REVIEW
doi: 10.1111/age.12178
Inbreeding depression in livestock species: review and meta-analysis G. Leroy*† *AgroParisTech, UMR 1313 Genetique Animale et Biologie Int egrative, F-75231 Paris, France. †INRA, UMR 1313 G en etique Animale et Biologie Integrative, F-78352 Jouy-en-Josas, France.
Summary
Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta-analysis conducted on 57 studies and seven livestock species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon. Keywords domestic animals, genetic diversity, inbreeding, production traits
Introduction In livestock species, most breeds can be considered as populations of limited size in relation to an unequal contribution of a limited number of reproducers to the next generation, as well as in relation to the fact that, in a quantitative scheme, selected reproducers are likely to be related (Robertson 1961). As a consequence, in relation to effective population sizes that generally range between a few tens and several hundreds of individuals (Leroy et al. 2013), the occurrence of inbreeding over generations cannot be avoided. Therefore, breeders have to deal with the inbreeding phenomenon and, in particular, with the consequences of inbreeding depression on characters of interest. Falconer & Mackay (1996) defined inbreeding depression as the reduction of the mean phenotypic value shown by characters connected with reproductive capacity or physiological efficiency, although the literature shows that inbreeding depression may impact any trait under selection. The genetic basis of this phenomenon is related to three hypotheses (Kristensen et al. 2010), namely partial Address for correspondence G. Leroy, AgroParisTech, UMR 1313 Genetique Animale et Biologie Int egrative, F-75231 Paris, France; INRA, UMR 1313 Genetique Animale et Biologie Integrative, F-78352 Jouy-en-Josas, France. E-mail: [email protected] Accepted for publication 01 May 2014 © 2014 Stichting International Foundation for Animal Genetics
dominance (increased expression of deleterious recessive alleles; Davenport 1908), overdominance (superiority of heterozygotes over both kinds of homozygotes; East 1908; Shull 1908) and epistasis (increased probability of favorable gene combinations for heterozygotes; Jain & Allard 1965). According to the predominance of one of the hypotheses, inbreeding depression is supposed to be a linear (partial dominance and overdominance) or non-linear function (epistasis) of inbreeding (Kristensen & Sorensen 2005; Croquet et al. 2007). In relation to the elimination of deleterious genes under selection pressure (inbreeding purge), deleterious consequences of inbreeding depression may eventually decrease overtime (Latter et al. 1995). Therefore, the level of inbreeding depression is expected to vary across breeds, given that populations do not share the same demographic and selection history (Mc Parland et al. 2009). These different elements raise numerous questions for populations under artificial selection. For instance, it would be interesting to investigate whether, in livestock species, one of the three hypotheses is preponderant over the others, given that it may have some consequences on the regression models used for the estimation of inbreeding depression. One may also wonder if some traits or populations are more affected by inbreeding depression than are others and what the subsequent economic consequences are. It also would be interesting to investigate to what extent the inbreeding purge phenomena may have occurred and 1
2
Leroy under what circumstances. Finally, one may investigate the perspective brought by genomics on knowledge of specific mechanisms of inbreeding depression or its converse, heterosis, as well as its management. The aim of the study was to answer, as far as possible, the aforementioned questions based on the existing literature, using in particular a meta-analysis approach considering 57 studies dealing with seven species.
Inbreeding depression: mechanisms involved It is considered that a change in genotypic value due to inbreeding is related to the existence of a directional dominance interaction between alleles (Falconer & Mackay 1996). Overdominance and partial dominance constitute the two historical hypotheses explaining inbreeding depression. These two hypotheses differ by the fact that, with partial dominance, heterozygotes are supposed to be superior to the mean of homozygotes, whereas with overdominance, they are supposed to have higher levels than both homozygotes (Kristensen & Sorensen 2005). Also, although in the second case, a heterozygote advantage will lead to a kind of balancing selection maintaining polymorphism, under partial dominance, deleterious alleles are supposed to be eliminated after some generations (Charlesworth & Charlesworth 1999). The importance of overdominance vs. partial dominance has been largely debated recently (Roff 2002). The question is indeed of interest, given that, among other things, inbreeding purge may exist only under the partial dominance hypothesis (Benesh et al. 2014). Differentiation between both hypotheses has been classically estimated by crossing inbred lines, considering that, according to the overdominance hypothesis mean fitness value of crosses should be equal to the outbred population, whereas under the partial dominance hypothesis, it should be higher due to purging of deleterious alleles (Roff 2002). Other approaches consider the identification of deleterious mutations as well as the use of marker data (Kristensen et al. 2010). Over the last number of years, most geneticists have considered that the role of overdominance toward inbreeding depression was minor in comparison with partial dominance (Lacy et al. 1996; Charlesworth & Charlesworth 1999; Roff 2002). The fact is that, in some cases, patterns of overdominance may be due to pseudo-overdominance phenomena, that is, a combination of recessive deleterious mutations at tightly linked loci (Graham et al. 1997; Charlesworth & Willis 2009). Using a genome-wide approach to assess the genomic basis of inbreeding depression, Ayroles et al. (2009) identified 567 genes involved in inbreeding depression among inbred Drosophilia melanogaster lines, 75 percent of them being additive, partially additive or dominant, and 25 percent expressing patterns of overdominance. In livestock species, it appears difficult to properly assess some of the questions related to the genetic basis of inbreeding for different reasons (ethics, generation intervals;
Kristensen & Sorensen 2005). Yet, Misztal et al. (1997) showed in Holstein cattle that large negative estimates of the inbreeding depressions were associated with higher estimates of the dominance variance. The importance of the role of overdominance compared with partial dominance also appears unclear and still deserves further investigation. Epistasy between genes constitutes the third hypothesis that may explain the inbreeding depression phenomenon, as heterozyogtes may likely combine favorable gene interactions. From a general point of view, little is known about the genomics mechanism behind those epistatic interactions and their importance in inbreeding depression (Kristensen & Sorensen 2005). However, because the relation between inbreeding and genotype differs under such a hypothesis, departure from linearity within regression models may allow identification of to what extent epistasy is involved within the inbreeding depression phenomenon.
