Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight

Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H-Line), 766 individuals for the low variability line (L-Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED ) information, on ROH identified using the SW method (FROHSW ) and on ROH identified using the CR method (FROHCR ). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW . Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH-based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED . Differences in robustness between lines were not attributable to a higher homozygosis in the L-Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness.

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance

This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (F NEJ), Li and Horvitz (F L&H), Van Raden method 1 (F VR1) and method 2 (F VR2), and Yang (F YAN). Inbreeding based on runs of homozygosity (F ROH) and pedigree inbreeding (F PED) were also computed. F ROH, F NEJ, and F L&H were also adjusted for their average values in the first generation of selection and named F ROH0, F NEJ0, and F L&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆F PEDt) and individual increases in inbreeding (∆F PEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆F NEJ0, ∆F L&H, ∆F L&H0, ∆F VR1, ∆F VR2, ∆F YAN, and ∆F ROH0). The Ne was obtained from different ∆F, such as Ne PEDt, Ne PEDi, Ne NEJ0, Ne L&H, Ne L&H0, Ne VR1, Ne VR2, Ne YAN, and Ne ROH0. Comparing with F PED , F ROH , F NEJ and F VR2 overestimated inbreeding while F NEJ0 , F L&H , F L&H0 , F VR1 and F YAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. F ROH had the highest correlation with F PED (0.89); F YAN had correlations >0.95 with all the other molecular inbreeding coefficients. Ne PEDi was more reliable than Ne PEDt and presented similar behaviour to Ne L&H0 and Ne NEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation Ne PEDi was 42.20, Ne L&H0 was 45.04 and Ne NEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively F ROH presented the highest correlation with F PED, which addresses the identity by descent probability (IBD). The evolution of Ne L&H0 and Ne NEJ0 was the most similar to that of Ne PEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.

Embryo survival and fertility differ in lines divergently selected for birth weight homogeneity in mice

The selection of animals for lower environment sensitivity around the optimum trait value can also provide benefits in productivity and welfare. A divergent selection experiment for birth weight environmental variability in mice was successfully conducted over 17 generations. Animals from low variability selected line (L-line) were more robust by having a higher litter size and survival at weaning in a common breeding environment, than those from high variability line (H-line). The objective of this study was to analyze the differences between those divergently selected lines for embryo and fetal survival and for fertility and prolificacy rate. To study embryo survival and ovulation rate, a total of 98 females (34 H-line and 50 L-line) were studied in four generations of the divergent experiment. To analyze fetal survival and fertility rate, 378 female mice (138 H-line and 240 L-line) in 10 generations or the divergent experiment were studied. Ultrasound scans were performed at day 14 of gestation to establish the number of total fetal and the embryo absorptions. Mortality was addressed as the difference between litter size at birth and the number of fetuses at 14 days of gestation. The number of pregnant females in the first 3 days after mating was used to measure fertility. A linear model was also fitted to analyze embryo mortality, litter size, and the number of embryos at 14 days of gestation. A categorical model was then used to study fertility, including line, generation, and its interaction as effects. Despite the fact that there were no significant differences in the ovulation rate, litter size at birth was significantly higher in the L-line than in the H-line (9.82 vs. 8.36 pups, p < 0.001). Moreover, embryo mortality was significantly lower in the L-line than in the H-line (1.39 vs. 2.87 fetuses, p < 0.001). L-line females were more fertile (53.49% vs. 23.26% for the H-line). According to these results, the line selected for low environmental variance would be preferable for robustness and animal welfare.

Genetic parameters for fleece uniformity in alpacas

Fiber diameter is the main selection objective and criterion in alpaca breeding programs, but it can vary across anatomic regions of the animal. As fiber diameter is usually registered from a unique sample from the mid side of the body, fiber diameter variability within fleece is never addressed and phenotypic and genetic differences may exist for fleece uniformity in alpaca populations. The objective of this work was to estimate the genetic parameters of fleece uniformity in an alpaca population. Fiber diameters measured in three different locations were used as repeated records of the same animal and studied for fitting a model that considers heterogeneous the residual variance of the model. Also, the logarithm of the standard deviation of the three measures was used as a measure of the fleece variability. Estimate of the additive genetic variance of the environmental variability was 0.43±0.14, enough high to suggest the existence of wide room to select for fleece uniformity. Genetic correlation of the trait with its environmental variability was 0.76±0.13 showing that fleece uniformity will be indirectly selected when aiming to reduce the fiber diameter. In the light of these parameters, and due to the cost of registering and the cost of opportunity, it looks no worthy to include uniformity as a selection criterion in alpaca breeding programs.

Differential sensitivity of climate conditions on birth weight genetic values in mice divergently selected for birth weight residual variance

After 32 generations of a divergent selection experiment for residual variance of birth weight in mice, two divergent lines were thus obtained: the heterogeneous line (H-line) and the homogeneous line (L-line). Throughout the generations, differences were observed between the two lines in traits such as litter size, survival at weaning, and birth weight variability caused by unidentified environmental conditions. The L-line exhibited advantages in terms of higher survival rates, larger litter sizes, and less sensitivity to changes in food intake. The study is an examination of the effects of climate as an environmental factor on the performance of these animals. Climate factors including maximum, minimum, and mean temperature (T), humidity (H), and TH index; at three stages (the fecundation, a week before the parturition and the parturition), were linked to a birth weight dataset consisting of 22,614 records distributed as follows: 8,853 corresponding to the H-line, 12,649 to the L-line, and 1,112 to the initial population. Out of the 27 analyzed climatic variables, the maximum temperature 1 wk before parturition (MXTW) was identified as the most influential when comparing heteroscedastic models with the deviance information criterion. The order of Legendre polynomial to apply in the following random regression model was tested by a cross-validation using homoscedastic models. Finally, MXTW was compared on how it affected the two divergent lines by analyzing predicted breeding values (PBV) obtained from a random regression heteroscedastic model. The mean PBV of the H-line in the first generation showed a range of 0.070 g with a negative slope, which was 35 times higher than the range obtained for the L-line, which varied within 0.002 g. In the last generation of selection, the H-line exhibited greater instability of PBV across temperatures, with a difference of 0.101 g between the maximum and minimum mean PBV, compared to 0.017 g for the L-line. The standard deviations of the slopes in the H-line were more dispersed than in the L-line. Unlike the H-line, the L-line had slopes that were not significantly different from 0 throughout the generations of selection, indicating greater stability in response to MXTW variations. The H-line exhibited a higher sensitivity to changes in MXTW, particularly in birth weight, with the L-line being more stable. The selection for uniformity of birth weight could lead to less sensitive animals under environmental changes.

