I. Cervantes

Improving the estimation of realized effective population sizes in farm animals

Computation of inbreeding rate (DeltaF) must consider that inbreeding is delayed with one generation with respect to the idealized population when addressed using individual inbreeding coefficients. The expression relating inbreeding in generation t with inbreeding rate F(t) = 1 - (1-DeltaF)(t) should be more correctly written in real animal populations as F(t) = 1 - (1-DeltaF)(t-1), as changes in allele frequencies occur in the equivalent co-ancestries in the previous generation. This simple approach is tested on simulated and real pedigrees thus demonstrating that: (i) the adjusted individual increase in inbreeding becomes stable in populations under random mating while the unadjusted parameter does not; (ii) regression of the unadjusted parameter over generations in pedigrees under random mating is highly significant while after correction it is not significant; and (iii) the variance of the adjusted parameter is reduced with the generations.

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.

Genetic relationships among calving ease, gestation length, and calf survival to weaning in the Asturiana de los Valles beef cattle breed.

The aim of this paper was to estimate the genetic relationships among calving ease (CE), calf survival (CS), and gestation length (GL) to assess the possibility of including this information in beef cattle breeding programs. A total of 35,395 field records were available for CE, 30,684 for GL, and 36,132 for CS from the Asturiana de los Valles beef cattle breed. The 3 traits were analyzed as traits of the calf fitting a multivariate linear mixed model. Estimates of heritability (+/-SE) for the direct genetic effects (CEd, GLd, and CSd) were 0.325 +/- 0.022, 0.331 +/- 0.026, and 0.226 +/- 0.018, respectively, whereas the estimates for maternal genetic effects (CEm, GLm, and CSm) were 0.066 +/- 0.018, 0.066 +/- 0.017, and 0.034 +/- 0.011. The estimates for the ratio of permanent environmental variance to phenotypic variance were CEc 0.090 +/- 0.011, GLc 0.066 +/- 0.011, and CSc 0.024 +/- 0.007. Genetic correlations between direct, maternal genetic, or permanent environmental effects involving CE and GL were, in general, positive and moderate, whereas those involving CE and CS were high. All were significant except for the pair CEm-GLm (0.277 +/- 0.172). Correlations between GL and CS were nonsignificant. Genetic correlations for CEd-CEm, GLd-GLm, and CSd-CSm were negative and high, ranging from -0.461 +/- 0.120 for GLd-GLm to -0.821 +/- 0.145 for CSd-CSm. The genetic correlations for CEd-CSm and for CSd-CEm were negative, significant, and high, whereas that for GLd-CEm was moderate (-0.323 +/- 0.124) and that for GLd-CSm was nonsignificant. The genetic correlations for GLm with the direct effects of the other traits were non-significant. Strong selection for CE will result in a significant correlated response in CS. Therefore, CE can be considered an early indicator of CS performance. The benefit of using GL as a correlated trait in a genetic evaluation with CE and CS seems limited.

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.

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.

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.

Genetic improvement for alpaca fibre production in the Peruvian Altiplano: the Pacomarca experience

Pacomarca es un rancho experimental fundado por el grupo INCA para actuar como un nucleo de seleccion que permita extender la mejora genetica de la fibra de alpaca en el altiplano peruano. En Pacomarca se aplican tecnicas estandar en produccion animal, como el control de rendimientos o la reproduccion asistida incluyendo la transferencia de embriones, para demostrar su utilidad en las condiciones productivas del altiplano. Pacomarca ha desarrollado una aplicacion informatica (Paco Pro) que permite una gestion adecuada de la informacion productiva, reproductiva y genealogica necesaria para llevar a cabo un programa de mejora genetica: los apareamientos se llevan a cabo de forma individualizada, la gestacion se diagnostica mediante ecografia, los meritos geneticos estimados mediante modernas tecnicas de evaluacion genetica se usan para la seleccion de reproductores y la transferencia de embriones se utiliza para aumentar la intensidad de seleccion. En todo caso, el objetivo de Pacomarca se cumple esencialmente organizando periodicamente cursos de formacion para miembros de pequenas comunidades rurales del altiplano en los que se produce la diseminacion de sus avances en manejo, reproduccion y produccion de la alpaca resultado de las experimentaciones realizadas en Pacomarca.

Genetic parameters for growth of fiber diameter in alpacas 1

The alpaca is the most important fiber producer of the South American camelid species, and is an important source of income for the Andean communities. Nowadays, fiber diameter is considered the main selection objective in alpaca populations throughout the world. However, fiber diameter increases with the age of the animals, and it would be preferable to select those animals that maintain a thin fiber throughout their life span. The goal of this study was to describe the genetic relationship between fiber diameter at weaning age (6 mo) and the evolution of fiber diameter along the life span. The analysis of the evolution of fiber diameter was studied as a useful model for canalization and as a longitudinal trait by hierarchical Bayesian analysis. The results suggested that substantial genetic variation exists for fiber diameter and also for the variability and linear growth of the fiber diameter. Thus, a genetic selection program is plausible to modify the evolution of fiber diameter with time, together with a favorable correlated decrease in fiber diameter.

Weighting fibre and morphological traits in a genetic index for an alpaca breeding programme

Nowadays, the fibre diameter (FD) is considered the main selection objective in alpaca populations all over the world. International Committee for Animal Recording recommendations define the FD and its CV as the first two traits to be considered in breeding programmes for this specie. In addition to these main criteria, other selection criteria of economic value used are comfort factor (CF) or standard deviation (s.d.); also other less important traits being used as selection objectives are these morphological traits: density (DE), crimp (CR) or lock structure (LS) for, respectively, Huacaya (HU) and Suri (SU) ecotypes, head (HE), coverage (CO) and balance (BA). The goal of this study was to establish how to implement a combined selection index starting from genetic parameters and to study the expected correlation between genetic trends by considering different alternative procedures of weighting all the involved traits, and the consequences of a wrongly proceeding way. Heritabilities and genetic and phenotypic correlations were estimated from the data set belonging to the PACOMARCA experimental farm for SU and HU. Two approaches were used to check the consequences of a set of subjective weights essayed. The coefficients of selection indexes were obtained for two sets of reference weights. In addition, equivalent weights were drawn if applied those reference values as coefficients of hypothetical selection indexes directly on phenotypes; relative expected genetic responses were computed in different cases. Results showed that almost in all cases for both ecotypes, the weight applied to CF should be surprisingly negative. Concerning genetic responses, only CO was compromised in some cases for the HU ecotype. The essayed methodology allowed explaining the differences between ecotypes in the genetic trends. The proposed methodology was shown to be effective to study the relative importance of the traits granted by the manager of a breeding scheme.