Estimation of inbreeding depression and regression models Basically, inbreeding depression (genetic load) is assessed in outcrossing species by measuring the rate at which the trait of interest declines with the inbreeding coefficient (Charlesworth & Willis 2009). More precisely, in livestock species the standard procedure has been to consider a regression of individual performance on the individual pedigree inbreeding coefficient (Curik et al. 2001). However, there are several biases inherent to this choice, as pedigree estimators are highly sensitive to the limitation of pedigree knowledge and error rate (Leroy 2011; Leroy et al. 2012). As a consequence, accuracy of inbreeding depression estimation is reduced in cases of missing pedigree, as illustrated by Cassel et al. (2003) in Jersey and Holstein cattle. The distribution of inbreeding coefficients may also appear as problematic, as in general most of individuals within a population show no or little inbreeding, whereas only a minority of individuals has large values of inbreeding. Also, as pedigree inbreeding assumes identity by descent for an infinite number of unselected loci, it responds differently to selection, dominance epistasis or linkage in comparison with heterozygosity or true autozygosity (Curik et al. 2002). Consequently, the use of pedigree inbreeding can lead to underestimation under the overdominance hypothesis or overestimation under the partial dominance hypothesis (Curik et al. 2001). To take into account discrepancies in pedigree knowledge, some recent studies used individual inbreeding rate DF, developed by Gutierrez et al. (2009), instead of the pedigree coefficient. Such estimators seem to overcome the underestimation of inbreeding depression related to incomplete pedigree (Gonzalez-Recio et al. 2007; Gomez et al. 2009; Santana et al. 2012). When based on genomic information, runs of homozygosity (ROH) is considered the best approach to estimate inbreeding, as it allows,
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
Inbreeding depression in livestock species among others, the distinction between identity by descent and identity by state (Keller et al. 2011). The principle of the approach is to consider continuous lengths of homozygous loci, corresponding to haplotype transmission from parent to offspring, long ROH being likely to be due to identity by descent, that is, inbreeding. Several studies on cattle and pig breeds showed relatively high correlation (0.50–0.81) between ROH and genealogical estimators of inbreeding, indicating that ROH provide an accurate estimation of inbreeding (Purfield et al. 2012; Ferencakovic et al. 2013a; Silio et al. 2013). The estimation of inbreeding depression with ROH was applied in Holstein cattle with results consistent with what was estimated when using pedigree inbreeding (Bjelland et al. 2013). Silio et al. (2013) suggested ROH should be advisable in the absence of pedigree data. Keller et al. (2011) went further in their simulation study, concluding that ROH should be used preferentially over genealogical inbreeding for detecting inbreeding purge. Independent of the fact that dominance is partial or complete, when loci effects combine additively, the relation between inbreeding and genotypic value is supposed to be linear. However, this was not the case when dealing with epistatic interaction, because genotypic value may then decline proportionally to F² (Falconer & Mackay 1996). In the study by Wiener et al. (1992) on sheep breeds, greater or fewer large deviations were found from linearity depending on traits considered, suggesting the involvement of epistasy. However, note that it is quite difficult to interpret whether deviation of linearity is due to statistical artifacts or to real reflection of directional epistasis (Lynch & Walsh 1997). Also, deviation from linearity can also be explained by other events such as a shift in the environment (Kristensen & Sorensen 2005). Finally, heterogeneity of variance for the trait measured when inbreeding increases can also introduce some bias into the regression analysis, which assumes homogeneity of those variances (Burdon & Russel 1998). In practice, different studies in livestock species considering both linear and non-linear models (Croquet et al. 2007; Carrillo & Siewerdt 2010) have concluded that, for low to moderate inbreeding values (under 10–20%), linear models fit well. Depending on the species, traits and information available in the different studies, a large variability of environment variables was included in the model used to estimate inbreeding depression, additive genetic effects also being considered or not. For traits that could be related to both direct and maternal inbreeding, such as litter size, maternal inbreeding impact on traits could also be estimated. Note that there can be bias inherent to measures of inbreeding for some traits, for instance whether there is compensatory mating which was not registered (horse breeding). Finally, some studies also have differentiated between old vs. new inbreeding to assess the existence of inbreeding purge (see section ‘Occurrence of inbreeding purge in livestock species’).
Inbreeding depression according to species and traits: a meta-analysis As previously underscored, the different studies assessing inbreeding depression in livestock species have been based on a large variety of models and hypotheses. Yet in most of them, inbreeding depression is estimated as a linear regression coefficient between a phenotypic value and inbreeding coefficient. Therefore, whatever trait or population is considered, it is possible to consider a scaled estimation by dividing the regression coefficient by the mean of the phenotypic trait (Flock et al. 1991; DeRose & Roff 1999; Gomez-Raya et al. 2009); the other solution would be to consider phenotypic standard deviation instead of mean. To test whether there was some variation in inbreeding depression according to traits and populations, we performed a meta-analysis based on 57 studies (see Appendix S1) and seven species, namely cattle (24 studies), sheep (12 studies), pig (seven studies), horse (six studies), chicken (four studies), goat (two studies) and rabbit (two studies). The data set included inbreeding depression estimations grouped into 37 traits and five trait categories (see Tables 1 & S1), those categories corresponding to reproduction/survival traits (life history traits), weight/ growth traits, conformation traits (morphological traits), production traits [i.e., traits related to production (milk, eggs, fleece, litter weight) not directly corresponding to other categories] and other traits (locomotion and behavior). For each trait, we defined inbreeding depression bm and br as the regression coefficient of inbreeding (genealogical coefficient or ROH) on the trait divided by the mean or the standard deviation of the trait respectively. Because inbreeding depression is supposed to correspond to a decrease in phenotypic value, for characters where selection aims at minimizing the trait (mortality, calving interval, etc.), we changed the sign of the regression coefficient. Eleven and six outliers (values outside three standard deviations from the mean; Sauvant et al. 2008) were removed for bm and br respectively. The following model was used: Yijkl ¼ l þ Si þ Cj þ Tk ðCj Þ þ Fl þ Eijkl ; where Yijkl was a measure of inbreeding depression (either bm or br) for a given trait k of a population l on a study i with following explanatory variables (fixed effects) and covariables: study Si, trait category Cj, trait Tk, Fl the average inbreeding of population l (considering the range of F may impact the estimation of inbreeding depression) and Eijk the error term. Egg number and egg weight were not included as traits for br as there were not enough results for those two traits. Because species did not show any significant impact on inbreeding depression, and most of the breeds considered were specific to one study, those effects were not included within the model. Least square (LS) means were
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
3
4
Leroy Table 1 Least square means for inbreeding depression over the different traits scaled on mean (bm) and standard deviation (br). Trait category
Trait
bm
br
Reproduction/survival
Age at first egg or weaning Fertility Calving ease Gestation length Fecundity Litter size Litter size (maternal) Number offspring weaned Number offspring weaned (maternal) Offspring survival Offspring survival (maternal) Adult Survival Functional longevity Birth weight Body weight Weight (maternal) Growth Growth (maternal) Body dimensions Body condition score Bone quality Carcass/meat quality Conformation dairy Conformation other Scrotal circumference Milk yield Protein yield Fat yield SCC Milk others Egg number Egg weight Litter weight Litter weight (maternal) Production fleece Locomotion Behavior
0.117NS (0.118) 0.191* (0.082) 0.322* (0.135) 0.021NS (0.119) 0.309*** (0.067) 0.182NS (0.105) 0.254* (0.112) 0.686*** (0.146) 0.462** (0.169) 0.322** (0.099) 0.002NS (0.123) 0.489** (0.151) 0.19NS (0.104) 0.195** (0.074) 0.29*** (0.06) 0.253* (0.111) 0.299*** (0.089) 0.163NS (0.171) 0.171** (0.059) 0.113NS (0.145) 0.038NS (0.137) 0.023NS (0.095) 0.093NS (0.06) 0.079NS (0.059) 0.31* (0.129) 0.367*** (0.092) 0.225* (0.093) 0.249** (0.093) 0.414*** (0.125) 0.155NS (0.15) 0.235NS (0.334) 0.301NS (0.196) 0.853*** (0.15) 0.34* (0.166) 0.369* (0.151) 0.215NS (0.146) 0.029NS (0.137)
0.691* (0.35) 0.414NS (0.262) 0.713NS (0.396) 0.039NS (0.328) 0.227NS (0.198) 0.384NS (0.301) 0.28NS (0.321) 1.092** (0.396) 0.4NS (0.461) 0.431NS (0.281) 0.147NS (0.345) 1.047* (0.412) 0.299NS (0.329) 0.429NS (0.23) 0.771*** (0.191) 0.384NS (0.325) 0.741* (0.347) 0.489NS (0.552) 0.707*** (0.177) 0.235NS (0.399) 0.201NS (0.38) 0.667NS (0.383) 0.074NS (0.182) 0.383* (0.174) 1.194* (0.488) 1.277*** (0.278) 1.144*** (0.284) 1.049*** (0.284) 0.205NS (0.353) 0.461NS (0.411)
Weight/growth
Conformation
Production
Other traits
1.144** (0.409) 0.259NS (0.452) 0.996* (0.435) 1.009* (0.402) 0.032NS (0.443)
non significant, *P < 0.05, **P < 0.01, ***P < 0.001.