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

BACKGROUND

Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -F_HOM-, the diagonal elements of the genomic -F_G-, and hybrid matrixes -F_H-) and ROH measures (F_RZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.

RESULTS

The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (F_RZ for three generations, F_H and F_HOM) to 0.11 (F_RZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with F_HOM) and 0.79 (F with F_RZ). In addition, the correlations between F_RZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated.

CONCLUSIONS

Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

Impact of selection for birth weight variability on reproductive longevity: A mice model

Uniformity, understood as a similar performance in relevant livestock traits, such as birth weight within the litter, is being included as one of the selection objectives in breeding programmes, especially for polytocous livestock species. A divergent selection experiment for birth weight within‐litter variability in mice during 23 generations showed that homogeneous animals were better for litter size, survival and feed efficiency but less heavy than heterogeneous animals. The aim of this study was to compare the reproductive longevity in both divergent lines as time to the end of the reproductive period. Two generations from both lines with an initial number of 43 females and 43 males were mated one to one and stayed together to have consecutive parturitions until the end of the reproductive life. Females were discarded when the time elapsed from the last parturition was longer than 63 days. The time to the end of the reproductive period between both lines was compared by fitting a Cox proportional hazard regression model adjusting for line, generation and its interaction. The rate of parturitions in both lines was also compared using a Prentice–Williams–Peterson model adjusted for the same effects. The low variability line was associated with a higher parturition rate, e.g., adjusted hazard ratio was 2.93 (95% CI 2.17–3.94). The Cox model showed that the low variability females also presented benefits of time to the end of the reproductive period, with an adjusted hazard ratio of 0.26 (95% CI 0.16–0.41). The median of reproductive days was 55.50 in the high variability line whilst the median was 252.50 days for the low variability females. The homogeneous line presented important reproductive advantages suggesting higher robustness and animal welfare. Further research should confirm whether the findings presented here of a better performance in the low variability line could be properly applied to some livestock species.

Impact of the event effect in genetic evaluation for ranking traits in horses

In genetic evaluation of horses, the genetic trend does not correspond into a phenotypic trend when using ranking as a phenotype due to its uniform distribution, and some other effects might be absorbing that trend. From a founder population, a further four discrete generations of 100 individuals were simulated under random mating. Then, ten additional discrete generations were simulated by selecting the best 10% of the animals. Likewise, an underlying variable with heritability 0.1 or 0.2, affected by an event environmental influence, generation and permanent environment, was simulated to establish the ranking assignment of 10 random participants or according to the competitive level for each event, in 10 or 100 structured or unstructured events. The ranking trait genetic evaluation model was tested to include or exclude the event effect and the permanent environment effect, depending on the scenario. The results showed that the event effect fitted the different competitive level of each event, leading to a 5% to 23% of selection response improvement for structured competitions. Therefore, the event effect should be included in the genetic evaluation models of horses. The permanent environment fitted or simulated did not significantly improve the selection response. The event effect explained the competition genetic level, by compensating the genetic trend obtained by selection.

Breeding Strategies to Optimize Effective Population Size in Low Census Captive Populations: The Case of Gazella cuvieri

Simple Summary

Small-sized populations frequently undergo a significant loss of genetic variability that can lead to their extinction. Therefore, research on animal breeding has focused on mating systems for minimizing the disappearance of genetic variability. Minimizing the average coancestry of offspring has been described as the best strategy for this purpose. Traditionally, the preservation of genetic variability has been approached via breeding strategies for increasing the effective population size (Ne). The main objective of this study was to compare, via computer simulations, the performance of different breeding schemes to limit the losses of genetic diversity in small populations. This objective was achieved by monitoring the evolution of the effective size obtained by different strategies across 20 generations with a starting point of two pedigree real populations of Gazella cuvieri. The results showed that minimizing average coancestry in a cohort did not maximize the effective size as compared with new strategies that were designed for this study. Furthermore, the best strategy may vary for each population and should be studied individually.

Abstract

Small-sized animal populations can undergo significant loss of genetic variability that can lead to their extinction. Therefore, studies on animal breeding have focused on mating systems for minimizing the disappearance of genetic variability. The main objective of this study was to compare, using computer simulations, the performance of different breeding schemes to limit the loss of genetic diversity in small-sized populations. This objective was achieved by monitoring the evolution of the effective population size obtained by 23 strategies throughout 20 generations in two populations of Gazella cuvieri. The scenarios were designed with different assumptions, in both reference subpopulations, regarding: the use of parents coancestry or offspring coancestry, the use of their increases or the coefficients themselves, and the number of males and females involved. Computations were performed using an experimental module of Endog v4.9 developed for this purpose. The results of the study showed that strategies for minimizing the coancestry of the parents were better in the short term; however, these strategies were worse in the long term. Minimizing the average coancestry of the offspring was a better approach in the long term. Nevertheless, in both populations, the best results were obtained when both the coancestry of the parents and the coancestry of the offspring were weighted at 5% each and neither males nor females were assumed to contribute to the next generation. In any case, not all strategies had the same evolutionary pattern throughout generations in both populations. The current results show that neither traditional nor new strategies have any general use. Therefore, it is important to carefully test these strategies before applying them to different populations with different breeding needs under different conditions, such as different generation intervals, and different natural breeding systems such as monogamy or polygyny.

