Genetic correlation and response to selection in simulated populations

Summary Effects of truncation selection of a primary trait upon genetic correlation with a secondary trait were examined over 30 generations in genetic populations simulated by computer. Populations were 24 males and 24 females mated randomly with replacement; number of offspring was determined by intensity of selection. Each trait was controlled by 48 loci segregating independently, effects were equal at every locus, and gene frequency was arbitrarily set at 0.5 at each locus in the initial generation. All combinations of three genetic correlations, three intensities of selection, and three environmental variances were simulated. Gene action was additive. Genetic correlation was set by number of loci which affected both traits and was measured each generation as the product-moment correlation of genotypic values and estimated by two methods of combining phenotypic covariances between parent and offspring.Genetic correlations in each offspring generation remained consistently near initial correlations for all environmental variances when fraction of offspring saved as parents was as large as one-half. When the fraction of offspring saved was as small as one-fifth, genetic correlations decreased but most rapidly with heritability high and after the 15th generation of selection. Truncation selection caused genetic correlation to decrease in those offspring selected to become parents of the next generation. Amount of reduction depended on heritability of the selected trait rather than on degree of truncation selection. Estimates of genetic correlation from phenotypic covariances between parent and offspring fluctuated markedly from real correlations in the small populations simulated.Michigan Agricultural Experiment Station Journal Article 4836. Part of North Central Regional Project NC-2.     

Genetic correlation and response to selection in simulated populations

Summary Effects of truncation selection of a primary trait upon genetic correlation between the primary trait and an unselected secondary trait were observed during 30 generations. Populations were 24 male and 24 female parents per generation randomly mated with replacement, the number of offspring set by intensity of selection. Each trait was controlled by genes with equal effects and complete dominance segregating independently from starting frequencies of 0.5 at each of 48 loci. Three levels each of genetic correlation, selection, and environmental variation were simulated.Genetic correlation decreased faster under more intense selection by lower than by upper truncation but behaved similarly in both by remaining near initial level when as many as one-half of the offspring were saved for parents. Truncation selection decreased genetic correlation in the offspring selected to be parents whether selection was by upper or lower truncation. Estimates of genetic correlation from covariances between phenotypes of parent and offspring were erratic for both directions of selection.Michigan Agricultural Experiment Station Journal Article4841. Part of North Central Regional Project NC-2.     

The effect of index selection on allele frequencies and future genetic gains when traits are correlated

The application of the selection index in the case of an additive two-trait model in which the genetic effect on each trait is determined by a finite number of loci is examined. Simulation results indicate that the direction of change in the frequency of favourable alleles is not necessarily in the positive direction at all loci when index selection is used as the basis for truncation selection. When the genetic correlation was positive (or favourable with respect to the economic weights), there was little difference (<5%) in genetic gain over 20 generations and no difference in the direction of change in allele frequencies or genetic correlation whether or not updated values for the genetic (co)variances were used in constructing the selection index. However, when the genetic correlation was negative or unfavourable, the effect of using genetic parameters which were not updated had unexpected effects on the allele frequencies and genetic correlation and reduced the genetic gain by a greater amount (< 12%).     

Two-trait selection response with marker-based assortative mating

 Marker-based assortative mating (MAM) – the mating of individuals that have similar genotypes at random marker loci – can increase selection response for a single trait by 3–8% over random mating (RM). Genetic gain is usually desired for multiple traits rather than for a single trait. My objectives in this study were to (1) compare MAM, phenotypic assortative mating (PAM), and RM of selected individuals for improving two traits and (2) determine when MAM will be most useful for improving two traits. I simulated 20 generations of selecting 32 out of 200 individuals in an F₂ population. The individuals were selected based on an index (SI) of two traits and were intermated by MAM, PAM, or RM. I studied eight genetic models that differed in three contrasts: (1) weight, number of quantitative trait loci (QTL), and heritability (h ²) for each trait; (2) linkage of QTL for each trait; and (3) trait means of the inbred parents of the F₂. For SI and the two component traits, MAM increased short-term selection response by 5–8% in six out of the eight genetic models. The MAM procedure was least effective in two genetic models, wherein the QTL for one trait were unlinked to the QTL for the other trait and the parents of the F₂ had divergent means for each trait. The loss of QTL heterozygosity was much greater with MAM than with PAM or RM. Consequently, the advantage of MAM over RM dissipated after 5–7 generations. Differences were small between selection responses with PAM and RM. The MAM procedure can enhance short-term selection response for two traits when selection is not stringent, h ² is low, and the means of the parents of the F₂ are equal for each trait. Received: 10 June 1998 / Accepted: 5 August 1998     

