A note on the use of inbreeding in progeny test schemes

SUMMARY: In this note some theoretical and simulated results are presented comparing the selection response in a progeny test scheme that utilizes inbred offspring for testing, with respect to a standard progeny test. The theory indicates a substantial increase in selection response, although the advantage decreases as the number of dams mated to a sire and the number of offspring per dam increases. The advantage is at a maximum when the variation of the trait is due to segregation of recessive alleles at low frequencies unfavourable to the direction of selection. Computer simulation confirmed the advantage of the method. ZUSAMMENFASSUNG: Verwendung von Inzuchttieren bei der Nachkommenschaftsprüfung Hier wurden theoretische und simulierte Selektionserfolge konventioneller Nachkommenschaftsprüfung mit Prüfung von Inzuchtnachkommen verglichen. Theoretisch zeigt sich ein erheblicher Vorteil der letzteren, wenn dieser auch mit steigende Zahl von Partnern und deren Nachkommen abnimmt und nach null tendiert. Der Vorteil der Nachkommenschaftsprüfung ingezüchteter Nachkommen ist am h?chsten, wenn seltene ungünstige rezessive Gene eine Rolle spielen. Rechner-Simulation best?tigt den Vorteil dieser Vorgangsweise.     

Predicting rates of inbreeding for livestock improvement schemes

This article presents a deterministic method to predict rates of inbreeding (deltaF) for typical livestock improvement schemes. The method is based on a recently developed general theory to predict rates of inbreeding, which uses the concept of long-term genetic contributions. A typical livestock breeding population was modeled, with overlapping generations, BLUP selection, and progeny testing of male selection candidates. Two types of selection were practiced: animals were either selected by truncation on estimated breeding values (EBV) across age classes, or the number of parents selected from each age class was set to a fixed value and truncation selection was practiced within age classes. Bulmer's equilibrium genetic parameters were obtained by iterating on a pseudo-BLUP selection index and deltaF was predicted for the equilibrium situation. Predictions were substantially more accurate than predictions from other available methods, which ignore the effect of selection on deltaF. Predictions were accurate for schemes with up to 20 sires. Predicted deltaF was somewhat too low for schemes with more than 20 sires, which was due to the use of simple linear models to predict genetic contributions. The present method provides a computationally feasible (i.e., deterministic) tool to consider both the rate of inbreeding and the rate of genetic gain when optimizing livestock improvement schemes.     

The influence of selection and epistasis on inbreeding depression estimates

Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coefficients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coefficients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coefficient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was difficult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.     

The joint regulation of genetic gain and inbreeding under mate selection

SUMMARY: Stochastic simulation was used to evaluate a range of selection strategies with respect to both additive genetic response and inbreeding. Strategies involving selection on BLUP ebvs or individual phenotype, followed by random mating, were compared with mate selection strategies which used portfolio analysis to give joint consideration to genetic merit and inbreeding. An adapted Mean Of Total Absolute Deviations (MOTAD) method was used in a mate selection model to define optimal matings with regard to aggregate genetic merit and inbreeding for a base population h(2) of 0.2. Compared with random mating following selection on BLUP ebvs, inbreeding levels after 10 years of selection were able to be reduced under BLUP plus mate selection from ～.23 to as little as .11. Additive genetic gain was either little compromised or increased. The results suggest that information linking expected levels of genetic merit and inbreeding can be used to find the preferred selection strategy. ZUSAMMENFASSUNG: Gemeinsame Kontrolle von Zuchtfortschritt und Inzucht bei Partnerselektion Es wurde stochastische Simulation zur Auswertung einer Reihe von Selektionsstrategien hinsichtlich Zuchtwertzuwachs und Inzucht verwendet. Strategien mit Selektion auf der Basis von BLUP ebvs oder individuellem Ph?notyp mit nachfolgender Zufallspaarung wurden mit Partnerselektionsstrategien verglichen, die Portfolioanalyse zur gemeinsamen Beachtung von Zuchtwert und Inzucht verwendeten. Eine Methode adaptierter MITTELWERTE TOTALER ABSOLUTER ABWEICHUNGEN (MOTAD) Methode wurde beim Partnerselektionsmodell zur Definition optimaler Paarungen in Hinblick auf Gesamtzuchtwert und Inzucht bei einer Populationsheritabilit?t von 0,2 verwendet. Verglichen mit Zufallspaarung nach Selektion auf BLUP ebvs waren die Inzuchtgrade nach 10 Selektionsjahren von 0,23 auf 0,11 reduziert und additiver Zuchtfortschritt war dabei wenig beeintr?chtigt oder nahm sogar zu. Die Ergebnisse weisen darauf hin, da? Information, die Zuchtwert und Inzucht verbindet, zur Identifikation erwünschter Selektionsstrategien führen kann.     