Genetic parameters for uniformity of harvest weight in Pacific white shrimp (Litopenaeus vannamei)

Background

Uniformity of body weight is a trait of great economic importance in the production of white shrimp (Litopenaeus vannamei). A necessary condition to improve this trait through selective breeding is the existence of genetic variability for the environmental variance of body weight. Although several studies have reported such variability in other aquaculture species, to our knowledge, no estimates are available for shrimp. Our aim in this study was to estimate the genetic variance for weight uniformity in a farmed population of shrimp to determine the potential of including this trait in the selection program. We also estimated the genetic correlation of weight uniformity between two environments (selection nucleus and commercial population).

Methods

The database contained phenotypic records for body weight on 51,346 individuals from the selection nucleus and 38,297 individuals from the commercial population. A double hierarchical generalized linear model was used to analyse weight uniformity in the two environments. Fixed effects included sex and year for the nucleus data and sex and year-pond combination for the commercial data. Environmental and additive genetic effects were included as random effects.

Results

The estimated genetic variance for weight uniformity was greater than 0 (0.06 ± 0.01) in both the nucleus and commercial populations and the genetic coefficient of variation for the residual variance was 0.25 ± 0.01. The genetic correlation between weight and weight uniformity was close to zero in both environments. The estimate of the genetic correlation of weight uniformity between the two environments (selection nucleus and commercial population) was 0.64 ± 0.06.

Conclusions

The existence of genetic variance for weight uniformity suggests that genetic improvement of this trait is possible. Selection for weight uniformity should not decrease weight, given the near zero genetic correlation between these two traits. The strong genetic correlation of weight uniformity between the two environments indicates that response to selection for uniformity in the nucleus will be at least partially transmitted to the commercial population if this trait is included in the breeding goal.

Genetic parameters for canalization analysis of morphological traits in the Pura Raza Español horse

Measurements from 13 different morphological traits of importance in the Pura Raza Español (PRE) horse were used to estimate genetic and environmental parameters following a heteroscedastic model in which data were assigned to stallions. Data sets used ranged from 20,610 (height at withers) to 48,486 measurements (length of shoulder), and the number of animals analysed in the pedigrees varied from 17,662 (height at withers) to 23,962 (dorsal-sternal diameter). Results of heritabilities of the traits varied from 0.09 (width of chest and upper neck line) to 0.30 (muscular development). Further, genetic correlations between traits and their environmental variability were estimated, obtaining values from -0.56 (muscular development) to 0.69 (height at withers). Also, predicted breeding values for the mean and for the environmental variability were obtained for all horses in the pedigrees, providing individual information about not only the expected phenotypic value of their offspring but also the expected heterogeneity among them. Results proved the possibility of improving morphological traits and reducing the heterogeneity of offspring at a time by the selection of animals and levels of systematic effects.

Combining Threshold, Thurstonian and Classical Linear Models in Horse Genetic Evaluations for Endurance Competitions

The racing time and rank at finish traits are commonly used for endurance horse breeding programs as a measure of their performance. Even so, given the nature of endurance competitions, many horses do not finish the race. However, the exclusion of non placed horses from the dataset could have an influence on the prediction of individual breeding values. The objective of the present paper was to develop a multitrait model including race time (T), rank (R) and placing (P), with different methodologies, to improve the genetic evaluation in endurance competitions in Spain. The database contained 6135 records from 1419 horses, with 35% of the records not placed. Horse pedigree included 10868 animals, with 52% Arab Horses. All models included gender, age and race effect as systematic effects and combined different random effects beside the animal and residual effects: rider, permanent environmental effect, and interaction horse-rider. The kilometers per race was included as a covariate for T. Heritabilities were estimated as moderately low, ranging from 0.06 to 0.14 for T, 0.09 to 0.15 for P, and 0.07 to 0.17 for R, depending on the model. T and R appeared mostly as inverse measures of the same trait due to their high genetic correlation, suggesting that T can be ignored in future genetic evaluations. P was the most independent trait from the genetic correlations. The possibility of simultaneously processing the threshold, Thurstonian and continuous traits has opened new opportunities for genetic evaluation in horse populations, and much more practical genetic evaluations can be done to help a proper genetic selection.

Selection Response in a Divergent Selection Experiment for Birth Weight Variability in Mice Compared with a Control Line

Birth weight (BW) in animal production is an economically important trait in prolific species. The laboratory mouse (Mus musculus) is used as an experimental animal because it is considered a suitable model for prolific species such as rabbits and pigs. Two mouse lines were divergently selected for birth weight variability with a third line of non-selected control population of the same origin as the animals starting the experiment. The objective of this study was, therefore, to compare and evaluate the differential response of each line. The animals were from the 17th generation of both low and high BW variability lines of the divergent selection experiment, including in addition animals from the control line. The dataset contained 389 records from 48 litters of the high line, 734 records from 73 litters of the low line, and 574 records from 71 litters of the control line. The studied traits were as follows: the BW, the BW variance, the BW standard deviation, the BW coefficient of variation within-litter, the weaning weight (WW), the litter size at birth and at weaning, the weight gain, and the preweaning survival. The model included the line effect jointly with the parturition number and its interaction, the linear and quadratic LS as covariates except for the LS trait itself when analyzing litter traits, as well as the pup sex when analyzing individual traits. The low line had a lower BW and WW, but a higher litter size, and greater robustness owing to a higher survival at weaning. As a model of livestock animals, the findings from this experiment led to a proposal of selection for pig production that would combine an increase in litter size with higher survival and welfare. Compared with the control line, a much higher response was observed in the low variability line than in the high line, making it extremely satisfactory given that homogeneity provides advantages in terms of animal welfare and robustness.

