Selection of grandparental combinations as a procedure designed to make use of dominance genetic effects

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Response: Commentary: Past, present and future of epigenetics applied to livestock breeding

Following our recent Review article (González-Recio et al., 2015), we received correspondence by Steele (2016). We thank Dr. Steele for his comments, which provide a thorough review of his work on human immunology, which has persuaded him that “hard types of soma-to-germline transfer are ongoing at very high frequency in human immune system germlines.” His and other researchers' studies on reverse transcriptase (RT) based feedback mechanisms showed that RNA could be retrotranscripted to DNA, and it can be inserted into the mammalian germline, and therefore be transferred to the progeny

Changes in allele frequencies when different genomic coancestry matrices are used for maintaining genetic diversity

A main objective in conservation programs is to maintain genetic variability. This can be achieved using the Optimal Contributions (OC) method that optimizes the contributions of candidates to the next generation by minimizing the global coancestry. However, it has been argued that maintaining allele frequencies is also important. Different genomic coancestry matrices can be used on OC and the choice of the matrix will have an impact not only on the genetic variability maintained, but also on the change in allele frequencies. The objective of this study was to evaluate, through stochastic simulations, the genetic variability maintained and the trajectory of allele frequencies when using two different genomic coancestry matrices in OC to minimize the loss of diversity: (i) the matrix based on deviations of the observed number of alleles shared between two individuals from the expected numbers under Hardy-Weinberg equilibrium (θLH); and (ii) the matrix based on VanRaden's genomic relationship matrix (θVR). The results indicate that the use of θLH resulted in a higher genetic variability than the use of θVR. However, the use of θVR maintained allele frequencies closer to those in the base population than the use of θLH.The research leading to these results has received funding from the Ministerio de Ciencia, Innovación y Universidades, Spain (grant CGL2016-75904-C2-2-P). R. Pong-Wong is funded by the European Union’s Horizon 2020 research and innovation programme under the Grant Agreement n◦772787 (SMARTER) and the Biotechnology and Biological Sciences Research Council through Institute Strategic Programme Grant funding (BBS/E/D/30002275).Peer reviewe

A note on mate allocation for dominance handling in genomic selection

Estimation of non-additive genetic effects in animal breeding is important because it increases the accuracy of breeding value prediction and the value of mate allocation procedures. With the advent of genomic selection these ideas should be revisited. The objective of this study was to quantify the efficiency of including dominance effects and practising mating allocation under a whole-genome evaluation scenario. Four strategies of selection, carried out during five generations, were compared by simulation techniques. In the first scenario (MS), individuals were selected based on their own phenotypic information. In the second (GSA), they were selected based on the prediction generated by the Bayes A method of whole-genome evaluation under an additive model. In the third (GSD), the model was expanded to include dominance effects. These three scenarios used random mating to construct future generations, whereas in the fourth one (GSD + MA), matings were optimized by simulated annealing. The advantage of GSD over GSA ranges from 9 to 14% of the expected response and, in addition, using mate allocation (GSD + MA) provides an additional response ranging from 6% to 22%. However, mate selection can improve the expected genetic response over random mating only in the first generation of selection. Furthermore, the efficiency of genomic selection is eroded after a few generations of selection, thus, a continued collection of phenotypic data and re-evaluation will be required

QTL detection for Aeromonas salmonicida resistance related traits in turbot (Scophthalmus maximus)

<p>Abstract</p> <p>Background</p> <p>Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new disease pressures. The turbot is one of the most promising European aquaculture species. Furunculosis, caused by the bacterium <it>Aeromonas salmonicida</it>, produces important losses to turbot industry. An appealing solution is to achieve more robust broodstock, which can prevent or diminish the devastating effects of epizooties. Genomics strategies have been developed in turbot to look for candidate genes for resistance to furunculosis and a genetic map with appropriate density to screen for genomic associations has been also constructed. In the present study, a genome scan for QTL affecting resistance and survival to <it>A. salmonicida </it>in four turbot families was carried out. The objectives were to identify consistent QTL using different statistical approaches (linear regression and maximum likelihood) and to locate the tightest associated markers for their application in genetic breeding strategies.</p> <p>Results</p> <p>Significant QTL for resistance were identified by the linear regression method in three linkage groups (LGs 4, 6 and 9) and for survival in two LGs (6 and 9). The maximum likelihood methodology identified QTL in three LGs (5, 6 and 9) for both traits. Significant association between disease traits and genotypes was detected for several markers, some of them explaining up to 17% of the phenotypic variance. We also identified candidate genes located in the detected QTL using data from previously mapped markers.</p> <p>Conclusions</p> <p>Several regions controlling resistance to <it>A. salmonicida </it>in turbot have been detected. The observed concordance between different statistical methods at particular linkage groups gives consistency to our results. The detected associated markers could be useful for genetic breeding strategies. A finer mapping will be necessary at the detected QTL intervals to narrow associations and around the closely associated markers to look for candidate genes through comparative genomics or positional cloning strategies. The identification of associated variants at specific genes will be essential, together with the QTL associations detected in this study, for future marker assisted selection programs.</p