NS
computed to investigate an eventual difference between traits and between trait categories. Statistical analysis was performed using the SAS GLM procedure. Over the 1218 and 1016 results analyzed for bm and br respectively, 876 and 727 were found to be less than or equal to zero. Average inbreeding depression corresponded to 0.137 (median = 0.105, SD = 0.523), that is, a decrease of 0.137 percent of the mean of the trait per 1 percent of inbreeding (bm) (Fig. S1). When scaled by the standard deviation of the trait (br), inbreeding depression was found on average equal to 0.56 (median = 0.527, SD = 1.882). For bm, 814 of the results corresponded to cattle species and 197 to sheep species (Table S1). According to traits, the median of bm ranged between 0.464 (adult survival) and 0.015 (offspring survival), whereas the median of br ranged between 1.406 (production fleece) and 0.244 (functional longevity; Table S2), median results reflecting both estimations being highly correlated
(r = 0.84). As shown in Fig. 1, production traits seemed to be strongly affected by inbreeding depression, in comparison with other trait categories. Models were applied for 988 and 801 estimations of bm and br respectively. P-values related to fixed effects differed according to the two estimates of inbreeding depression. For bm, significant impacts were found related to the study (P < 0.001) and related to the trait category (P = 0.015) and the trait (P < 0.001), but average inbreeding coefficient did not have a significant effect in the model (P = 0.122). For br study (P < 0.001), traits (P = 0.003) and average inbreeding coefficient (P = 0.010) showed a significant effect on inbreeding depression, whereas trait category did not have a significant effect (P = 0.050). The estimate for the average inbreeding coefficient effect on br was 0.037 per percentage of inbreeding. R2 was found to be equal to 0.146 and 0.157 for bm and br models respectively. Considering bm (and br), LS means were found equal to 0.092 (0.473),
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
Inbreeding depression in livestock species
bm
0.351 (0.817), 0.222 (0.336), 0.24 (0.563) and 0.093 (0.488) for conformation, production, reproduction/survival, weight/growth and ‘other traits’ trait categories respectively. Inbreeding depression for production trait categories was found to be significantly lower for production traits than for all aggregated category traits, considering either bm (P = 0.005) or br (P = 0.034). According to the traits (Table 1), LS means ranged between 0.853 (litter weight) and +0.321 (calving ease) for bm and between 1.277 (milk yield) and +0.713 (calving ease) for br. Considering either bm (or br), for 33 (or 30) of the 37 (or 35) traits, inbreeding depression was significantly (P < 0.05) negative for 20 (or 14) of them. In this study, the fact that no species effect was identified confirms the hypothesis that inbreeding depression is more population (breed) specific, that is, related to allele frequencies segregating within each breed, than due to physiological specificities of a given species. In their meta-analysis considering inbreeding depression in animal species, DeRose & Roff (1999) estimated values for bm (and br) to be around 0.472 (and 1.453) and 0.089 (and 0.594; sign was inversed here) for life history (fecundity, survival and development) and morphological (adult body size) traits respectively, which is of the same order as our results. However, note that in the DeRose & Roff study, regression coefficients for which inbred values exceeded outbred values were put to zero, leading to a probable larger estimation of inbreeding depression effects. Nevertheless, in this study, inbreeding depression showed a larger effect for traits related to production. Therefore, our results do not support
Other traits
Production
Conformation
Weight/Growth
Figure 1 Box plots of inbreeding depression scaled on mean (bm) and standard deviation (br) over the different trait categories (for a given trait category; box represents 0.75 quantile, middle bar is median value and + is mean value).
Reproduction/survival
bσ
the assumption that fitness traits are particularly sensitive to inbreeding depression (Falconer & Mackay 1996) for livestock species, in agreement with results by Analla et al. (1998). Note that the meta-analysis performed on animal populations by Chapman et al. (2009) did not find a particular difference between life history, morphological and physiological trait types for correlation between traits and molecular heterozygosity. DeRose & Roff (1999) interpreted their difference by considering that there is less directional dominance for morphological traits compared with those for fitness. Indeed, considering the dominance effect d for a given locus, inbreeding depression can be expressed as 2dpqF (Falconer & Mackay 1996). Therefore, inbreeding will be detrimental if, overall, loci d is positive, which happens in the case of selection, as fixation occurs more quickly for loci with negative d. We may then hypothesize that directional dominance within a given trait is a function of the fact that the trait has been more or less strongly selected. In wild species, selection occurs mainly for fitness traits, whereas in livestock species, selection is made on fitness traits but also on other traits, related to production for instance. Those traits would be impacted by inbreeding all the more given that they are intensively selected, whereas in nature they would not show any inbreeding depression. We may also expect better precision for estimating inbreeding depression for traits with high heritability. Note that the classification of traits among the different categories could be discussed in relation to this hypothesis. In meat sheep and pigs, for instance, over the last decades selection goals have focused on improvement of
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
5
6
Leroy traits related to growth, body weight and number of offspring weaned, and those traits showed a large inbreeding depression impact here. Also, a trait such as litter weight can be considered a production trait, considering for instance that meat sheep are bred for producing meat, but also as a life history (weight/growth reproduction) trait, as it also is a function of prolificacy. This meta-analysis does not particularly support either the hypothesis that inbreeding depression impact is larger earlier in life (Adamec et al. 2006; Sorensen et al. 2006). Yet, in some cases, traits that constitute a combination of other traits showed larger inbreeding depression than did the traits included for their combination; for instance, considering bm, LS means for direct and maternal inbreeding depression were found to be 0.182 and 0.254 for litter size, 0.322 and 0.002 for offspring survival but 0.686 and 0.462 for number of offspring weaned. When comparing direct and maternal effect of inbreeding on traits, in general, the direct effects were found to be larger, except for litter size, which could be explained by the fact that relative to ‘later’ traits, litter size is largely related to the physiological status of the mother (ovulation rate, uterine capacity). The results of this meta-analysis illustrate that, in livestock species, any kind of selected trait may be affected by inbreeding depression. For a given trait and population, intensity of inbreeding depression may depend on the importance of dominance variance within the trait (Misztal et al. 1997), that is, to the number of genes involved, their mode of action under inbreeding depression (Curik et al. 2001) and to the selection history of population studied, as illustrated below.
Heterogeneity of inbreeding depression The ability to compute partial inbreeding coefficients (i.e. inbreeding coefficient related to alleles transmitted by a specific ancestor) has provided a way to test whether genetic load is equally distributed among founder genomes. Considering rodents (Lacy et al. 1996) and domestic species (Miglior et al. 1994; Rodriganez et al. 1998; Gulisija et al. 2006; Casellas et al. 2008, 2009, 2010), several studies have shown a large magnitude of neutral or negative (or eventually positive) effects of partial inbreeding coefficients, whole inbreeding being in any case deleterious to traits measured. This finding supports the hypothesis that a large part of genetic load could be due to a small number of alleles with major deleterious effects. The study by Casellas et al. (2010) also reported interactions between partial inbreeding coefficients of different founders, revealing what could be epistatic inbreeding depression phenomena. The fact that there is variation among lineages in inbreeding depression may have some consequence for genetic management. This indeed implies that detrimental effect of founder alleles should be measured for a given
number of traits and the status of candidates with respect to founder alleles impacting inbreeding depression should be taken into account when implementing conservation strategies (Rodriganez et al. 1998).