Calving date and its variability as a potential trait in the breeding objective to account for reproductive seasonality in alpacas

The low fertility and offspring survival indicators in alpacas can be partially due to their particularity seasonal reproduction that reduces the opportunities of the females to become pregnant within a season, with the survival of the offspring concerned by the availability of food and exposure to diseases that depends on the calving date. Optimizing the date of delivery and reducing its variability are shown as eligible criteria that could be used as selection criteria within the genetic improvement programmes in alpacas, the calving date being a much more appropriate trait to measure and optimize fertility unlike of age at first calving and the calving interval, this due to the reproductive seasonality in camelids. For this study, 6,533 birth date records were taken between 2001 and 2018 of Peruvian alpacas, to estimate the genetic parameters. Models assuming heterogeneity in the residuals were fitted besides classical homogeneous models to address, not only the possibility of forwarding or delaying the calving date, but also the trend to have parturitions in similar dates. The heritability and repeatability ranged from 0.07 to 0.20 for a homogeneity model and from 0.08 to 0.23 for a heterogeneity model, and suggest the possibility of advancing or delaying the calving date. It should be taken into account that the gestation length of camelids makes it difficult to adapt many reproductive traits, and trying to centre the calving date could delay it. It was concluded the feasibility to genetically select the calving date, also in the production of camels and dromedaries, which have the same reproductive characteristics as alpacas. This selection can be combined with other traits. The heterogeneity model was shown to provide a better fit.

Challenging the selection for consistency in the rank of endurance competitions

Background

Control of the environmental variability by genetic selection offers possibilities for new selection objectives for productive traits. This methodology aims at reducing heterogeneity in productive traits and has been applied to several traits and species for which animal homogeneity is profitable. In horse breeding programmes, rank in competitions is a common selection objective but has been challenging to model. In this study, the parameters of environmental variability for the rank of a horse were computed to analyse the capability of a horse to maintain the best ranking across competitions that consist of long-distance races in which the adapted physical condition of the horse is essential. The genetic component of the environmental variance for the rank in endurance competitions was evaluated, which resulted in proposing a new transformation of horse scores in competitions.

Results

Homogeneous and heterogeneous variance models were compared by assaying three random effects that affect both the rank and its variability, using endurance ride data consisting of 2863 records. The pedigree relationship matrix contained 5931 animals. The rank trait was transformed into a normalized variable to prevent false estimates of the genetic correlation by inappropriate artificial skewness. The models included the number of participants in the race, sex, and age as systematic effects. The rider, the rider-horse interaction, or an environmental permanent effect were tested as random effects, in addition to additive genetic and residual effects. The models were analysed using the GSEVM program. Estimates of heritability for rank ranged from 0.12 to 0.15. The heterogeneous variance model that fitted the rider was assessed as the best model based on the deviance information criterion. Estimates of genetic variance for rank variability ranged from 0.12 to 0.13. The genetic correlation between the rank and its environmental variability was low and did not differ from 0.

Conclusions

These results offer an opportunity to select animals for canalization by reducing the variability of race results and achieving the best positions, which could be a new selection objective by weighting estimated breeding values for rank and its variability in a selection index.

The Statistical Scale Effect as a Source of Positive Genetic Correlation Between Mean and Variability: A Simulation Study

The selection objective for animal production is the highest income with the lowest production cost, while ensuring the highest animal welfare. A selection experiment for environmental variability of birth weight in mice showed a correlated response in the mean after 20 generations starting from a crossed panmictic population. The relationship between the birth weight and its environmental variability explained the correlated response. The scale effect represents a potential cause of this correlation. The relationship between the mean and the variability implies: the higher the mean, the higher the variability. The study was to quantify by simulation the genetic correlation between a trait and its environmental variability. This can be attributable to the scale effect in a range of coefficients of variation and heritabilities between 0.05 and 0.50. The resulting genetic correlation ranged from 0.1335 to 0.7021 being the highest for the highest heritability and the lowest CV. The scale effect for a trait with heritability between 0.25 and 0.35 and CV between 0.15 and 0.25 generated a genetic correlation between 0.43 and 0.57. The genetic coefficient of variation (GCV) affecting residual variability was modulated by the strength reducing the impact of the scale effect. GCV ranged from 0.0050 to 1.4984. The strength of the scale effect might be in the range between 0 and 1. The scale effect would explain many reported genetic correlation and the additive genetic variance for the variability. This is relevant when increasing the mean of a trait jointly with the reduction of its variability.

Effect of feed restriction on the environmental variability of birth weight in divergently selected lines of mice

BACKGROUND

Selection of mice for decreased environmental variability of birth weight has achieved higher survivability and larger litter size as a correlated response to canalized selection, which suggests higher welfare and robustness, and animals that are more homogeneous. However, in these studies, animals were not exposed to an environmental challenge. To demonstrate the advantages of this mouse line with a low environmental variability of birth weight, animals from two divergent lines (high and low variability of birth weight) were subjected to feed restriction. The objective of this study was to use these divergent lines to compare their response in terms of robustness against an environmental challenge. At weaning, 120 females, i.e. four full-sib females from 10 random litters of three consecutive generations of selection, were chosen from these divergent lines. The total number of females was divided into four groups, which were subjected to a feeding regimen by imposing different levels of feed restriction (i.e. 75, 90 and 85% of full ad libitum feed across three generations, respectively) in different combinations during the growth and reproduction periods.