Genetic correlation and response to selection in simulated populations

Summary One of two quantitative traits was selected and correlated response in the other trait was measured in each of 30 generations for models of additive genes and of complete dominance. Each trait was controlled by 48 loci with equal effects, segregating independently from frequencies of 0.5 in the initial generation. Intensity of selection regulated the number of offspring from randomly mating 24 males and 24 females each generation. Three each of genetic correlations between traits, intensities of selection, and amounts of environmental variation were simulated.In the additive model correlated responses of the unselected trait to selection of the primary trait agreed closely with responses expected from theoretical considerations. In the model of complete dominance, responses of genotypic means of the unselected trait to selection of the primary trait in opposite directions were quite symmetrical for the first few generations but became distinctly asymmetrical in later generations. With little selection, response was fairly linear but became distinctly curvilinear as intensity of selection increased and environmental variance decreased. Between 15th and 30th generations some gains in the correlated trait to the 15th generation were lost.Michigan Agricultural Experiment Station Journal Article 4847. Part of North Central Regional Project NC-2.     

Indirect genetic effects in a sex‐limited trait: the case of breeding time in red‐billed gulls

Female reproductive performance can be strongly affected by male care, so that breeding time, a trait expressed only by females, can be seen as one trait determined by both male and female genotypes. Animal model analyses of a 46‐year study of red‐billed gulls (Larus novaehollandiae scopulinus) revealed that laying date was not heritable in females (h² = 0.001 ± 0.030), but significantly so in males (h² = 0.134 ± 0.029). Heritability of breeding time in males probably reflects genetic variability in some other trait such as courtship feeding ability. In line with predictions of evolutionary models incorporating indirect genetic effects, the strong and consistent directional selection for advanced breeding time has not resulted in detectable selection response in males. Our results demonstrate that a female trait is largely determined by genetic characteristics of its mate, and hence, any evolutionary change in red‐billed gull breeding time depends critically on genetic variation in males.     

Effect of selection on genetic parameters of correlated traits

Summary Changes in genetic parameters of correlated traits due to the buildup of linkage (gametic phase) disequilibrium from repeated truncation selection on a single trait are studied. After several generations of selection, an equilibrium is approached where there are no further changes in genetic parameters and limiting values are reached. Formulae are derived under an infinitesimal model for these limiting values of genetic variances and covariances, heritabilities, and genetic correlations between traits directly and indirectly selected. Changes from generation zero to the limit in all these parameters become greater as heritability of the trait under direct selection increases and, to a lesser extent, as intensity of selection increases. Change in heritability of a trait under indirect selection also increases as the absolute value of the correlation between the trait under indirect and the trait under direct selection increases. The change is maximum when the initial value of heritability is close to 0.5 and insignificant when the initital value is close to zero or one. Change in the genetic correlation between the trait under direct selection and the trait under indirect selection is maximum when its initial value is close to ±0.6 and insignificant when its initial value is close to zero or ±1. Heritability of the trait indirectly selected and genetic correlation between that trait and the trait directly selected always decrease in absolute value, whereas genetic correlation between two traits indirectly selected can either decrease or increase in absolute value. It is suggested that use be made of formulae at selection equilibrium in the prediction of correlated responses after several generations of selection.     