Maximizing genetic gain over multiple generations with quantitative trait locus selection and control of inbreeding

Stochastic computer simulation was used to investigate the potential extra genetic gains obtained from gene-assisted selection (GAS) by combining 1) optimization of genetic contributions for maximizing gain, while restricting the rate of inbreeding with 2) optimization of the relative emphasis given to the QTL over generations. The genetic model assumed implied a mixed inheritance model in which a single quantitative trait locus (i.e., QTL) is segregating together with polygenes. When compared with standard GAS (i.e., fixed contributions and equal emphasis on the QTL and polygenic EBV), combined optimization of contributions of selection candidates and weights on the QTL across generations allowed substantial increases in gain at a fixed rate of inbreeding and avoided the conflict between short- and long-term responses in GAS schemes. Most of the increase of gain was produced by optimization of selection candidates' contributions. Optimization of the relative emphasis given to the QTL over generations had, however, a greater effect on avoiding the long-term loss usually observed in GAS schemes. Optimized contribution schemes led to lower gametic phase disequilibrium between the QTL and polygenes and to higher selection intensities both on the QTL and polygenes than with standard truncation selection with fixed contributions of selection candidates.     

Comparison of selection methods at the same level of inbreeding.

Animal geneticists predict higher genetic responses to selection by increasing the accuracy of selection using BLUP with information on relatives. Comparison of different selection methods is usually made with the same total number tested and with the same number of parents and mating structure so as to give some acceptable (low) level of inbreeding. Use of family information by BLUP results in the individuals selected being more closely related, and the levels of inbreeding are increased, thereby breaking the original restriction on inbreeding. An alternative is to compare methods at the same level of inbreeding. This would allow more intense selection (fewer males selected) with the less accurate methods. Stochastic simulation shows that, at the same level of inbreeding, differences between the methods are much smaller than if inbreeding is unrestricted. If low to moderate inbreeding levels are targeted, as in a closed line of limited size, then selection on phenotype can yield higher genetic responses than selection on BLUP. Extra responses by BLUP are at the expense of extra inbreeding. The results derived here show that selection on BLUP of breeding values may not be optimal in all cases. Thus, current theory and teaching on selection methods are queried. Revision of the methodology and a reappraisal of the optimization results of selection theory are required.     

近亲交配对牛群危害及其控制措施

研究分析了近交对荷斯坦牛群产奶性状、繁殖性状以及体型性状的影响，针对我国奶牛业的现状，提出了控制近交的措施。     

A mating system to reduce inbreeding in selection programmes: Theoretical basis and modification of compensatory mating

Increased rate of inbreeding in selection programmes may have an important effect on mid- and long-term selection response and reproductive performance through reduction in genetic variance and inbreeding depression. Selection on an inherited trait inflates the rate of inbreeding and reduces the effective population size (R obertson 1961; S antiago and C aballero 1995). This can be particularly important in selection based on index with information from relatives (L ush 1947) or best liner unbiased prediction (BLUP) with an animal model (H enderson 1984). In recent years, various methods have been proposed to reduce the rates of inbreeding in selection programmes while keeping genetic gains at the same level. These methods assume various selection and mating strategies. G rundy et al. (1994) showed that the use of biased heritability estimates for BLUP evaluation is one of the simplest and most efficient methods. A direct reduction in the weight on family mean in index selection (T oro and P erez -E nciso 1990), selection for weighted ancestral Mendelian sampling estimates (W oolliams and T hompson 1994; G rundy et al. 1998) and limited use of selected parents (T oro and N ieto 1984; W ei 1995) have also been shown to be efficient methods. Other methods include nonrandom matings of selected parents, such as factorial mating designs (W oolliams 1989), minimum coancestry mating (T oro et al. 1988) and compensatory mating (S antiago and C aballero 1995). Simultaneous optimization of the selection of candidates and their mating allocations has been also considered through mate selection with linear programming techniques (T oro and P erez -E nciso 1990). Among these methods, compensatory mating is a very simple and efficient method (G rundy et al. 1994; S antiago and C aballero 1995; C aballero et al. 1996). This mating system was derived from the theoretical consideration on effective population size under selection (S antiago and C aballero 1995). Although S antiago and C aballero (1995) considered that implementation of this mating could counteract the cumulative effect of selection on the effective population size, the theoretical basis has been little studied. In this paper, the author gives the theoretical basis of compensatory mating. A modification to enhance the effect of compensatory mating is also proposed and the efficiency is examined by stochastic simulation.     