RESULTS

Animals from the "low" line were less sensitive to a change in feed level than those from the "high" line. Regarding reproduction, the "low" line performed better in terms of number of females having parturitions, number of parturitions, and litter size. Imposing a feed restriction on female mice during their growth period did not affect the birth weight of their pups. The "low" line was preferred because of its higher reproductive efficiency and survival under an environmental challenge.

CONCLUSIONS

Selection for decreased environmental variability of birth weight produces animals that are less sensitive to environmental conditions, which can be interpreted as having greater robustness.

Genetic parameters for medullated fiber and its relationship with other productive traits in alpacas

The alpaca fiber diameter (FD) varies from 18 to 36 μm, being the finer fiber categories highly appreciated. However, the alpaca fiber presents some limitations in the textile industry due to the high incidence of fiber medullation and diameter variability, both reduces the comfort feeling of the garments. Decreasing or even removing medullation could be a possible selection objective in alpaca breeding programs for increasing economic value of the alpaca fiber. Therefore, the present work aimed to estimate genetic parameters regarding medullation traits, as well as the genetic correlations with other economical important traits, to be able to select the appropriate criteria to reduce or remove medullation on alpaca fiber and help to reduce the prickle factor in the garments. The data was collected from 2000 to 2017 and belonged to the Pacomarca experimental farm. There were 3698 medullation records corresponding to 1869 Huacaya and 414 Suri genetic types. The fiber samples were taken from the mid side, and were analyzed in an OFDA 100® device. The traits analyzed were percentage of medullation (PM), medullated fiber diameter (MFD), FD, standard deviation of FD, greasy fleece weight as fiber traits; density, crimp in Huacaya and lock structure in Suri, head conformation, leg coverage as morphological traits; weaning weight and age at first calving as secondary and functional traits. Genetic parameters were estimated via a multitrait restricted maximum likelihood. The heritabilities for PM and MFD were 0.225 and 0.237 in Huacaya genetic type and 0.664 and 0.237 in Suri genetic type, respectively; heritabilities for other traits were moderate for productive and morphological traits, and low to moderate for secondary and functional traits. The genetic correlations PM-FD and MFD-FD were high and favorable in both genetic types, between 0.531 and 0.975; the genetic correlation PM-MFD was 0.121 in Huacaya and 0.427 in Suri. The rest of genetic correlations with other traits were in general moderate and favorable. The repeatabilities were 0.556 and 0.668 for PM, and 0.322 and 0.293 for MFD in Huacaya and Suri genetic types, respectively. As a conclusion, PM was identified to be a good selection criterion, probably combined in an index with FD to reduce prickling factor.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

Feed and reproductive efficiency differences between divergently selected lines for birthweight environmental variability in mice

Sustainability has come to play an important role in agricultural production. A way to combine efficiency with sustainability might be by searching for robust animals that can be selected for the homogeneity of certain traits. Furthermore, the optimization of feed efficiency is one of the challenges to improve livestock genetics programmes, but this might compromise reproductive efficiency. Animals from two divergent mouse lines, regarding variability of birthweight, were used to check whether homogeneity was also related to both feed and reproductive efficiency. The objective of this study was to use these divergent lines of mice to compare them with their feed efficiency and the reproductive capacity. Animal weight, weight gain, feed intake, relative intake and cumulated transformation index were considered as feed efficiency traits. Animals from the low line had both lower weight and feed intake from 21 to 56 days. They had a worse transforming index in the three last weeks when litter size was fitted as an effect of the model, but the lines become similar if the higher litter size of the low line was not included. Reproductively, the low line performed better considering the number of females having parturitions, the number of parturitions, and with higher litter size and survival in both parturitions. Hence, the low variability line was preferred because of reproductive efficiency without seriously affecting its feed efficiency. Homogeneity seemed to be related to robustness with similar feed efficiency but higher reproductive efficiency.

Modulating birth weight heritability in mice

Expected genetic response is proportional to the heritability of the trait, and this parameter is considered inherent of a specific trait in a particular population. However, models assuming heterogeneity in residual variance lead to different estimates of heritability across combinations of systematic (environmental) effects. Modifying the residual variance of the birth weight by artificial selection was shown to be feasible in a divergent selection experiment in mice. The objectives of this work were to 1) estimate the evolution of the heritability of birth weight in mice in the mentioned experiment, and 2) estimate different heritability regarding systematic effects. Data came from eleven generations of a divergent selection experiment to modify the residual variability of birth weight in mice. A total of 15,431 birth weight records from 959 females and 1,641 litters in combination with 14,786 pedigree records were used. The model used for analysis included generation, litter size, sex, and parity number as systematic effects. Each record of birth weight was assigned to the mother of the pup in the model which assumes that the residual variance is heterogeneous and partially under genetic control. Differences in heritability between lines reached values of 0.06 in the last generations. Choosing the most extreme values of systematic effects, the birth weight heritability ranged from 0.04 to 0.22. From these results, the possibility of modulating the heritability for this trait could be explored in 1 of 2 ways: selecting to decrease the residual variability, or choosing the specific levels of the systematic effects.

Response to selection while maximizing genetic variance in small populations

Background

Rare breeds represent a valuable resource for future market demands. These populations are usually well-adapted, but their low census compromises the genetic diversity and future of these breeds. Since improvement of a breed for commercial traits may also confer higher probabilities of survival for the breed, it is important to achieve good responses to artificial selection. Therefore, efficient genetic management of these populations is essential to ensure that they respond adequately to genetic selection in possible future artificial selection scenarios. Scenarios that maximize the maximum genetic variance in a unique population could be a valuable option. The aim of this work was to study the effect of the maximization of genetic variance to increase selection response and improve the capacity of a population to adapt to a new environment/production system.