Economic consequences of inbreeding depression As underscored by Gama & Smith (1993), economic constraints related to inbreeding depression are first related to the extent of purebreeding within the species. For poultry, production systems are based almost entirely on cross-breeding schemes, and inbreeding depression can probably be economically neglected. By contrast, a large majority of dairy cows is purebred. Therefore management of inbreeding depression can be an important concern, whereas the situation would probably be intermediate for other species. This and the quality of the dataset for dairy cattle explains probably why a large portion of studies dealing with inbreeding depression (18 of the 57 studies here) focused on those breeds. For a trait such as milk yield, we estimated a decrease of 0.37 percent per 1 percent of inbreeding (Table 1). In a breed such as Holstein, the annual inbreeding rate can be approximated to 0.12 percent per year, considering an inbreeding rate per generation of approximately 0.6 percent (Danchin-Burge et al. 2011) and generation interval of around five years. Therefore, because the annual genetic progress in Holstein is estimated to be close to 100 kg per lactation, that is, 1 percent of the current phenotypic mean (around 10 000 kg), inbreeding depression per year will correspond to 0.044 percent of the phenotypic mean, that is, to 4.4 percent of the genetic progress. On this result alone, the impact of inbreeding depression can be considered relatively limited, yet the impact of inbreeding depression on total performance is likely to be larger than when considering traits separately, as economic return can be considered as a multiplicative combination of single traits (Kristensen & Sorensen 2005). Several studies investigated an economic quantification of inbreeding depression considering either one trait or an aggregate of several traits. For instance, considering impact on mastitis incidence alone in Danish Holstein, Sorensen et al. (2006) estimated a reduction of $11 in lifetime net return per cow on average. Also for the Holstein breed, Croquet et al. (2006) computed a loss of lifetime profit of €6.13 per 1 percent increase of inbreeding, that is, €22.7 on average, whereas in the study by Smith et al. (1998), the loss of lifetime net income ranged between $22 and 24 per 1 percent of inbreeding, that is, between $65 and 73 on average. The difference between both results, even considering rate change, could be eventually explained by the fact the results of the Croquet et al. study were probably underestimated, as the traits related to fertility, longevity and health were not taken into account in their study. In
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
Inbreeding depression in livestock species sheep, the average economic loss per ewe in value of production was estimated at $17 for average inbreeding (Ercanbrack & Knight 1991). All these results confirm that inbreeding depression, through the different impacts it may have on traits of interest, may reduce the economic income of breeders. The control of inbreeding rate within livestock population selection schemes, through optimal contribution for instance (Clark et al. 2013), therefore appears as a necessity, at least for species raised mainly as purebreds.
Occurrence of inbreeding purge in livestock species As previously stated, under the partial dominance hypothesis, inbreeding should expose deleterious alleles to selection. Different reviews have supported the existence of purging within plants and animals, however, with generally limited effects and large discrepancies among the results (Ballou 1997; Crnokrak & Barret 2002). According to Kristensen & Sorensen (2005), it is assumed that purging is likely to occur (i) if partial dominance is of major importance relative to other hypotheses (overdominance and espistasy), (ii) if selection is strong relative to drift allowing deleterious alleles to be eliminated and not randomly fixed (the deleterious effect should therefore be large) and (iii) if deleterious alleles cannot be introduced through gene flow (closed population). Also, a larger amount of time during which alleles are exposed to selection, relative to the amount of inbreeding, may increase the possibility of occurrence of inbreeding purge. Therefore, to assess the existence of the phenomenon, one may either differentiate the consequence of ‘fast’ vs. ‘slow’ inbreeding, or ‘new’ vs. ‘old’ inbreeding (Hinrichs et al. 2007). In the first case, it is considered that slow inbreeding increases the number of generations needed to purge the genetic load. In the second case, it can be considered that individuals with inbred ancestry are less likely to be carriers of deleterious alleles in comparison with individuals with more recent inbreeding. One may also suppose that ‘old’ deleterious mutations are likely to have been purged in comparison with new ones. A few studies assessed the existence of inbreeding purge in livestock species, based mainly on the comparison between new and old inbreeding. Based on a simulation study within the Jersey cattle population, Gulisija & Crow (2007) agreed with Hedrick (1994), concluding that inbreeding purge could occur efficiently only for alleles with large effects, with reduction of genetic load around 12.6 percent for alleles with a strong effect (fitness near 0). For alleles with small effects, purging would probably be negligible. In practice, Mc Parland et al. (2009) provided evidence of an inbreeding purge for milk production traits in Holstein cattle, a larger part of inbreeding depression being attributable to new inbreeding. In the same study, however,
no evidence of inbreeding purge was found for fertility traits, either due to limited selection on those trait (antagonism with milk production traits) or to predominance of overdominance. In pigs, K€ ock et al. (2009) showed that litter size performance as well was affected by old and new inbreeding, thus providing no evidence of inbreeding purge. It has to be noted that some examples may exist of strains having naturally purged their genetic load, such as the Chillingham cattle feral herd, remaining viable and fertile despite an almost complete homozygosity (Visscher et al. 2001). Therefore, investigation of inbreeding purge within livestock species deserves further investigation.
Inbreeding by environment (I 3 E) interactions The question of the interactions between inbreeding and environment is strongly related to the question of genetic homeostasis, developed by Lerner (1954), stating that heterozygotes (individuals) are less responsive to environmental stresses than are homozygotes, as far as traits directly related to fitness are concerned. Adaptive capacities to environment modifications constitute traits of growing interest for breeders, especially given the concerns relative to climate change (Piling & Hoffmann 2011). In different parts of the world, temperature increases associated with climate change are expected to significantly impact levels of animal production and their economic viability unless management and genetic resources are adapted (Mader et al. 2009). The results from theoretical and experimental results have shown that inbred individuals are particularly sensitive to environment changes. For instance, the study of Jimenez et al. (1994) showed more severe effects of inbreeding on mice survival in natural environment when compared to captive one. The meta-analysis of Armbruster & Reed (2005) on plant and model species showed for instance that, when changing from a benign to stressful environment, there was an increase of inbreeding depression in 76 percent of the cases. Indeed, inbreeding seems to have an impact on canalization, that is, the capacity to maintain the main phenotype under various environments, which is probably reduced under inbreeding (Kristensen et al. 2010). Reed et al. (2012) proposed three hypotheses behind this interaction: (i) an increased expression of genetic load, that is, deleterious alleles with higher fitness cost, or larger number of deleterious alleles expressed (neutral alleles under a benign environment and deleterious under a stressful one); (ii) a global physiological weakening of inbred individuals, therefore more sensitive to stress; and (iii) an increased phenotypic variation under stress, increasing expression of inbreeding depression. In livestock species, there is a noteworthy lack of investigation surrounding I 9 E interaction, probably related to the difficulty in implementing experimental
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
7
8
Leroy designs in comparison with model species. From a general point of view, livestock selection schemes need better incorporation of genotype–environment effect within selection models (Reed et al. 2012). There is also a strong need for experiments to define more clearly what adaptive traits for livestock species are and what the basis and molecular mechanisms behind I 9 E environment for those species are.
Perspectives brought by genomics Recent developments of genomic and other ‘omic’ approaches are, of course, of paramount interest for estimation, understanding and management of inbreeding depression. First, as previously stated, genomic estimators of inbreeding do not suffer from drawbacks inherent to genealogical tools (reliability, limited pedigree knowledge, assumption that founders are unrelated, etc.). Also, genealogical approaches generally do not take into account the stochastic nature of recombination. Among genomic approaches, ROH is considered the optimal one to measure inbreeding (Keller et al. 2011; Bjelland et al. 2013). Moreover, because long ROH correspond to recent inbreeding, whereas shorter ROH indicate more distant ancestral effects such as breed founder effects (Purfield et al. 2012), the ROH approach could therefore be used to differentiate more clearly between old and new inbreeding. The approach may therefore provide interesting results about the inbreeding purge phenomenon, independently from pedigree knowledge limitations. Yet, the ROH approach has its own limits. Silio et al. (2013) indicated that some ROH metrics could be weakly correlated with inbreeding due to unequal repartition of ROH within chromosomes in that study. In their study on cattle breeds, Ferencakovic et al. (2013b) reported overestimation of inbreeding when using the 50k SNP chip with a short ROH segment (
doi: 10.1111/age.12178
Inbreeding depression in livestock species: review and meta-analysis G. Leroy*† *AgroParisTech, UMR 1313 Genetique Animale et Biologie Int egrative, F-75231 Paris, France. †INRA, UMR 1313 G en etique Animale et Biologie Integrative, F-78352 Jouy-en-Josas, France.