Restricting inbreeding while maintaining selection response for weight gain in Mus musculus

An experiment with mice was designed to test the relative efficiency of three selection methods that help to minimize the rate of inbreeding during selection. A common house mice (Mus musculus) population was selected for 17 generations to increase the weight gain between 21 and 42 days. The population was split at random into three lines A, B and C where three selection methods were applied: individual selection and random mating, weighted selection with random mating and individual selection with minimum coancestry mating, respectively. There were three replicates for each line. Cumulated selection response was similar in the three lines, but there were differences in the level of inbreeding attained (in percentage): 31.24 (method A), 24.72 (method B) and 27.88 (method C). As consequence, lines B and C (weighted selection and minimum coancestry) showed a lower value of deterioration of fitness traits (the intrauterine mortality and the mortality at birth) than line A (random mating).     

Assessing genetic gain, inbreeding, and bias attributable to different flock genetic means in alternative sheep sire referencing schemes

Flocks participating in sire referencing schemes can achieve greater genetic gains than those achievable by within-flock selection. However, requirements for joining these schemes can be prohibitive to some producers. The objectives of this study were to determine whether less restrictive schemes or schemes of shorter duration could achieve rates of gain and reduce inbreeding as efficiently as continuous sire referencing schemes (SRS) and to investigate whether bias from different genetic means could be reduced by these alternative schemes. Pedigree and performance data for a single trait with a within-flock heritability of 0.25 were simulated (50 replications) for 15 flocks with 40 to 140 ewes per flock. Founder genetic means for each flock were sampled from a normal distribution with mean 0 and SD equal to the trait's genetic SD. After 10 yr of random mating, flocks had the opportunity to join an SRS and begin selection for the simulated trait. Yearling rams were chosen as reference sires randomly from the top one-sixth of the population ranked on BLUP EBV. Every year, in each flock, 3 reference sires were mated to 10 ewes. Six sire referencing scenarios were considered, in which all flocks participated in a SRS for 1) 15 yr; 2) 5 yr before discontinuing the scheme; 3) 10 yr before discontinuing the scheme; 4) 2 out of every 3 yr; 5) 15 yr with reference sire mating by natural service; and 6) no years (no use of SRS). Ewes not mated to reference sires were mated either to their own home-bred sires exclusively or to a mixture of homebred and unrelated purchased rams of unknown merit. Genetic gain was equivalent whether the SRS used AI or natural service matings, although inbreeding was lower with natural service. Across all scenarios, genetic gain and inbreeding were greater when excess ewes were mated exclusively to homebred sires. Genetic gains without SRS were 80 to 82% lower than when the scheme operated for 15 yr, whereas inbreeding was considerably greater. Other scenarios were intermediate in both gain and inbreeding levels. In all SRS scenarios, bias in EBV attributable to differing flock genetic means rapidly decreased in the first 5 yr of sire referencing. Levels of bias did not substantially increase when flocks discontinued SRS after 5 or 10 yr, suggesting that further participation in an SRS may not be necessary to manage risk. Natural service and noncontinuous SRS are viable options to continuous AI SRS in terms of genetic gain, inbreeding, and bias reduction.     