Results

We simulated a random scenario (A), a full-sib scenario (B), a scenario applying the maximum variance total (MVT) method (C), a MVT scenario with a restriction on increases in average inbreeding (D), a MVT scenario with a restriction on average individual increases in inbreeding (E), and a minimum coancestry scenario (F). Twenty replicates of each scenario were simulated for 100 generations, followed by 10 generations of selection. Effective population size was used to monitor the outcomes of these scenarios. Although the best response to selection was achieved in scenarios B and C, they were discarded because they are unpractical. Scenario A was also discarded because of its low response to selection. Scenario D yielded less response to selection and a smaller effective population size than scenario E, for which response to selection was higher during early generations because of the moderately structured population. In scenario F, response to selection was slightly higher than in Scenario E in the last generations.

Conclusions

Application of MVT with a restriction on individual increases in inbreeding resulted in the largest response to selection during early generations, but if inbreeding depression is a concern, a minimum coancestry scenario is then a valuable alternative, in particular for a long-term response to selection.

Crossbreed genetic performance study in the eventing horse competition

Eventing is an equestrian discipline combining dressage, show jumping and cross-country exercises. The Spanish Sport Horse (SSH) was used in this study as an example to develop a method to ascertain the influence of parental breeds on particular performances by linking their parental genetic contribution with the individual phenotype value computing the optimal breed contribution for each trait evaluated in eventing. Data included 1220 eventing records from 210 SSH animals. The genetic contribution of six main founder populations were computed for each SSH: the Spanish Purebreed (SPB), Arab Horse (A), Thoroughbred (TB), Selle Français (SF), German breeds (G) and North(-west) European (N) breeds. For this analysis we used BLUP (best linear unbiased predictor) animal models for five defined traits and for the total score. The genetic contribution as linear and quadratic adjustment and the interaction between genetic contributions were included as covariates in the genetic model to separate the possible combining ability from the breeding values. The optimal breed genetic contribution for each trait was maximised by using a simplex method. The best combination for conformation was 51% SPB and 49% N, for cross-country aptitude 23% SPB and 77% N, for dressage 48% SF and 52% N, and for show jumping 64% A and 36% N. For cross-country the best performance was predicted using 100% N genetic contribution and for the total score of 24% SF and 76% N. The combination of two breeds (group of breeds) seemed to be the best option for most of the traits. Although the results should be interpreted with caution, the importance of this paper is that it can be considered as a starting point of the analysis. The methodology applied here performed nicely in searching for the best contribution of several breeds to find the best combination for particular interests and could, therefore, be useful for other species/populations.

Estimation of genetic parameters for reproductive traits in alpacas

One of the main deficiencies affecting animal breeding programs in Peruvian alpacas is the low reproductive performance leading to low number of animals available to select from, decreasing strongly the selection intensity. Some reproductive traits could be improved by artificial selection, but very few information about genetic parameters exists for these traits in this specie. The aim of this study was to estimate genetic parameters for six reproductive traits in alpacas both in Suri (SU) and Huacaya (HU) ecotypes, as well as their genetic relationship with fiber and morphological traits. Dataset belonging to Pacomarca experimental farm collected between 2000 and 2014 was used. Number of records for age at first service (AFS), age at first calving (AFC), copulation time (CT), pregnancy diagnosis (PD), gestation length (GL), and calving interval (CI) were, respectively, 1704, 854, 19,770, 5874, 4290 and 934. Pedigree consisted of 7742 animals. Regarding reproductive traits, model of analysis included additive and residual random effects for all traits, and also permanent environmental effect for CT, PD, GL and CI traits, with color and year of recording as fixed effects for all the reproductive traits and also age at mating and sex of calf for GL trait. Estimated heritabilities, respectively for HU and SU were 0.19 and 0.09 for AFS, 0.45 and 0.59 for AFC, 0.04 and 0.05 for CT, 0.07 and 0.05 for PD, 0.12 and 0.20 for GL, and 0.14 and 0.09 for CI. Genetic correlations between them ranged from -0.96 to 0.70. No important genetic correlations were found between reproductive traits and fiber or morphological traits in HU. However, some moderate favorable genetic correlations were found between reproductive and either fiber and morphological traits in SU. According to estimated genetic correlations, some reproductive traits might be included as additional selection criteria in HU.

Genetic control of the environmental variance for birth weight in seven generations of a divergent selection experiment in mice

Data from seven generations of a divergent selection experiment designed for environmental variability of birth weight were analysed to estimate genetic parameters and to explore signs of selection response. A total of 10 783 birth weight records from 638 females and 1127 litters in combination with 10 007 pedigree records were used. Each record of birth weight was assigned to the mother of the pup in a heteroscedastic model, and after seven generations of selection, evidence of success in the selection process was shown. A Bayesian analysis showed that success of the selection process started from the first generation for birth weight and from the second generation for its environmental variability. Genetic parameters were estimated across generations. However, only from the third generation onwards were the records useful to consider the results to be reliable. The results showed a consistent positive and low genetic correlation between the birth weight trait and its environmental variability, which could allow an independent selection process. This study has demonstrated that the genetic control of the birth weight environmental variability is possible in mice. Nevertheless, before the results are applied directly in farm animals, it would be worth confirming any other implications on other important traits, such as robustness, longevity and welfare.