Genetic Variance and Correlation after Selection for Two Traits by Index, Independent Culling Levels and Extreme Selection

Three two-trait selection methods were analyzed for their effects on genetic variance and correlation by multivariate methods, two-locus methods and computer simulation. The two-trait selection methods studied were independent culling levels (ICL), index (IND) and extreme (EXT) selection. The effects of the selection methods on genetic variance and correlation were partitioned into permanent effects due to changes in gene frequencies and temporary effects due to nonrandom association of alleles at different loci. Multivariate methods were used to predict temporary effects from a single generation of selection by each method and from several generations of index selection. Two-locus theory was used to determine the stability and rank of temporary effects on genetic correlation for all three methods. Predictions were compared to computer simulation results. When selection increased the means of both traits, EXT had the lowest (closest to -1.0) genetic correlation and highest variances, while ICL tended to have the highest (closest to 1.0) genetic correlation. When selection increased the mean of one trait and decreased the mean of the other, EXT had the highest genetic variances and correlation, while ICL had the lowest genetic variances and correlation.     

Selection for fertility in mice — the selection plateau and how to overcome it

Summary A long-term experiment for increasing the traits first day litter size (LS1) and litter weight (LW1) was conducted with two populations for 33 generations. The selection plateau was reached in population DU-C (selection and estrus synchronization (h² = 0.02±0.01); in population DU-K (selection) the plateau (h² = 0.05±0.2) was nearly reached. Selection progress per generation was in LS1 b = 0.11±0.02; b = 0.12±0.04 (1st to 18th generation DU-K, DU-C) and b = 0.10±0.03; b = 0.07±0.05 (19th to 33rd generation, DU-K, DU-C) in LW1 b = 0.16±0.04 g; 0.19±0.07 g (DU-K, DU-C) b = 0.20±0.09 g; 0.001±0.09 g (DU-K, DU-C). Reverse and relaxe selection as well as systematic inbreeding was applied for 10 generations. Reverse selection yielded h² = 0.28±0.11 (R-DU-K) and h² = 0.17±0.05 (R-DU-C) and showed that there was still additive genetic variance. Relaxe selection did not cause alterations in the selection parameters, whereas inbreeding lead to inbred depressions (b = LS1 = –0.42±0.15; –0.45±0.12; b = LW1 = –1.13±0.20; –0.82±0.18 I-DU-K, I-DU-C). The plateau was based upon the heterozygote advantage. Several methods for overcoming the plateau were applied. A new selective useful variance could be created by crossing the plateau populations (h² = 0.14±0.04). A short-term progress in overcoming the plateau (1st to 3rd generation) could be obtained by litter size standardization (LS = 388). Tandem selection (selection for body weight — BW42) as well as crossing of inbred strains were not suitable for overcoming the selection plateau. Altering the environmental conditions as a possibility for overcoming the plateau has been discussed.     

Pleiotropic Models of Polygenic Variation, Stabilizing Selection, and Epistasis

We show that in polymorphic populations many polygenic traits pleiotropically related to fitness are expected to be under apparent ``stabilizing selection' independently of the real selection acting on the population. This occurs, for example, if the genetic system is at a stable polymorphic equilibrium determined by selection and the nonadditive contributions of the loci to the trait value either are absent, or are random and independent of those to fitness. Stabilizing selection is also observed if the polygenic system is at an equilibrium determined by a balance between selection and mutation (or migration) when both additive and nonadditive contributions of the loci to the trait value are random and independent of those to fitness. We also compare different viability models that can maintain genetic variability at many loci with respect to their ability to account for the strong stabilizing selection on an additive trait. Let V(m) be the genetic variance supplied by mutation (or migration) each generation, V(g) be the genotypic variance maintained in the population, and n be the number of the loci influencing fitness. We demonstrate that in mutation (migration)-selection balance models the strength of apparent stabilizing selection is order V(m)/V(g). In the overdominant model and in the symmetric viability model the strength of apparent stabilizing selection is approximately 1/(2n) that of total selection on the whole phenotype. We show that a selection system that involves pairwise additive by additive epistasis in maintaining variability can lead to a lower genetic load and genetic variance in fitness (approximately 1/(2n) times) than an equivalent selection system that involves overdominance. We show that, in the epistatic model, the apparent stabilizing selection on an additive trait can be as strong as the total selection on the whole phenotype.     