Optimization of selection and mating schemes in closed broiler lines

Minimum coancestry mating (MC) is a simple mating system to reduce inbreeding in populations, in which matings are allocated so as to minimize the average inbreeding coefficient of progeny. This system was compared with random mating (RM) in simulated broiler lines. The population structure and genetic parameters were determined on the basis of an existing broiler line. Comparison of mating systems was made under two selection methods. The first method (DIS) was based on selection index for achieving desired genetic gains. In the second method (LPS), a combination of the family index and linear programming technique was applied to obtain the desired genetic gains. The selected traits were body weight at 6 weeks of both sexes and age at sexual maturity of hen. Four schemes by all the possible combinations of selection and mating methods (DIS + RM, DIS + MC, LPS + RM and LPS + MC) were compared in terms of genetic gains and inbreeding during 15 generations of selection and mating. The results obtained are summarized as follows: (i) the four schemes produced similar genetic gains averaged over replicates; (ii) the variations of genetic gains under LPS + RM and LPS + MC schemes were much smaller than under DIS + RM and DIS + MC schemes; (iii) irrespective of the selection methods, MC reduced the average inbreeding coefficients to about 80% of RM and; (iv) the inbreeding coefficients of individuals in the schemes with RM were distributed in a wide range, while the inbreeding coefficients in the schemes with MC showed a high uniformity. From these results, the LPS + MC scheme was recommended as a selection and mating strategy in closed broiler lines.     

The use of selection and strain crossing to reduce egg shell breakage

1. Selection for low egg shell deformation and high egg production was carried out in two White Leghorn strains, M and H, in order to test the feasibility of reducing the incidence of egg breakage without loss in egg production.

2. Selected and control lines were maintained within each strain.

3. After three generations of selection, egg shell deformation was reduced in the M selected line as compared to its control counterpart but this change in deformation was not accompanied by a reduction in egg breakage; however, no reduction in deformation or egg breakage was achieved in the H selected line.

4. Crossing the M and H strains resulted in a reduction of egg breakage in the crosses as compared to the average breakage of the parental strains, suggesting the potential of utilising strain crosses to reduce the incidence of egg shell breakage.     

闭锁群体BLUP选择下遗传方差和近交系数的变化

采用计算机随机模拟方法模拟了在一个闭锁群体内连续对单个性状进行 1 5个世代选择的情况。选择过程中世代不重叠 ,每个世代的种畜根据动物模型最佳线性无偏预测 (BLUP)法估计的育种值进行选留 ,并在此基础上系统地比较了不同群体规模、公母比例和性状遗传力对群体遗传方差和近交系数变化的影响。结果表明 ,扩大育种群规模、增加公畜比例以及对低遗传力性状进行选择时 ,群体遗传方差降低的速度和近交系数上升的速度会更慢 ,在长期选择时可望获得更大的持续进展和适宜的近交增量     

Role of selection and inbreeding on the incidence of cutaneous malignant melanoma in Sinclair swine

Summary This paper reports the quantitative analysis of the historical database of a herd of Sinclair swine affected by cutaneous malignant melanoma. The herd was under partial and non-systematic selection for melanoma susceptibility (animals having at least one tumour during the first 6 weeks of life). Weighted selection differentials for the number of tumours at birth and the number of tumours at 6 weeks were generally positive and between −0.43 and 4.76 tumours for the number of tumours at 6 weeks. Estimates of the heritability for number of tumours at birth and at 6 weeks using 1934 animals were 0.27 (±0.03) and 0.25 (±0.03), respectively. The estimate of the genetic correlation between these two traits was 0.95 (±0.03). Genetic trends were positive for the number of tumours at birth and at 6 weeks. In spite of positive selection differentials and a moderate heritability, there was a negative phenotypic trend in the number of tumours. Natural selection might be acting in a direction opposite to artificial selection in the Sinclair herd. The slopes of the regression of the number of tumours at birth, at 6 weeks, and melanoma susceptibility on individual inbreeding coefficients were non-significant, indicating no evidence of dominance. The number of live-born pigs was lower in litters from parents susceptible to the disease (p < 0.01).     