Summary
Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta-analysis conducted on 57 studies and seven livestock species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon. Keywords domestic animals, genetic diversity, inbreeding, production traits
Introduction In livestock species, most breeds can be considered as populations of limited size in relation to an unequal contribution of a limited number of reproducers to the next generation, as well as in relation to the fact that, in a quantitative scheme, selected reproducers are likely to be related (Robertson 1961). As a consequence, in relation to effective population sizes that generally range between a few tens and several hundreds of individuals (Leroy et al. 2013), the occurrence of inbreeding over generations cannot be avoided. Therefore, breeders have to deal with the inbreeding phenomenon and, in particular, with the consequences of inbreeding depression on characters of interest. Falconer & Mackay (1996) defined inbreeding depression as the reduction of the mean phenotypic value shown by characters connected with reproductive capacity or physiological efficiency, although the literature shows that inbreeding depression may impact any trait under selection. The genetic basis of this phenomenon is related to three hypotheses (Kristensen et al. 2010), namely partial Address for correspondence G. Leroy, AgroParisTech, UMR 1313 Genetique Animale et Biologie Int egrative, F-75231 Paris, France; INRA, UMR 1313 Genetique Animale et Biologie Integrative, F-78352 Jouy-en-Josas, France. E-mail: [email protected] Accepted for publication 01 May 2014 © 2014 Stichting International Foundation for Animal Genetics
dominance (increased expression of deleterious recessive alleles; Davenport 1908), overdominance (superiority of heterozygotes over both kinds of homozygotes; East 1908; Shull 1908) and epistasis (increased probability of favorable gene combinations for heterozygotes; Jain & Allard 1965). According to the predominance of one of the hypotheses, inbreeding depression is supposed to be a linear (partial dominance and overdominance) or non-linear function (epistasis) of inbreeding (Kristensen & Sorensen 2005; Croquet et al. 2007). In relation to the elimination of deleterious genes under selection pressure (inbreeding purge), deleterious consequences of inbreeding depression may eventually decrease overtime (Latter et al. 1995). Therefore, the level of inbreeding depression is expected to vary across breeds, given that populations do not share the same demographic and selection history (Mc Parland et al. 2009). These different elements raise numerous questions for populations under artificial selection. For instance, it would be interesting to investigate whether, in livestock species, one of the three hypotheses is preponderant over the others, given that it may have some consequences on the regression models used for the estimation of inbreeding depression. One may also wonder if some traits or populations are more affected by inbreeding depression than are others and what the subsequent economic consequences are. It also would be interesting to investigate to what extent the inbreeding purge phenomena may have occurred and 1
2
Leroy under what circumstances. Finally, one may investigate the perspective brought by genomics on knowledge of specific mechanisms of inbreeding depression or its converse, heterosis, as well as its management. The aim of the study was to answer, as far as possible, the aforementioned questions based on the existing literature, using in particular a meta-analysis approach considering 57 studies dealing with seven species.
Inbreeding depression: mechanisms involved It is considered that a change in genotypic value due to inbreeding is related to the existence of a directional dominance interaction between alleles (Falconer & Mackay 1996). Overdominance and partial dominance constitute the two historical hypotheses explaining inbreeding depression. These two hypotheses differ by the fact that, with partial dominance, heterozygotes are supposed to be superior to the mean of homozygotes, whereas with overdominance, they are supposed to have higher levels than both homozygotes (Kristensen & Sorensen 2005). Also, although in the second case, a heterozygote advantage will lead to a kind of balancing selection maintaining polymorphism, under partial dominance, deleterious alleles are supposed to be eliminated after some generations (Charlesworth & Charlesworth 1999). The importance of overdominance vs. partial dominance has been largely debated recently (Roff 2002). The question is indeed of interest, given that, among other things, inbreeding purge may exist only under the partial dominance hypothesis (Benesh et al. 2014). Differentiation between both hypotheses has been classically estimated by crossing inbred lines, considering that, according to the overdominance hypothesis mean fitness value of crosses should be equal to the outbred population, whereas under the partial dominance hypothesis, it should be higher due to purging of deleterious alleles (Roff 2002). Other approaches consider the identification of deleterious mutations as well as the use of marker data (Kristensen et al. 2010). Over the last number of years, most geneticists have considered that the role of overdominance toward inbreeding depression was minor in comparison with partial dominance (Lacy et al. 1996; Charlesworth & Charlesworth 1999; Roff 2002). The fact is that, in some cases, patterns of overdominance may be due to pseudo-overdominance phenomena, that is, a combination of recessive deleterious mutations at tightly linked loci (Graham et al. 1997; Charlesworth & Willis 2009). Using a genome-wide approach to assess the genomic basis of inbreeding depression, Ayroles et al. (2009) identified 567 genes involved in inbreeding depression among inbred Drosophilia melanogaster lines, 75 percent of them being additive, partially additive or dominant, and 25 percent expressing patterns of overdominance. In livestock species, it appears difficult to properly assess some of the questions related to the genetic basis of inbreeding for different reasons (ethics, generation intervals;
Kristensen & Sorensen 2005). Yet, Misztal et al. (1997) showed in Holstein cattle that large negative estimates of the inbreeding depressions were associated with higher estimates of the dominance variance. The importance of the role of overdominance compared with partial dominance also appears unclear and still deserves further investigation. Epistasy between genes constitutes the third hypothesis that may explain the inbreeding depression phenomenon, as heterozyogtes may likely combine favorable gene interactions. From a general point of view, little is known about the genomics mechanism behind those epistatic interactions and their importance in inbreeding depression (Kristensen & Sorensen 2005). However, because the relation between inbreeding and genotype differs under such a hypothesis, departure from linearity within regression models may allow identification of to what extent epistasy is involved within the inbreeding depression phenomenon.