Estimates of direct and indirect effects for early juvenile survival in captive populations maintained for conservation purposes: the case of Cuvier's gazelle

Together with the avoidance of any negative impact of inbreeding, preservation of genetic variability for life-history traits that could undergo future selective pressure is a major issue in endangered species management programmes. However, most of these programmes ignore that, apart from the direct action of genes on such traits, parents, as contributors of offspring environment, can influence offspring performance through indirect parental effects (when parental genotype and phenotype exerts environmental influences on offspring phenotype independently of additive genetic effects). Using quantitative genetic models, we estimated the additive genetic variance for juvenile survival in a population of the endangered Cuvier's gazelle kept in captivity since 1975. The dataset analyzed included performance recording for 700 calves and a total pedigree of 740 individuals. Results indicated that in this population juvenile survival harbors significant additive genetic variance. The estimates of heritability obtained were in general moderate (0.115-0.457) and not affected by the inclusion of inbreeding in the models. Maternal genetic contribution to juvenile survival seems to be of major importance in this gazelle's population as well. Indirect genetic and indirect environmental effects assigned to mothers (i.e., maternal genetic and maternal permanent environmental effects) roughly explain a quarter of the total variance estimated for the trait analyzed. These findings have major evolutionary consequences for the species as show that offspring phenotypes can evolve strictly through changes in the environment provided by mothers. They are also relevant for the captive breeding programme of the species. To take into account, the contribution that mothers have on offspring phenotype through indirect genetic effects when designing pairing strategies might serve to identify those females with better ability to recruit, and, additionally, to predict reliable responses to selection in the captive population.

Modelling genetic evaluation for dressage in Pura Raza Español horses with focus on the rider effect

The most popular use of the Pura Raza Español horse in sport is for dressage competitions. Tests on young sport horses were first established in 2004 in Spain to collect data for the genetic evaluation of this breed's suitability for dressage. The aim of this study was to compare eight different models to find out the most appropriate way to include the rider in the genetic evaluation of dressage. A progressive removal of systematic effects from model was also analysed. A total of 8867 performance records collected between 2004 and 2011 from 1234 horses aged between 4 and 6 years old were used. The final score in the dressage test was used as the performance trait. The pedigree matrix contained 8487 individuals. A BLUP animal model was applied using a Bayesian approach with TM software. The horse's age, gender, travelling time, training level, stud of birth and event were included as systematic effects in all the models. Apart from the animal and residual effects that were present in all models, different models were compared combining random effects such as the rider, match (i.e. rider-horse interaction) and permanent environmental effects. A cross-validation approach was used to evaluate the models' prediction ability. The best model included the permanent environmental, rider and match random effects. As far as systematic effects are concerned, the event or the stud of birth was essential effects needed to fit the data.

Genetic parameters for birthweight environmental variability in mice

Data from a divergent experiment for birthweight (BrW) environmental variability were used to estimate genetic parameters for BrW trait and its environmental variability by fitting both homoscedastic (HO) and heteroscedastic (HE) models. A total of 5 475 records of BrW from animals born from inbred dams, and 7 140 pedigree records were used. The heritability of BrW using the model HO was 0.27, with the litter effect much more important, 0.43. The model HE provided a genetic correlation between the trait and its environmental variability that was very high and negative, -0.97, and a high value for the additive genetic variance for environmental variability, suggesting an artefact in the model. The residual skewness was found to be essentially null. A model considering the genetic correlation null was also fitted, and used to obtain the breeding values for the selection process. Moreover, the trait was considered as maternal resulting in similar estimates under the model HO, but more reasonable for the genetic correlation between the trait and its environmental variability of 0.48 with a value of 0.25 for the additive genetic variance regarding environmental variability under the model HE. This led to the conclusion that environmental variability of BrW in mice must be selected via dams. Estimated parameters in a reduced dataset without inbred animals did not substantially change this conclusion.

Maximization of total genetic variance in breed conservation programmes

The preservation of the maximum genetic diversity in a population is one of the main objectives within a breed conservation programme. We applied the maximum variance total (MVT) method to a unique population in order to maximize the total genetic variance. The function maximization was performed by the annealing algorithm. We have selected the parents and the mating scheme at the same time simply maximizing the total genetic variance (a mate selection problem). The scenario was compared with a scenario of full-sib lines, a MVT scenario with a rate of inbreeding restriction, and with a minimum coancestry selection scenario. The MVT method produces sublines in a population attaining a similar scheme as the full-sib sublining that agrees with other authors that the maximum genetic diversity in a population (the lowest overall coancestry) is attained in the long term by subdividing it in as many isolated groups as possible. The application of a restriction on the rate of inbreeding jointly with the MVT method avoids the consequences of inbreeding depression and maintains the effective size at an acceptable minimum. The scenario of minimum coancestry selection gave higher effective size values, but a lower total genetic variance. A maximization of the total genetic variance ensures more genetic variation for extreme traits, which could be useful in case the population needs to adapt to a new environment/production system.

Estimation of effective population size from the rate of coancestry in pedigreed populations

We introduce a simple method to estimate effective population size from increase in coancestry (Δc(jk)) for all pairs of individuals j and k in a reference subpopulation. An increase in pairwise coancestry for any pair of individuals j and k can be defined assuming that a hypothetical mating between them would give an individual with an inbreeding coefficient equal to c(jk), where c(jk) is the coancestry coefficient between the individuals j and k. The equivalent measure to discrete generations value (g(jk)) corresponding to the individual jk can be computed by averaging discrete equivalents generations of its parents (g(j) and g(k)). The mean increase in coancestry for all pairs of individuals in a reference subpopulation can be used to estimate a realized effective population size based on coancestries that would provide information on the effective size of a population under random mating. Performance of the new parameter was tested on simulated and empirical (horse) populations with different mating strategies and population structures. The routines needed to compute the introduced parameters have been included in a new version of the program ENDOG.