Effects of data structure and selection on estimated inbreeding depression in experimental Tribolium castaneum lines

SUMMARY: Inbreeding depression was estimated for four experimental Tribolium castaneum lines. Each line, containing approximately 7000 animals, was selected for 16 generations either randomly (control), on pupae weight (PWT), on family size (FST) or on an index containing both PWT and FST. The inbreeding trend was 0.9, 0.5, 0.5 and 0.4 % inbreeding per generation in PWT-selected, FST-selected, index-selected, and control line, respectively. The model used to estimate the inbreeding depression included a linear regression on individual inbreeding coefficients, and random additive genetic effects. Using all the performance and pedigree data, estimated inbreeding depressions in the control line were -0.13 (SE = 0.16; #) and -8.50 (SE = 2.66; μg) per 1 % inbreeding for FST and PWT, respectively. Using only performance data of the latest generation in the control line, the estimated inbreeding depressions changed considerably: -0.17 (SE = 0.82) and -37.4 (SE= 11.9) for FST and PWT, respectively. Estimated inbreeding depression for FST in the FST-selected line was - 0.40 (SE = 0.31). Inbreeding depression for PWT in the PWT-selected line was 21.6 (SE = 25.8). This study indicates that estimating inbreeding depression might best be based on the performance data of animals with an equal and sufficiently-large number of ancestral generations known. ZUSAMMENFASSUNG: Wirkung von Datenstruktur und Selektion auf gesch?tzte Inzuchtdepression in experimentellen Triboleum castaneum Linien Jede der vier experimentellen Linien, aus je etwa 7000 Individuen, wurde durch 16 Generationen selektiert, zuf?llig die Kontrolle, auf Puppengewicht (PWT), Familiengr??e (FST), oder auf einen beide Merkmale kombinierenden Index. Inzucntzuw?chse in diesen vier Linien waren 0.4, 0.9, 0.5 und 0.5% je Generation. Das Modell zur Sch?tzung der Inzuchtdepression beinhaltete eine lineare Regression auf individuelle Inzuchtkoeffizienten und zuf?llige additive-genetische Wirkungen. Aus allen Daten, Leistung und Pedigree, ergaben sich -0.13 (SE = 0.16; #) und - 8.5 (SE = 2.66; mg) je 1% Inzucht für FST und PWT, Daten der letzten Generation ergaben deutlich andere Werte: -0.17 (SE = 0.82) und -37.4 (SE = 11.9) für FST und PWT. Inzuchtdepressionen für FST bzw. PWT in den jeweils hierfür selektierten Linien waren -0.40 (SE = 0.31) und 21.6 (SE = 25.8). Es wird gefolgert, da? Sch?tzungen auf Leistungen von hinreichend gro?er Zahl von Vorfahrengenerationen beruhen sollten.     

Optimizing female allocation to reproductive technologies considering merit,inbreeding and cost in nucleus breeding programmes with genomic selection

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro fertilization and embryo transfer (JIVET) have been shown to accelerate genetic gain by increasing selection intensity and decreasing generation interval. Genomic selection (GS) increases the accuracy of selection of young candidates which can further accelerate genetic gain. Optimal contribution selection (OCS) is an effective method of keeping the rate of inbreeding at a sustainable level while increasing genetic merit. OCS could also be used to selectively and optimally allocate reproductive technologies in mate selection while accounting for their cost. This study uses stochastic simulation to simulate breeding programmes that use a combination of artificial insemination (AI) or natural mating (N), MOET and JIVET with GS. OCS was used to restrict inbreeding to 1.0% increase per generation and also to optimize use of reproductive technologies, considering their effect on genetic gain as well as their cost. Two Australian sheep breeding objectives were used as an example to illustrate the methodology—a terminal sire breeding objective (A) and a dual‐purpose self‐replacing breeding objective (B). The objective function used for optimization considered genetic merit, constrained inbreeding and cost of technologies where costs were offset by a premium paid to the seedstock breeder investing in female reproductive technologies. The premium was based on the cumulative discounted expression of genetic merit in the progeny of a commercial tier in the breeding programme multiplied by the proportion of that benefit received by the breeder. With breeding objective B, the highest premium of 64% paid to the breeder resulted in the highest allocation of reproductive technologies (4%–10% for MOET and 19%–54% for JIVET) and hence the highest annual genetic gain. Conversely, breeding objective A, which had a lower dollar value of the breeding objective and a maximum of 5% mating types for JIVET and zero for MOET were optimal, even when highest premiums were paid. This study highlights that the level of investment in breeding technologies to accelerate genetic gain depends on the investment of genetic improvement returned to the breeder per index point gain achieved. It also demonstrates that breeding programmes can be optimized including allocation of reproductive technologies at the individual animal level. Accounting for revenue to the breeder and cost of the technologies can facilitate more practical decision support for beef and sheep breeders.     

