar to those of traditional introgression schemes.

Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect.

BACKGROUND: When estimating marker effects in genomic selection, estimates of marker effects may simply act as a proxy for pedigree, i.e. their effect may partially be attributed to their association with superior parents and not be linked to any causative QTL. Hence, these markers mainly explain polygenic effects rather than QTL effects. However, if a polygenic effect is included in a Bayesian model, it is expected that the estimated effect of these markers will be more persistent over generations without having to re-estimate the marker effects every generation and will result in increased accuracy and reduced bias. METHODS: Genomic selection using the Bayesian method, 'BayesB' was evaluated for different marker densities when a polygenic effect is included (GWpEBV) and not included (GWEBV) in the model. Linkage disequilibrium and a mutation drift balance were obtained by simulating a population with a Ne of 100 over 1,000 generations. RESULTS: Accuracy of selection was slightly higher for the model including a polygenic effect than for the model not including a polygenic effect whatever the marker density. The accuracy decreased in later generations, and this reduction was stronger for lower marker densities. However, no significant difference in accuracy was observed between the two models. The linear regression of TBV on GWEBV and GWpEBV was used as a measure of bias. The regression coefficient was more stable over generations when a polygenic effect was included in the model, and was always between 0.98 and 1.00 for the highest marker density. The regression coefficient decreased more quickly with decreasing marker density. CONCLUSIONS: Including a polygenic effect had no impact on the selection accuracy, but showed reduced bias, which is especially important when estimates of genome-wide markers are used to estimate breeding values over more than one generation.