An experimental comparison of selection alternatives to plateaued response

Three alternative selection methods for extending selection limits or breaking response plateaus were compared over ten generations in a replicated model experiment using two unrelated populations of Drosophila melanogaster that no longer responded to purebred selection for high egg number, a heterotic polygenic trait. The three methods were: (1) reciprocal recurrent selection (RRS) with selection within each of the plateaued populations based solely on crossbred performance, (2) a modification of reciprocal recurrent selection (MRRS) with selection within each population based on both purebred and crossbred performance, and (3) purebred selection within a new synthetic population formed by crossing the two plateaued populations.--Conflicting estimates were obtained for heritability of purebred egg number in each of the plateaued populations. The realized heritability values and estimates from diallel analyses indicated an absence of additive genetic variation for both populations; however, estimates from conventional intraclass correlation methods were positive. The diallel analyses revealed significant amounts of nonadditive gene effects for purebred egg number in each population, while the significant gene effects for crossbred egg numbers were additive. Estimates of the genetic correlation between purebred and crossbred egg number were negative (-0.85 +/- 0.68 and -0.32 +/- 0.25) for the two base populations.--All three alternatives to continued purebred selection gave significant responses, with the average gain per generation from MRRS being significantly superior to the other two methods. Observed purebred and crossbred responses under RRS were in agreement with quantitative genetic theory. Such was not the case for MRRS, which suggested the possibility of major gene segregation.--Evidence supporting a negative genetic correlation between purebred and crossbred performance and the possibility of overdominance is presented and discussed.     

Estimation of additive genetic variance in commercial layer poultry and simulated populations under selection

Changes in genetic parameters over generations for a selected commercial population and simulated populations of poultry with different sizes were studied. The traits analyzed from the commercial population were rate of lay, age at first egg, egg weight, deformation, and body weight. In the simulated population, a trait measured on both sexes and a sex-limited trait, measured only on one sex, each with a heritability of 0.1 and 0.5, were analyzed. In the commercial and simulated populations, males and females were selected on the basis of family selection indexes and data was available only after many generations of selection. Parameters for each generation were estimated by fitting an animal model using derivative free maximum likelihood (DFREML) with different data structures. In structure 1, data included the given (base) generation for which the parameters were to be estimated, and all subsequent generations. In structure 2, only data on birds in the given generation and their progeny were included. In both structures, parents of base-generation birds were assumed unrelated and pedigrees traced back to these parents. With commercial data using structure 1, estimates of _a ² and h² decreased by 14 to 37% across five generations. With structure 2, no trends were observed, though estimates were lower than for structure 1. For simulated data, with a heritability of 0.1, both structures yielded apparently unbiased estimates of the observed additive genetic variances in the (selected) base generation, no matter how many generations of data were utilized, for both sex-limited and normal traits. However, with a heritability of 0.5 the estimated additive genetic variance for both types of trait decreased with a decrease in the number of generations used in the estimation. Estimates based on the first two generations underestimated, while estimates based on five generations of data overestimated, the observed genetic variances in the defined base. The combinations of conditions that lead to varying degrees of bias remain undefined.     