A note on the use of DNA fingerprints to assess the coefficient of inbreeding in populations with unknown pedigree

SUMMARY: The relationship between the inbreeding coefficient and characteristics of DNA fingerprints is described to show opportunities of using DNA fingerprinting in assessing the inbreeding coefficient in populations with unknown pedigree. Characteristics studied include the number of bands per individual and the average level of bandsharing among individuals in a population. Conceptually simple functions relating allelic frequencies, inbreeding coefficient, and DNA fingerprint characteristics are derived. An increase in the inbreeding coefficient, with constant allelic frequencies, decreases both the number of bands and bandsharing. Allelic fixation will give rise to low numbers of bands but also to higher levels of bandsharing. It is concluded, that when empirically positive correlations between bandsharing and inbreeding are found, this should be due to drift and family structure in small populations subjected to drift and not to the effect of inbreeding per se. ZUSAMMENFASSUNG: Verwendung von DNA-Fingerprints zur Inzuchtsch?tzung in Populationen ohne Herdbuchaufzeichnungen Der Zusammenhang zwischen Inzuchtkoeffizienten und DNA-Fingerprints ist in Hinblick auf Nutzung von DNA-Fingerprints zur Ermittlung der Inzuchtkoeffizienten in Populationen mit unbekannter Abstammung dargestellt worden. Bei DNA-Fingerprints sind Anzahl der Bande eines Individuums und das durchschnittliche Niveau der Bandengleichheit zwischen Individuen me?bar. Zwischen Frequenz von Genen, Inzuchtkoeffizienten und Eigenschaften von DNA Fingerprints existiert ein relativ einfacher Zusammenhang. Eine Zunahme des Inzuchtkoeffizienten bei gleichbleibender Frequenz der Gene ergibt eine Abnahme der Bandenzahl je Individuum und der Bandengleichheit. Genfixierung ergibt niedrigere Anzahl von Banden, aber auch h?here Bandengleichheit. Zusammenfassend, ein empirisch positiver Zusammenhang zwischen Bandengleichheit und Inzuchtkoeffizient kann infolge Zufallsdrift und Verwandtschaft von Individuen in kleinen Populationen auftreten und nicht unbedingt infolge Inzucht an sich.     

Marker‐assisted selection reduces expected inbreeding but can result in large effects of hitchhiking

We used computer simulations to investigate to what extent true inbreeding, i.e. identity‐by‐descent, is affected by the use of marker‐assisted selection (MAS) relative to traditional best linear unbiased predictions (BLUP) selection. The effect was studied by varying the heritability (h² = 0.04 vs. 0.25), the marker distance (MAS vs. selection on the gene, GAS), the favourable QTL allele effect (α = 0.118 vs. 0.236) and the initial frequency of the favourable QTL allele (p = 0.01 vs. 0.1) in a population resembling the breeding nucleus of a dairy cattle population. The simulated genome consisted of two chromosomes of 100 cM each in addition to a polygenic component. On chromosome 1, a biallelic QTL as well as 4 markers were simulated in linkage disequilibrium. Chromosome 2 was selectively neutral. The results showed that, while reducing pedigree estimated inbreeding, MAS and GAS did not always reduce true inbreeding at the QTL relative to BLUP. MAS and GAS differs from BLUP by increasing the weight on Mendelian sampling terms and thereby lowering inbreeding, while increasing the fixation rate of the favourable QTL allele and thereby increasing inbreeding. The total outcome in terms of inbreeding at the QTL depends on the balance between these two effects. In addition, as a result of hitchhiking, MAS results in extra inbreeding in the region surrounding QTL, which could affect the overall genomic inbreeding.