Estimation of inbreeding depression and regression models Basically, inbreeding depression (genetic load) is assessed in outcrossing species by measuring the rate at which the trait of interest declines with the inbreeding coefficient (Charlesworth & Willis 2009). More precisely, in livestock species the standard procedure has been to consider a regression of individual performance on the individual pedigree inbreeding coefficient (Curik et al. 2001). However, there are several biases inherent to this choice, as pedigree estimators are highly sensitive to the limitation of pedigree knowledge and error rate (Leroy 2011; Leroy et al. 2012). As a consequence, accuracy of inbreeding depression estimation is reduced in cases of missing pedigree, as illustrated by Cassel et al. (2003) in Jersey and Holstein cattle. The distribution of inbreeding coefficients may also appear as problematic, as in general most of individuals within a population show no or little inbreeding, whereas only a minority of individuals has large values of inbreeding. Also, as pedigree inbreeding assumes identity by descent for an infinite number of unselected loci, it responds differently to selection, dominance epistasis or linkage in comparison with heterozygosity or true autozygosity (Curik et al. 2002). Consequently, the use of pedigree inbreeding can lead to underestimation under the overdominance hypothesis or overestimation under the partial dominance hypothesis (Curik et al. 2001). To take into account discrepancies in pedigree knowledge, some recent studies used individual inbreeding rate DF, developed by Gutierrez et al. (2009), instead of the pedigree coefficient. Such estimators seem to overcome the underestimation of inbreeding depression related to incomplete pedigree (Gonzalez-Recio et al. 2007; Gomez et al. 2009; Santana et al. 2012). When based on genomic information, runs of homozygosity (ROH) is considered the best approach to estimate inbreeding, as it allows,
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
Inbreeding depression in livestock species among others, the distinction between identity by descent and identity by state (Keller et al. 2011). The principle of the approach is to consider continuous lengths of homozygous loci, corresponding to haplotype transmission from parent to offspring, long ROH being likely to be due to identity by descent, that is, inbreeding. Several studies on cattle and pig breeds showed relatively high correlation (0.50–0.81) between ROH and genealogical estimators of inbreeding, indicating that ROH provide an accurate estimation of inbreeding (Purfield et al. 2012; Ferencakovic et al. 2013a; Silio et al. 2013). The estimation of inbreeding depression with ROH was applied in Holstein cattle with results consistent with what was estimated when using pedigree inbreeding (Bjelland et al. 2013). Silio et al. (2013) suggested ROH should be advisable in the absence of pedigree data. Keller et al. (2011) went further in their simulation study, concluding that ROH should be used preferentially over genealogical inbreeding for detecting inbreeding purge. Independent of the fact that dominance is partial or complete, when loci effects combine additively, the relation between inbreeding and genotypic value is supposed to be linear. However, this was not the case when dealing with epistatic interaction, because genotypic value may then decline proportionally to F² (Falconer & Mackay 1996). In the study by Wiener et al. (1992) on sheep breeds, greater or fewer large deviations were found from linearity depending on traits considered, suggesting the involvement of epistasy. However, note that it is quite difficult to interpret whether deviation of linearity is due to statistical artifacts or to real reflection of directional epistasis (Lynch & Walsh 1997). Also, deviation from linearity can also be explained by other events such as a shift in the environment (Kristensen & Sorensen 2005). Finally, heterogeneity of variance for the trait measured when inbreeding increases can also introduce some bias into the regression analysis, which assumes homogeneity of those variances (Burdon & Russel 1998). In practice, different studies in livestock species considering both linear and non-linear models (Croquet et al. 2007; Carrillo & Siewerdt 2010) have concluded that, for low to moderate inbreeding values (under 10–20%), linear models fit well. Depending on the species, traits and information available in the different studies, a large variability of environment variables was included in the model used to estimate inbreeding depression, additive genetic effects also being considered or not. For traits that could be related to both direct and maternal inbreeding, such as litter size, maternal inbreeding impact on traits could also be estimated. Note that there can be bias inherent to measures of inbreeding for some traits, for instance whether there is compensatory mating which was not registered (horse breeding). Finally, some studies also have differentiated between old vs. new inbreeding to assess the existence of inbreeding purge (see section ‘Occurrence of inbreeding purge in livestock species’).
Inbreeding depression according to species and traits: a meta-analysis As previously underscored, the different studies assessing inbreeding depression in livestock species have been based on a large variety of models and hypotheses. Yet in most of them, inbreeding depression is estimated as a linear regression coefficient between a phenotypic value and inbreeding coefficient. Therefore, whatever trait or population is considered, it is possible to consider a scaled estimation by dividing the regression coefficient by the mean of the phenotypic trait (Flock et al. 1991; DeRose & Roff 1999; Gomez-Raya et al. 2009); the other solution would be to consider phenotypic standard deviation instead of mean. To test whether there was some variation in inbreeding depression according to traits and populations, we performed a meta-analysis based on 57 studies (see Appendix S1) and seven species, namely cattle (24 studies), sheep (12 studies), pig (seven studies), horse (six studies), chicken (four studies), goat (two studies) and rabbit (two studies). The data set included inbreeding depression estimations grouped into 37 traits and five trait categories (see Tables 1 & S1), those categories corresponding to reproduction/survival traits (life history traits), weight/ growth traits, conformation traits (morphological traits), production traits [i.e., traits related to production (milk, eggs, fleece, litter weight) not directly corresponding to other categories] and other traits (locomotion and behavior). For each trait, we defined inbreeding depression bm and br as the regression coefficient of inbreeding (genealogical coefficient or ROH) on the trait divided by the mean or the standard deviation of the trait respectively. Because inbreeding depression is supposed to correspond to a decrease in phenotypic value, for characters where selection aims at minimizing the trait (mortality, calving interval, etc.), we changed the sign of the regression coefficient. Eleven and six outliers (values outside three standard deviations from the mean; Sauvant et al. 2008) were removed for bm and br respectively. The following model was used: Yijkl ¼ l þ Si þ Cj þ Tk ðCj Þ þ Fl þ Eijkl ; where Yijkl was a measure of inbreeding depression (either bm or br) for a given trait k of a population l on a study i with following explanatory variables (fixed effects) and covariables: study Si, trait category Cj, trait Tk, Fl the average inbreeding of population l (considering the range of F may impact the estimation of inbreeding depression) and Eijk the error term. Egg number and egg weight were not included as traits for br as there were not enough results for those two traits. Because species did not show any significant impact on inbreeding depression, and most of the breeds considered were specific to one study, those effects were not included within the model. Least square (LS) means were
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
3
4
Leroy Table 1 Least square means for inbreeding depression over the different traits scaled on mean (bm) and standard deviation (br). Trait category
Trait
bm
br
Reproduction/survival
Age at first egg or weaning Fertility Calving ease Gestation length Fecundity Litter size Litter size (maternal) Number offspring weaned Number offspring weaned (maternal) Offspring survival Offspring survival (maternal) Adult Survival Functional longevity Birth weight Body weight Weight (maternal) Growth Growth (maternal) Body dimensions Body condition score Bone quality Carcass/meat quality Conformation dairy Conformation other Scrotal circumference Milk yield Protein yield Fat yield SCC Milk others Egg number Egg weight Litter weight Litter weight (maternal) Production fleece Locomotion Behavior
0.117NS (0.118) 0.191* (0.082) 0.322* (0.135) 0.021NS (0.119) 0.309*** (0.067) 0.182NS (0.105) 0.254* (0.112) 0.686*** (0.146) 0.462** (0.169) 0.322** (0.099) 0.002NS (0.123) 0.489** (0.151) 0.19NS (0.104) 0.195** (0.074) 0.29*** (0.06) 0.253* (0.111) 0.299*** (0.089) 0.163NS (0.171) 0.171** (0.059) 0.113NS (0.145) 0.038NS (0.137) 0.023NS (0.095) 0.093NS (0.06) 0.079NS (0.059) 0.31* (0.129) 0.367*** (0.092) 0.225* (0.093) 0.249** (0.093) 0.414*** (0.125) 0.155NS (0.15) 0.235NS (0.334) 0.301NS (0.196) 0.853*** (0.15) 0.34* (0.166) 0.369* (0.151) 0.215NS (0.146) 0.029NS (0.137)
0.691* (0.35) 0.414NS (0.262) 0.713NS (0.396) 0.039NS (0.328) 0.227NS (0.198) 0.384NS (0.301) 0.28NS (0.321) 1.092** (0.396) 0.4NS (0.461) 0.431NS (0.281) 0.147NS (0.345) 1.047* (0.412) 0.299NS (0.329) 0.429NS (0.23) 0.771*** (0.191) 0.384NS (0.325) 0.741* (0.347) 0.489NS (0.552) 0.707*** (0.177) 0.235NS (0.399) 0.201NS (0.38) 0.667NS (0.383) 0.074NS (0.182) 0.383* (0.174) 1.194* (0.488) 1.277*** (0.278) 1.144*** (0.284) 1.049*** (0.284) 0.205NS (0.353) 0.461NS (0.411)
Weight/growth
Conformation
Production
Other traits
1.144** (0.409) 0.259NS (0.452) 0.996* (0.435) 1.009* (0.402) 0.032NS (0.443)
non significant, *P < 0.05, **P < 0.01, ***P < 0.001.