Analysis of the existence of major genes affecting alpaca fiber traits

The aim of this study was to determine the presence of major genes for fiber diameter (FD), SD of FD (SDFD), CV of FD, and comfort factor (CF) in Huacaya (HU) and Suri (SU) Peruvian alpaca breeds. Bayesian segregation analyses with relaxed transmission probabilities were performed using 1,906 and 6,592 available records for SU and HU breeds. Evidence for the presence of major genes was statistically supported when the 95% posterior density did not include zero. Significant major genes were found associated with decreased FD, SDFD, CV values, and increased CF values. Additive effects of the major genes were 4.18 and 4.23 μm for FD, 1.67 and 1.61 μm for SDFD, 3.32 and 3.76% for CV, and 15.03 and 14.90% for CF in HU and SU breeds, respectively. Dominance effects were -1.98 and -2.03 μm for FD, -0.88 and -1.11 μm for SDFD, -1.37 and -2.17% for CV, and 13.0 and 11.8% for CF in HU and SU breeds, respectively. Major gene variance was larger than the polygenic variance for all traits. Major gene allelic frequencies for FD, SDFD, and CV ranged from 0.81 to 0.86 for HU breed and from 0.70 to 0.77 for the SU breed and were 0.24 and 0.36, respectively, for CF. It can be concluded that a major gene affecting these traits could be segregating. Then, molecular identification and monitoring of animals carrying favorable genes throughout the worldwide alpaca population would allow for a quick genetic improvement.

Genealogical analyses in open populations: the case of three Arab-derived Spanish horse breeds

This research assesses the genetic composition of three Arab-derived Spanish horse breeds as an example to highlight the major shortcomings related to genealogical analyses in open populations and to propose approaches useful to deal with this task. The studbooks of three Spanish Arab (SA)-derived horse breeds, Spanish Anglo-Arab (dAA), Hispano-Arab (dHA) and Spanish Sport Horse (dSSH) and those of their parental breeds SA, Spanish Purebred (SPB) and Thoroughbred (TB), totalling 211 754 individuals, were available. The genealogies of the dAA, dHA and dSSH were analysed not only using the corresponding studbook (breed exclusive dataset) but also including the genealogies of the founders from parental breeds (completed dataset). Coancestry analyses revealed that the present SA-derived populations share more genes with the Arab than with the other parental breeds. Effective population size was computed by accounting for migration rates to obtain an equivalent closed-population effective size ((eq)N(e)) of 39.2 for the dAA, 56.3 for dHA and 114.1 for dSSH. The essayed methodologies were useful for characterising populations involving migration. The consequences of the management of the analysed breeds are discussed. The results emphasize the need to include the complete genealogies of the individuals to attain reliable genealogical parameters.

Genetic diversity and population structure of the synthetic Pannon White rabbit revealed by pedigree analyses

Demographic history, current status, and efficiency of the mating strategy were analyzed using the pedigree of Pannon White (PW) rabbits born between 1992 and 2007. Potential accumulation of detrimental effects and loss of genetic diversity were also considered. Calculations and estimates were done most often for rabbits born in 2007, whereas other reference populations (REFPOPXXXX) were specified explicitly. The pedigree contained 4,749 individuals and 580 founders, and its completeness was 82.1% up to 10 and 94.5% up to 5 generations, respectively. Generation intervals through different pathways averaged 1.2 yr. When adjusted to the pedigree completeness, the amount of inbreeding (F(i)) of rabbits was comparable (5.54%) with that of other livestock populations, whereas the 10 (30) founders contributing the most to inbreeding explained a large part of the population inbreeding [i.e., 42.24% (73.18%)]. The ancestral inbreeding coefficient of REFPOP2004 (10.67%) was one-half that of REFPOP2007 (20.66%), showing its strong dependence on pedigree length. Family variance, inbreeding, and realized effective population size were 84.18 (REFPOP2006; this variable could not be calculated for the last year examined), 37.19, and 91.08, respectively. The effective numbers of ancestors, founders, and founder genomes were 48, 26, and 7.33, respectively. Although the circular mating scheme applied was generally effective, the large accumulated reduction in genetic variability indicates the need to revise and improve the current breeding strategy.

Fluorangiographic study of the ocular fundus in normal horses

PURPOSE

To describe the protocol and appearance of fluorescein angiography (FA) in normal horses.

ANIMALS

A total of 25 healthy horses aged between 5 and 15 years.

MATERIALS AND METHODS

The horses were sedated with 15 microg/kg detomidine and 50 microg/kg butorphanol and dilated with topical tropicamide 1%. All angiograms were recorded after intravenous bolus injection of 10 mg/kg of fluorescein sodium solution.

RESULTS

Two successive angiographic phases could be discerned: the choriopapillary phase, starting at 46.95 +/- 9.48 s, and the retinal vascular phase, starting at 47.79 +/- 10.38 s. The retinal vascular phase was divided in three parts: filling phase, maximum fluorescence point, and fading phase. During the filling phase, the dye progressed into the retinal vessels, obtaining maximum fluorescence at 59.79 +/- 10.39 s, termed the maximum fluorescence point. The fading phase started immediately following the maximum fluorescence point. During this phase, vascular fluorescence decreased to complete reduction at 74.76 +/- 9.81 s. Also, areas of delayed choroidal filling, the presence of short retinal vessels in the ventral region of the optic disc, and a particular filling of the optic disc were also observed.

CONCLUSIONS

The normal angiographic sequence was described in horses. FA may be a useful method for studying the integrity of the blood-retinal barriers in horses.

Individual increase in inbreeding allows estimating effective sizes from pedigrees

We present here a simple approach to obtain reliable estimates of the effective population size in real world populations via the computation of the increase in inbreeding for each individual (delta F_i) in a given population. The values of delta F_i are computed as t-root of 1 - (1 - F_i) where F_i is the inbreeding coefficient and t is the equivalent complete generations for each individual. The values of delta F computed for a pre-defined reference subset can be averaged and used to estimate effective size. A standard error of this estimate of N_e can be further computed from the standard deviation of the individual increase in inbreeding. The methodology is demonstrated by applying it to several simulated examples and to a real pedigree in which other methodologies fail when considering reference subpopulations. The main characteristics of the approach and its possible use are discussed both for predictive purposes and for analyzing genealogies.