Genetic determinism for within-litter birth weight variation and its relationship with litter weight and litter size in the Ripollesa ewe breed

Birth weight plays a central role in lamb survival and growth, and the knowledge of its genetic determinism has become essential in worldwide selection programmes. Within this context, within-litter birth weight variation (BWV) has been suggested as an attractive trait to homogenise litters in prolific species, although it has not been analysed in sheep. The objective of this study was to ascertain whether maternal additive genetic variance exists for BWV in Ripollesa ewes, and to study its genetic, permanent environmental and residual relationships with litter weight (LW) and litter size (LS) at birth. Data were recorded in the Ripollesa experimental flock of the Universitat Autònoma of Barcelona, between 1986 and 2005, and included 1 662 litters from 380 ewes, with 712 records of BWV and 1 530 records of LW. Traits were analysed with a multivariate animal model solved through Bayesian methodologies, and with a threshold characterisation of LS. Additionally, the effect of BWV on lamb survival was studied. Additive genetic variance was observed for BWV (h² = 0.061), as well as for LW (h² = 0.200) and LS (h² = 0.141). Nevertheless, genetic correlations among those traits were not substantial (BWV and LW = 0.151; BWV and LS = − 0.219; LW and LS = − 0.320) and suffered from a high degree of uncertainly, with the null correlation included within the highest posterior interval at 95%. Within-litter birth weight variation and LS showed a negative and large permanent environmental correlation ( − 0.872), and LW and LS were negatively correlated due to residual ( − 0.762) and permanent environmental ( − 0.449) random sources of variation. Within-litter birth weight variation influenced lamb mortality during the first 7 days of life (P < 0.05), increasing and decreasing survivability in heavier and lighter littermates, respectively. Nevertheless, stillbirths and lambs died after the 1st week of life were not affected by BWV (P>0.05). The low heritability found indicates that slow genetic progress may be expected from selecting for BWV. Close to zero genetic correlations suggest that this selection will probably not affect LS and LW, although some significant permanent and residual correlations must be taken into account. Further studies are needed to understand better the genetic architecture among these three reproductive traits.     

Soft selective sweep near a gene that increases plant height in wheat

Strong selection within a given population locally reduces genetic variability not only in the selected gene itself but also in neighbouring loci. This so-called hitch-hiking effect is related to the initial linkage disequilibrium between markers and the selected gene, and depends mainly on the number of copies of the beneficial allele at the start of the selection phase. Contrary to the classical case, in which selection acts on a single, newly arisen beneficial mutation, we considered selection from standing variation (soft selective sweeps) on a gene ( Rht-B1 ) with a major effect on plant height, a selected trait in an experimental wheat population grown for 17 generations, and we documented the evolution of gene diversity and linkage disequilibrium near this gene. As expected, Rht-B1 was found to be under strong selection ( s  = 0.15) and its variation in frequency accounted for 15% of the total trait evolution. This led to a smaller genetic effective population size at Rht-B1 ( N_eg  = 18) compared to the whole genome estimation ( N_eg  = 167). When compared with expectations under genetic drift only, no significant decrease in gene diversity was found at the closest loci. We computed expected di-locus frequencies for any linked marker– Rht-B1 pair due to hitch-hiking effects. We found that hitch-hiking was expected to affect the two most closely linked loci, but expected reduction in gene diversity was not greater than that due to genetic drift, which was consistent with the observations. Such limited effect was attributed to the low level of linkage disequilibrium (0.16) estimated after parental intercrosses, together with a relatively high initial frequency of the gene. This situation is favourable to candidate gene approaches where small linkage disequilibrium around selected genes is expected.     

Efficiency of indirect selection at selection equilibrium

Summary Efficiency of indirect selection compared with that of direct selection to increase the mean value of some trait has been usually studied by considering a single generation of indirect and direct responses to selection only. However, under continued selection, genetic variances and covariances, and therefore expected genetic responses, change each generation due to linkage disequilibrium. With directional and truncation selection, genetic parameters asymptote to limiting values after several generations. The efficiency of indirect selection is examined in this limiting situation. The ratio of correlated response to direct response for the trait to improve in the limit is compared with the ratio after the first generation of selection. For all initial parameter values for which indirect selection is more efficient than direct selection, relative efficiency of indirect selection is smaller in the limit than in the first generation. For some parameter values, indirect selection is more efficient than direct selection in the first generation, but less efficient in the limit. Expressions for minimum values of the initial genetic correlation and heritability of the alternative trait required for indirect selection to be preferred in the limit are derived. These values are higher when limiting responses are used instead of single generation responses. The loss in relative efficiency of indirect selection from changes in genetic parameters due to selection should be taken into account when applications of indirect selection are considered.     