NS
computed to investigate an eventual difference between traits and between trait categories. Statistical analysis was performed using the SAS GLM procedure. Over the 1218 and 1016 results analyzed for bm and br respectively, 876 and 727 were found to be less than or equal to zero. Average inbreeding depression corresponded to 0.137 (median = 0.105, SD = 0.523), that is, a decrease of 0.137 percent of the mean of the trait per 1 percent of inbreeding (bm) (Fig. S1). When scaled by the standard deviation of the trait (br), inbreeding depression was found on average equal to 0.56 (median = 0.527, SD = 1.882). For bm, 814 of the results corresponded to cattle species and 197 to sheep species (Table S1). According to traits, the median of bm ranged between 0.464 (adult survival) and 0.015 (offspring survival), whereas the median of br ranged between 1.406 (production fleece) and 0.244 (functional longevity; Table S2), median results reflecting both estimations being highly correlated
(r = 0.84). As shown in Fig. 1, production traits seemed to be strongly affected by inbreeding depression, in comparison with other trait categories. Models were applied for 988 and 801 estimations of bm and br respectively. P-values related to fixed effects differed according to the two estimates of inbreeding depression. For bm, significant impacts were found related to the study (P < 0.001) and related to the trait category (P = 0.015) and the trait (P < 0.001), but average inbreeding coefficient did not have a significant effect in the model (P = 0.122). For br study (P < 0.001), traits (P = 0.003) and average inbreeding coefficient (P = 0.010) showed a significant effect on inbreeding depression, whereas trait category did not have a significant effect (P = 0.050). The estimate for the average inbreeding coefficient effect on br was 0.037 per percentage of inbreeding. R2 was found to be equal to 0.146 and 0.157 for bm and br models respectively. Considering bm (and br), LS means were found equal to 0.092 (0.473),
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
Inbreeding depression in livestock species
bm
0.351 (0.817), 0.222 (0.336), 0.24 (0.563) and 0.093 (0.488) for conformation, production, reproduction/survival, weight/growth and ‘other traits’ trait categories respectively. Inbreeding depression for production trait categories was found to be significantly lower for production traits than for all aggregated category traits, considering either bm (P = 0.005) or br (P = 0.034). According to the traits (Table 1), LS means ranged between 0.853 (litter weight) and +0.321 (calving ease) for bm and between 1.277 (milk yield) and +0.713 (calving ease) for br. Considering either bm (or br), for 33 (or 30) of the 37 (or 35) traits, inbreeding depression was significantly (P < 0.05) negative for 20 (or 14) of them. In this study, the fact that no species effect was identified confirms the hypothesis that inbreeding depression is more population (breed) specific, that is, related to allele frequencies segregating within each breed, than due to physiological specificities of a given species. In their meta-analysis considering inbreeding depression in animal species, DeRose & Roff (1999) estimated values for bm (and br) to be around 0.472 (and 1.453) and 0.089 (and 0.594; sign was inversed here) for life history (fecundity, survival and development) and morphological (adult body size) traits respectively, which is of the same order as our results. However, note that in the DeRose & Roff study, regression coefficients for which inbred values exceeded outbred values were put to zero, leading to a probable larger estimation of inbreeding depression effects. Nevertheless, in this study, inbreeding depression showed a larger effect for traits related to production. Therefore, our results do not support
Other traits
Production
Conformation
Weight/Growth
Figure 1 Box plots of inbreeding depression scaled on mean (bm) and standard deviation (br) over the different trait categories (for a given trait category; box represents 0.75 quantile, middle bar is median value and + is mean value).
Reproduction/survival
bσ
the assumption that fitness traits are particularly sensitive to inbreeding depression (Falconer & Mackay 1996) for livestock species, in agreement with results by Analla et al. (1998). Note that the meta-analysis performed on animal populations by Chapman et al. (2009) did not find a particular difference between life history, morphological and physiological trait types for correlation between traits and molecular heterozygosity. DeRose & Roff (1999) interpreted their difference by considering that there is less directional dominance for morphological traits compared with those for fitness. Indeed, considering the dominance effect d for a given locus, inbreeding depression can be expressed as 2dpqF (Falconer & Mackay 1996). Therefore, inbreeding will be detrimental if, overall, loci d is positive, which happens in the case of selection, as fixation occurs more quickly for loci with negative d. We may then hypothesize that directional dominance within a given trait is a function of the fact that the trait has been more or less strongly selected. In wild species, selection occurs mainly for fitness traits, whereas in livestock species, selection is made on fitness traits but also on other traits, related to production for instance. Those traits would be impacted by inbreeding all the more given that they are intensively selected, whereas in nature they would not show any inbreeding depression. We may also expect better precision for estimating inbreeding depression for traits with high heritability. Note that the classification of traits among the different categories could be discussed in relation to this hypothesis. In meat sheep and pigs, for instance, over the last decades selection goals have focused on improvement of
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
5
6
Leroy traits related to growth, body weight and number of offspring weaned, and those traits showed a large inbreeding depression impact here. Also, a trait such as litter weight can be considered a production trait, considering for instance that meat sheep are bred for producing meat, but also as a life history (weight/growth reproduction) trait, as it also is a function of prolificacy. This meta-analysis does not particularly support either the hypothesis that inbreeding depression impact is larger earlier in life (Adamec et al. 2006; Sorensen et al. 2006). Yet, in some cases, traits that constitute a combination of other traits showed larger inbreeding depression than did the traits included for their combination; for instance, considering bm, LS means for direct and maternal inbreeding depression were found to be 0.182 and 0.254 for litter size, 0.322 and 0.002 for offspring survival but 0.686 and 0.462 for number of offspring weaned. When comparing direct and maternal effect of inbreeding on traits, in general, the direct effects were found to be larger, except for litter size, which could be explained by the fact that relative to ‘later’ traits, litter size is largely related to the physiological status of the mother (ovulation rate, uterine capacity). The results of this meta-analysis illustrate that, in livestock species, any kind of selected trait may be affected by inbreeding depression. For a given trait and population, intensity of inbreeding depression may depend on the importance of dominance variance within the trait (Misztal et al. 1997), that is, to the number of genes involved, their mode of action under inbreeding depression (Curik et al. 2001) and to the selection history of population studied, as illustrated below.
Heterogeneity of inbreeding depression The ability to compute partial inbreeding coefficients (i.e. inbreeding coefficient related to alleles transmitted by a specific ancestor) has provided a way to test whether genetic load is equally distributed among founder genomes. Considering rodents (Lacy et al. 1996) and domestic species (Miglior et al. 1994; Rodriganez et al. 1998; Gulisija et al. 2006; Casellas et al. 2008, 2009, 2010), several studies have shown a large magnitude of neutral or negative (or eventually positive) effects of partial inbreeding coefficients, whole inbreeding being in any case deleterious to traits measured. This finding supports the hypothesis that a large part of genetic load could be due to a small number of alleles with major deleterious effects. The study by Casellas et al. (2010) also reported interactions between partial inbreeding coefficients of different founders, revealing what could be epistatic inbreeding depression phenomena. The fact that there is variation among lineages in inbreeding depression may have some consequence for genetic management. This indeed implies that detrimental effect of founder alleles should be measured for a given
number of traits and the status of candidates with respect to founder alleles impacting inbreeding depression should be taken into account when implementing conservation strategies (Rodriganez et al. 1998).