Detection of growth-related QTL in turbot (Scophthalmus maximus)

<p>Abstract</p> <p>Background</p> <p>The turbot (<it>Scophthalmus maximus</it>) is a highly appreciated European aquaculture species. Growth related traits constitute the main goal of the ongoing genetic breeding programs of this species. The recent construction of a consensus linkage map in this species has allowed the selection of a panel of 100 homogeneously distributed markers covering the 26 linkage groups (LG) suitable for QTL search. In this study we addressed the detection of QTL with effect on body weight, length and Fulton's condition factor.</p> <p>Results</p> <p>Eight families from two genetic breeding programs comprising 814 individuals were used to search for growth related QTL using the panel of microsatellites available for QTL screening. Two different approaches, maximum likelihood and regression interval mapping, were used in order to search for QTL. Up to eleven significant QTL were detected with both methods in at least one family: four for weight on LGs 5, 14, 15 and 16; five for length on LGs 5, 6, 12, 14 and 15; and two for Fulton's condition factor on LGs 3 and 16. In these LGs an association analysis was performed to ascertain the microsatellite marker with the highest apparent effect on the trait, in order to test the possibility of using them for marker assisted selection.</p> <p>Conclusions</p> <p>The use of regression interval mapping and maximum likelihood methods for QTL detection provided consistent results in many cases, although the high variation observed for traits mean among families made it difficult to evaluate QTL effects. Finer mapping of detected QTL, looking for tightly linked markers to the causative mutation, and comparative genomics are suggested to deepen in the analysis of QTL in turbot so they can be applied in marker assisted selection programs.</p

Assessment of heterogeneity of residual variances using changepoint techniques

Several studies using test-day models show clear heterogeneity of residual variance along lactation. A changepoint technique to account for this heterogeneity is proposed. The data set included 100 744 test-day records of 10 869 Holstein-Friesian cows from northern Spain. A three-stage hierarchical model using the Wood lactation function was employed. Two unknown changepoints at times T1 and T2, (0 <T1 <T2 <tmax), with continuity of residual variance at these points, were assumed. Also, a nonlinear relationship between residual variance and the number of days of milking t was postulated. The residual variance at a time t() in the lactation phase i was modeled as: for (i = 1, 2, 3), where λι is a phase-specific parameter. A Bayesian analysis using Gibbs sampling and the Metropolis-Hastings algorithm for marginalization was implemented. After a burn-in of 20 000 iterations, 40 000 samples were drawn to estimate posterior features. The posterior modes of T1, T2, λ1, λ2, λ3, , , were 53.2 and 248.2 days; 0.575, -0.406, 0.797 and 0.702, 34.63 and 0.0455 kg2, respectively. The residual variance predicted using these point estimates were 2.64, 6.88, 3.59 and 4.35 kg2 at days of milking 10, 53, 248 and 305, respectively. This technique requires less restrictive assumptions and the model has fewer parameters than other methods proposed to account for the heterogeneity of residual variance during lactation

Effect of linkage on the control of inbreeding in selection programmes

Selection and mating methods for controlling inbreeding in selection programmes are based on relationships obtained from pedigrees. The efficiency of these methods has always been tested by studies using genetic models of independent loci. However, under linkage the rate of inbreeding obtained from pedigrees can be different from the probability of identity by descent of genes. We simulated a quantitative trait under artificial selection controlled by a large number of genes spread on genome regions of different sizes. A method to control inbreeding based on minimising the average coancestry of selected individuals with a restriction in the loss of selection response, and a mating procedure to control inbreeding were applied. These methods, that use coancestry relationships, were not effective in controlling inbreeding when the genome sizes were smaller than five morgans or so. However, for larger genome sizes the methods were sufficiently efficient. For very tight linkage, methods that utilise molecular information from markers should be used. We finally discuss the effects of the selection of individual major genes on the neutral variability of adjacent genome regions