The effect of trait type and strength of selection on heritability and evolvability in an island bird population

The heritability (h²) of fitness traits is often low. Although this has been attributed to directional selection having eroded genetic variation in direct proportion to the strength of selection, heritability does not necessarily reflect a trait's additive genetic variance and evolutionary potential (“evolvability”). Recent studies suggest that the low h² of fitness traits in wild populations is caused not by a paucity of additive genetic variance (V_A) but by greater environmental or nonadditive genetic variance (V_R). We examined the relationship between h² and variance‐standardized selection intensities (i or β_σ), and between evolvability (I_A:V_A divided by squared phenotypic trait mean) and mean‐standardized selection gradients (β_μ). Using 24 years of data from an island population of Savannah sparrows, we show that, across diverse traits, h² declines with the strength of selection, whereas I_A and I_R (V_R divided by squared trait mean) are independent of the strength of selection. Within trait types (morphological, reproductive, life‐history), h², I_A, and I_R are all independent of the strength of selection. This indicates that certain traits have low heritability because of increased residual variance due to the age at which they are expressed or the multiple factors influencing their expression, rather than their association with fitness.     

Response to joint selection on germination and flowering phenology depends on the direction of selection

Flowering and germination time are components of phenology, a complex phenotype that incorporates a number of traits. In natural populations, selection is likely to occur on multiple components of phenology at once. However, we have little knowledge of how joint selection on several phenological traits influences evolutionary response. We conducted one generation of artificial selection for all combinations of early and late germination and flowering on replicated lines within two independent base populations in the herb Campanula americana. We then measured response to selection and realized heritability for each trait. Response to selection and heritability were greater for flowering time than germination time, indicating greater evolutionary potential of this trait. Selection for earlier phenology, both flowering and germination, did not depend on the direction of selection on the other trait, whereas response to selection to delay germination and flowering was greater when selection on the other trait was in the opposite direction (e.g., early germination and late flowering), indicating a negative genetic correlation between the traits. Therefore, the extent to which correlations shaped response to selection depended on the direction of selection. Furthermore, the genetic correlation between timing of germination and flowering varies across the trait distributions. The negative correlation between germination and flowering time found when selecting for delayed phenology follows theoretical predictions of constraint for traits that jointly determine life history schedule. In contrast, the lack of constraint found when selecting for an accelerated phenology suggests a reduction of the covariance due to strong selection favoring earlier flowering and a shorter life cycle. This genetic architecture, in turn, will facilitate further evolution of the early phenology often favored in warm climates.     

Genetic response from marker assisted selection in an outbred population for differing marker bracket sizes and with two identified quantitative trait loci.

Effect of flanking quantitative trait loci (QTL)-marker bracket size on genetic response to marker assisted selection in an outbred population was studied by simulation of a nucleus breeding scheme. In addition, genetic response with marker assisted selection (MAS) from two quantitative trait loci on the same and different chromosome(s) was investigated. QTL that explained either 5% or 10% of phenotypic variance were simulated. A polygenic component was simulated in addition to the quantitative trait loci. In total, 35% of the phenotypic variance was due to genetic factors. The trait was measured on females only. Having smaller marker brackets flanking the QTL increased the genetic response from MAS selection. This was due to the greater ability to trace the QTL transmission from one generation to the next with the smaller flanking QTL-marker bracket, which increased the accuracy of estimation of the QTL allelic effects. Greater negative covariance between effects at both QTL was observed when two QTL were located on the same chromosome compared to different chromosomes. Genetic response with MAS was greater when the QTL were on the same chromosome in the early generations and greater when they were on different chromosomes in the later generations of MAS.     