Economic consequences of inbreeding depression As underscored by Gama & Smith (1993), economic constraints related to inbreeding depression are first related to the extent of purebreeding within the species. For poultry, production systems are based almost entirely on cross-breeding schemes, and inbreeding depression can probably be economically neglected. By contrast, a large majority of dairy cows is purebred. Therefore management of inbreeding depression can be an important concern, whereas the situation would probably be intermediate for other species. This and the quality of the dataset for dairy cattle explains probably why a large portion of studies dealing with inbreeding depression (18 of the 57 studies here) focused on those breeds. For a trait such as milk yield, we estimated a decrease of 0.37 percent per 1 percent of inbreeding (Table 1). In a breed such as Holstein, the annual inbreeding rate can be approximated to 0.12 percent per year, considering an inbreeding rate per generation of approximately 0.6 percent (Danchin-Burge et al. 2011) and generation interval of around five years. Therefore, because the annual genetic progress in Holstein is estimated to be close to 100 kg per lactation, that is, 1 percent of the current phenotypic mean (around 10 000 kg), inbreeding depression per year will correspond to 0.044 percent of the phenotypic mean, that is, to 4.4 percent of the genetic progress. On this result alone, the impact of inbreeding depression can be considered relatively limited, yet the impact of inbreeding depression on total performance is likely to be larger than when considering traits separately, as economic return can be considered as a multiplicative combination of single traits (Kristensen & Sorensen 2005). Several studies investigated an economic quantification of inbreeding depression considering either one trait or an aggregate of several traits. For instance, considering impact on mastitis incidence alone in Danish Holstein, Sorensen et al. (2006) estimated a reduction of $11 in lifetime net return per cow on average. Also for the Holstein breed, Croquet et al. (2006) computed a loss of lifetime profit of €6.13 per 1 percent increase of inbreeding, that is, €22.7 on average, whereas in the study by Smith et al. (1998), the loss of lifetime net income ranged between $22 and 24 per 1 percent of inbreeding, that is, between $65 and 73 on average. The difference between both results, even considering rate change, could be eventually explained by the fact the results of the Croquet et al. study were probably underestimated, as the traits related to fertility, longevity and health were not taken into account in their study. In
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
Inbreeding depression in livestock species sheep, the average economic loss per ewe in value of production was estimated at $17 for average inbreeding (Ercanbrack & Knight 1991). All these results confirm that inbreeding depression, through the different impacts it may have on traits of interest, may reduce the economic income of breeders. The control of inbreeding rate within livestock population selection schemes, through optimal contribution for instance (Clark et al. 2013), therefore appears as a necessity, at least for species raised mainly as purebreds.
Occurrence of inbreeding purge in livestock species As previously stated, under the partial dominance hypothesis, inbreeding should expose deleterious alleles to selection. Different reviews have supported the existence of purging within plants and animals, however, with generally limited effects and large discrepancies among the results (Ballou 1997; Crnokrak & Barret 2002). According to Kristensen & Sorensen (2005), it is assumed that purging is likely to occur (i) if partial dominance is of major importance relative to other hypotheses (overdominance and espistasy), (ii) if selection is strong relative to drift allowing deleterious alleles to be eliminated and not randomly fixed (the deleterious effect should therefore be large) and (iii) if deleterious alleles cannot be introduced through gene flow (closed population). Also, a larger amount of time during which alleles are exposed to selection, relative to the amount of inbreeding, may increase the possibility of occurrence of inbreeding purge. Therefore, to assess the existence of the phenomenon, one may either differentiate the consequence of ‘fast’ vs. ‘slow’ inbreeding, or ‘new’ vs. ‘old’ inbreeding (Hinrichs et al. 2007). In the first case, it is considered that slow inbreeding increases the number of generations needed to purge the genetic load. In the second case, it can be considered that individuals with inbred ancestry are less likely to be carriers of deleterious alleles in comparison with individuals with more recent inbreeding. One may also suppose that ‘old’ deleterious mutations are likely to have been purged in comparison with new ones. A few studies assessed the existence of inbreeding purge in livestock species, based mainly on the comparison between new and old inbreeding. Based on a simulation study within the Jersey cattle population, Gulisija & Crow (2007) agreed with Hedrick (1994), concluding that inbreeding purge could occur efficiently only for alleles with large effects, with reduction of genetic load around 12.6 percent for alleles with a strong effect (fitness near 0). For alleles with small effects, purging would probably be negligible. In practice, Mc Parland et al. (2009) provided evidence of an inbreeding purge for milk production traits in Holstein cattle, a larger part of inbreeding depression being attributable to new inbreeding. In the same study, however,
no evidence of inbreeding purge was found for fertility traits, either due to limited selection on those trait (antagonism with milk production traits) or to predominance of overdominance. In pigs, K€ ock et al. (2009) showed that litter size performance as well was affected by old and new inbreeding, thus providing no evidence of inbreeding purge. It has to be noted that some examples may exist of strains having naturally purged their genetic load, such as the Chillingham cattle feral herd, remaining viable and fertile despite an almost complete homozygosity (Visscher et al. 2001). Therefore, investigation of inbreeding purge within livestock species deserves further investigation.
Inbreeding by environment (I 3 E) interactions The question of the interactions between inbreeding and environment is strongly related to the question of genetic homeostasis, developed by Lerner (1954), stating that heterozygotes (individuals) are less responsive to environmental stresses than are homozygotes, as far as traits directly related to fitness are concerned. Adaptive capacities to environment modifications constitute traits of growing interest for breeders, especially given the concerns relative to climate change (Piling & Hoffmann 2011). In different parts of the world, temperature increases associated with climate change are expected to significantly impact levels of animal production and their economic viability unless management and genetic resources are adapted (Mader et al. 2009). The results from theoretical and experimental results have shown that inbred individuals are particularly sensitive to environment changes. For instance, the study of Jimenez et al. (1994) showed more severe effects of inbreeding on mice survival in natural environment when compared to captive one. The meta-analysis of Armbruster & Reed (2005) on plant and model species showed for instance that, when changing from a benign to stressful environment, there was an increase of inbreeding depression in 76 percent of the cases. Indeed, inbreeding seems to have an impact on canalization, that is, the capacity to maintain the main phenotype under various environments, which is probably reduced under inbreeding (Kristensen et al. 2010). Reed et al. (2012) proposed three hypotheses behind this interaction: (i) an increased expression of genetic load, that is, deleterious alleles with higher fitness cost, or larger number of deleterious alleles expressed (neutral alleles under a benign environment and deleterious under a stressful one); (ii) a global physiological weakening of inbred individuals, therefore more sensitive to stress; and (iii) an increased phenotypic variation under stress, increasing expression of inbreeding depression. In livestock species, there is a noteworthy lack of investigation surrounding I 9 E interaction, probably related to the difficulty in implementing experimental
© 2014 Stichting International Foundation for Animal Genetics, doi: 10.1111/age.12178
7
8
Leroy designs in comparison with model species. From a general point of view, livestock selection schemes need better incorporation of genotype–environment effect within selection models (Reed et al. 2012). There is also a strong need for experiments to define more clearly what adaptive traits for livestock species are and what the basis and molecular mechanisms behind I 9 E environment for those species are.
Perspectives brought by genomics Recent developments of genomic and other ‘omic’ approaches are, of course, of paramount interest for estimation, understanding and management of inbreeding depression. First, as previously stated, genomic estimators of inbreeding do not suffer from drawbacks inherent to genealogical tools (reliability, limited pedigree knowledge, assumption that founders are unrelated, etc.). Also, genealogical approaches generally do not take into account the stochastic nature of recombination. Among genomic approaches, ROH is considered the optimal one to measure inbreeding (Keller et al. 2011; Bjelland et al. 2013). Moreover, because long ROH correspond to recent inbreeding, whereas shorter ROH indicate more distant ancestral effects such as breed founder effects (Purfield et al. 2012), the ROH approach could therefore be used to differentiate more clearly between old and new inbreeding. The approach may therefore provide interesting results about the inbreeding purge phenomenon, independently from pedigree knowledge limitations. Yet, the ROH approach has its own limits. Silio et al. (2013) indicated that some ROH metrics could be weakly correlated with inbreeding due to unequal repartition of ROH within chromosomes in that study. In their study on cattle breeds, Ferencakovic et al. (2013b) reported overestimation of inbreeding when using the 50k SNP chip with a short ROH segment (
