M. Valera

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 Fi) in a given population. The values of delta Fiare computed as t-root of 1 - (1 - Fi) where Fiis 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 Ne 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.

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.

Application of individual increase in inbreeding to estimate realized effective sizes from real pedigrees

The objective of this study was to test the performance of a recently proposed methodology for the estimation of realized effective size (N(e)) based on individual increase in inbreeding (DeltaF(i)) on several real pedigrees: (a) an experimental mice population; (b) a closed pedigree of fighting bulls; (c) the Spanish Purebred (SPB, Andalusian) horse pedigree; (d) the Carthusian strain of SPB pedigree; (e) the Spanish Arab horse pedigree; and (f) the Spanish Anglo-Arab horse pedigree. Several reference subpopulations were defined on the basis of generation length in order to consider only animals in the last generation, to assess the influence of the pedigree content on the estimates of N(e). The estimates of realized N(e) computed from DeltaF(i) (Ne) tended to be higher than those obtained from regression on equivalent generations. The new parameter Ne remained approximately stable when pedigree depth achieved about five equivalent generations. Estimates of take into account the genetic history of the populations, the size of their founder population, and the mating policy or bottlenecks caused by poor use of reproducing individuals. The usefulness of the realized N(e) computed from individual increase in inbreeding in real pedigrees is also discussed.

Genetic characterization of the Spanish Trotter horse breed using microsatellite markers

To assist in selection schemes we carried out the first genetic characterization of the Spanish Trotter horse (Trotador Espanol). We used 16 microsatellite markers to genotype 40 unrelated Spanish trotters, 25 native Balearic horses (11 Menorquina and 14 Mallorquina horses) and 32 Andalusian horses. The observed heterozygosity for the Spanish Trotters was 0.647 ± 0.037 and the expected heterozygosity was 0.696 ± 0.026 while the average number of alleles per locus was 6.0 ± 0.341, these values being similar to the data published for other horse breeds. We also tried to establish the importance of the Mallorquina and Menorquina breeds in the present Spanish Trotter population. Only 9% of the total genetic variability could be attributed to differences between breeds (mean F ST = 0.09 ± 0.010). Recent migration rates were confirmed the low recent genetic relationship between the Balearic breeds and Spanish Trotters, indicating that the genetic background of the present Spanish Trotter population is not based on the native Balearic horse population.

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.

Using eye temperature and heart rate for stress assessment in young horses competing in jumping competitions and its possible influence on sport performance.

The aims of this study were, first, to evaluate eye temperature (ET) with infrared thermography and heart rate (HR) to measure stress in horses during show jumping competitions and their relationship with competition results, and second, to evaluate the influence of different extrinsic and intrinsic factors of the horse on the stress measurements analysed. One hundred and seventy-three Spanish Sport Horses were analysed for ET and HR, and these measurements were taken 3 h before the competition, just after and 3 h after it. Two interval measurements were also assessed for each parameter. Positive significant correlations were found between ET and HR, measured before (r=0.23), just after competition (r=0.28) and for the later interval (r=0.26), whereas negative correlations with competition results were found only for ET when measured just after competing (r=-0.25). Two intrinsic factors (genetic line and age) and no extrinsic factors showed significant differences for ET, whereas one intrinsic factor (age) and two extrinsic factors (journey duration and number of training hours) showed significant differences for HR. The marginal means showed significantly higher ET values for the Anglo-Arab genetic line and for 5-year-old animals. HR values were significantly higher for 4-year-old animals, for horses which had travelled 4 to 6 h and for horses that had 3 to 6 h of daily training. This study suggests that, although ET and HR seemed to share a similar physiological basis, the factors that most influenced each parameter were different. Finally, ET seems to be a suitable tool for assessing stress during show jumping competitions in horses.

Estimation of genetic parameters for racing speed at different distances in young and adult Spanish Trotter horses using the random regression model

A total of 71 522 records (from 3154 horses) with the times per kilometre (TPK), recorded in Spanish Trotter horses (individual races) from racing performances held from 1991 to 2007, were available for this study. The TPK values for the different age groups (young and adult horses) and different distances (1600-2700 m) were considered as different traits, and a bi character random regression model (RRM) was applied to estimate the (co)variance components throughout the trajectory of age groups and distances. The following effects were considered as fixed: the combination of hippodrome-date of race (404 levels); sex of the animals (3 levels); type of start (2 levels) and a fixed regression of Legendre polynomials (order 2). Those considered as random effects were the random regression Legendre polynomial (order 1) for animals (9201 animals in the pedigree); the individual environment permanent (3154 animals with data) and the driver (n = 957 levels). The residual variance was considered as heterogeneous with two classes (ages). The heritability estimated by distance ranged from 0.12 to 0.34, with a different trajectory for the two age groups. Within each age group, the genetic correlations between adjacent distances were high (>0.90), but decreased when the differences between them were over 400 metres for both age groups. The genetic correlations for the same distance across the age groups ranged from 0.47 to 0.78. Accordingly, the analysed trait (TPK) can be considered as positive genetic correlated but as different traits along the trajectory of distance and age. Therefore, some re-ranking should be expected in the breeding value of the horses at different characteristics of the racing. The use of RRM is recommended because it allows us to estimate the breeding value along the whole trajectory of race competition.