CONSTANCY OF POPULATION PARAMETERS FOR LIFE-HISTORY AND FLORAL TRAITS IN RAPHANUS SATIVUS L. II. EFFECTS OF PLANTING DENSITY ON PHENOTYPE AND HERITABILITY ESTIMATES

To determine the effect of growing conditions on population parameters in wild radish, (Raphanus sativus L.: Brassicaceae), we replicated maternal and paternal half-sib families of seed across three planting densities in an experimental garden. A nested breeding design performed in the greenhouse produced 1,800 F₁ seeds sown in the garden. We recorded survivorship, measured phenotypic correlations among and estimated narrow-sense and broad-sense heritabilities (h²) of: days to germination, days to flowering, petal area, ovule number/flower, pollen production/flower, and modal pollen grain volume. Survivorship declined with increasing density, but the relative abundances of surviving families did not differ significantly among densities. Seeds in high-density plots germinated significantly faster than seeds sown in medium- or low-density plots, but they flowered significantly later. Plants in high-density plots had fewer ovules per flower than those in the other treatments. Petal area and pollen characters did not differ significantly among densities. Densities differed with respect to the number and sign of significant phenotypic correlations. Analyses of variance were conducted to detect additive genetic variance (V_a) of each trait in each density. At low density, there were significant paternal effects on flowering time and modal pollen grain volume; in medium-density plots, germination time, flowering time and ovule number exhibited significant paternal effects; in high-density plots, only pollen grain volume differed among paternal sibships. The ability to detect maternal effects on progeny phenotype also depended on density. Narrow-sense h² estimates differed markedly among density treatments for germination time, flowering time, ovule number and pollen grain volume. Maternal, paternal and error variance components were estimated for each trait and density to examine the sources of variation in narrow-sense h² across densities. Variance components did not change consistently across densities; each trait behaved differently. To provide qualitative estimates of genetic correlations between characters, correlation coefficients were estimated using paternal family means; these correlations also differed among densities. These results demonstrate that: a) planting density influences the magnitude of maternal and paternal effects on progeny phenotype, and of h² estimates, b) traits differ with respect to the density in which heritability is greatest, c) density affects the variance components that comprise heritability, but each trait behaves differently, and d) the response to selection on any target trait should result in different correlated responses of other traits, depending on density.     

Identity-by-descent genomic selection using selective and sparse genotyping for binary traits

Background

Genomic selection (GS) allows estimation of the breeding value of individuals, even for non-phenotyped animals. The aim of the study was to examine the potential of identity-by-descent genomic selection (IBD-GS) in genomic selection for a binary, sib-evaluated trait, using different strategies of selective genotyping. This low-cost GS approach is based on linkage analysis of sparse genome-wide marker loci.

Findings

Lowly to highly heritable (h² = 0.15, 0.30 or 0.60) binary traits with varying incidences (10 to 90%) were simulated for an aquaculture-like population. Genotyping was restricted to the 30% best families according to phenotype, using three genotyping strategies for training sibs. IBD-GS increased genetic gain compared to classical pedigree-based selection; the differences were largest at incidences of 10 to 50% of the desired category (i.e. a relative increase in genetic gain greater than 20%). Furthermore, the relative advantage of IBD-GS increased as the heritability of the trait increased. Differences were small between genotyping strategies, and most of the improvement was achieved by restricting genotyping to sibs with the least common binary phenotype. Genetic gains of IBD-GS relative to pedigree-based models were highest at low to moderate (10 to 50%) incidences of the category selected for, but decreased substantially at higher incidences (80 to 90%).

Conclusions

The IBD-GS approach, combined with sparse and selective genotyping, is well suited for genetic evaluation of binary traits. Genetic gain increased considerably compared with classical pedigree-based selection. Most of the improvement was achieved by selective genotyping of the sibs with the least common (minor) binary category phenotype. Furthermore, IBD-GS had greater advantage over classical pedigree-based models at low to moderate incidences of the category selected for.