Quantifying the relative contribution of ante - and post - mortem factors to the variability in beef texture

This study aims to investigate the relative contribution of ante- and post-mortem factors to the final quality of beef. In all, 112 steers (four breed-crosses) were arranged in a 2 × 2 × 2 factorial experimental including production system, growth implant and β-adrenergic agonist strategies. Carcasses were suspended by the Achilles tendon or the aitch bone and meat was aged for 2/6/13/21/27 days (longissimus muscle) or 2/27 days (semimembranosus muscle). Meat quality traits related to beef texture were measured. Statistical analyses were developed including ante- and post-mortem factors and their relative contribution to the variability observed for each measured trait was calculated. The main factor responsible for the variability in sarcomere length was the suspension method (91.1%), which also influenced drip-loss (44.3%). Increasing the percentage of British breeds increased (P < 0.05) the intramuscular fat content in longissimus muscle, but only when implants were not used. Thus, the breed-cross, implant strategy and their interaction were responsible for >58% of the variability in this trait. The variability in instrumental and sensory tenderness was mainly affected by post-mortem factors (carcass suspension, ageing time and their interaction), explaining generally ∼70% of the variability in these traits. Breed-cross was the second most important effect (∼15%) when carcass suspension was not considered in the model, but still ageing time was responsible for a much larger proportion of the variability in tenderness (>45%). In conclusion, post-mortem handling of the carcasses may be much more effective in controlling beef tenderness than pre-mortem strategies.

Genetic improvement of wool production in Spanish Merino sheep: genetic parameters and simulation of selection strategies

Wool production of the Spanish Merino breed was analysed after several decades of genetic selection to improve meat production. Genetic parameters (heritability and correlations) were estimated for greasy fleece weight, staple length, crimp frequency and fibre diameter of 1869 Spanish Merino purebred sheep. Heritabilities ranged from 0.08 ± 0.050 (fibre diameter) to 0.22 ± 0.060 (staple length), and the genetic correlations ranged from –0.63 ± 0.159 (crimp frequency – staple length) to 0.75 ± 0.222 (fibre diameter – staple length). Genetic simulations were developed to show the consequences of eight selection strategies, which included single trait selection on wool traits and liveweight (the current selection criteria) and index selection combining traits. The results show that it is possible to improve wool and growth traits at the same time. Also, our results show there is indirect genetic progress for wool characteristics using the current liveweight selection criterion.

Sire × stud interaction for body measurement traits in Spanish purebred horses.

The mating policy for Spanish Purebred horses encourages the same or closely related stallions to be used for reproduction across studs differing in environments. Stallions may perform differently across studs, and if so, adjustment for the sire x stud (ss) interaction is recommended. However, there are no studies available that analyzed the influence of ss interaction on estimation of genetic parameters in horses. This research is aimed at assessing the implications of including ss interaction in models fitted for the estimation of genetic parameters for traits under selection using 8 body measurements in Spanish Purebred (Andalusian) horses: height at withers, height at chest, leg length, body length, width of chest, heart girth circumference, knee perimeter, and cannon bone circumference. Body measurements were available for 11,894 horses. Genetic parameters and EBV were estimated using animal models by REML. The inclusion of the ss interaction gives reduced estimates of heritability. Generally, the genetic correlations estimated using the models including the ss interaction were greater than those obtained using the simpler model. Estimates for the ss variance as a proportion of the total phenotypic variance ranged from 0.02 (height at withers) to 0.11 (width of chest). Estimates between the ss interaction correlations associated with each body measurement were positive, significant, and from moderate to low. The range of EBV estimated using the model including the ss interaction decreased with respect to those estimated using the simpler model, and the EBV ranking order was affected. The models including ss interaction fitted significantly better. Therefore, the genetic parameters estimated using the ss interaction may be more realistic, and the obtained (co)variances may be assumed to be closer to the true population parameters. This interaction may result from selective decisions or preferential management practices causing greater similarity between the progeny of a sire in the same stud. It is therefore advisable to include it in genetic models used in horse breeding schemes.