Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.     

Between-founder heterogeneity in inbreeding depression for production in Jersey cows

Severity of inbreeding depression depends on the hidden (i.e., recessive) genetic load carried by a population. If the load is distributed unevenly among founder genomes, or founder-lines were exposed to variable amounts of selection, descendants from different founders may be differentially affected by inbreeding. Between-founder heterogeneity in inbreeding depression for production traits and somatic cell score in milk (SCS) was studied using records from 59,788 Jersey cows. Inbreeding coefficients (F) were partitioned into components due to four founders, plus a remainder. A two-stage statistical analysis was performed. First, empirical best linear unbiased predictions (EBLUP) of residuals for milk, fat and protein yield, and for SCS, were computed using linear models including fixed effects of herd–year–season, age at calving and days in milk, and random additive genetic effects of individual cows. Second, models with total and partial inbreeding coefficients as predictor variables were fitted to EBLUP residuals, for each trait. Tests of differences between slopes indicated that regressions of milk, fat and protein yield on partial inbreeding coefficients were heterogeneous; SCS did not exhibit inbreeding depression. Hence, alleles contributing to inbreeding depression for production in this Jersey population seem to be associated with specific founders. This indicates that a homogeneous effect of inbreeding on production may be an incorrect statistical specification in genetic evaluation models that attempt to account for inbreeding depression. Furthermore, the observed variability between effects of partial inbreeding due to different founders implies that inbreeding effects on yield traits may be due to alleles with major effects.     

Genetic inbreeding depression load for fertility traits in Pura Raza Española mares

Fertility is a key factor in the economic success of horse farms. However, it has received little attention due to the difficulty of measuring fertility objectively. Since its studbook creation (1912), the Pura Raza Española (PRE) breed has been a closed population and become high in-bred resulting in inbreeding depression (poor phenotypic values). Nevertheless, heterogeneous effects of inbreeding depression have been detected among founders and nonfounders. The aims of this study were (1) to analyze the genetic parameters for reproductive traits in mares of the PRE horse breed and (2) to estimate, for the first time, the inbreeding depression load associated with common ancestors of the breed. A total of 22,799 mares were analyzed. Heritability estimates ranged from 0.05 (interval between first and second foaling) to 0.16 (age at first foaling), whereas inbreeding depression load ratios ranged from 0.06 (parturition efficiency at 6th foaling) to 0.17 (age at first foaling), for a partial inbreeding coefficient of 10%. Although heritability is related to the variability expressed in the population, inbreeding depression load ratios measure the potential variability, whether expressed in the population or not. Most correlations between additive and inbreeding depression load genetic values were significant (P < 0.001) and of low to moderate magnitude. Our results confirm that individual inbreeding depression loads allow us to select horses that have a genetic value resistant to the deleterious effects of inbreeding.     

Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32?% of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50?% of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8?% for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64?%. The average relatedness coefficient between individuals of the population was estimated to be 2.05?%??the highest individual coefficient was 10.31?%. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help breeders and farmers adopt better precautionary measures against inbreeding depression and other deleterious genetic effects.     

The influence of selection and epistasis on inbreeding depression estimates

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

Association analyses between the prion protein locus and reproductive and lamb weight traits in Ripollesa sheep

The objective of this study was to analyze the association between the haplotypes of the prion protein (PrP) locus and several reproductive and lamb weight traits in Ripollesa sheep. Prion protein genotypes were available for a total of 310 sheep (7 rams, 114 ewes, and 189 lambs), all of them belonging to the purebred Ripollesa flock of the Universitat Autònoma of Barcelona, for which all sheep had a known pedigree. In addition, the genotype of 24 historical descendants of the previously genotyped adult individuals was reconstructed, provided that both parents were homozygous for PrP haplotypes. Only 3 haplotypes (ARR, ARQ, and ARH) were observed in the PrP locus of the sheep sampled. Reproductive traits included conception rate and litter size, whereas birth BW and 90-d BW were the lamb weight traits studied. The additive effect of PrP haplotypes was analyzed through Bayesian animal threshold and linear models, for reproduction and weight traits, respectively. Ewe reproductive data belonged to 89 ewes that gave 492 conception rate records and 440 litter size records. Analyses of BW at birth and at 90 d of age were made on 323 and 164 lamb records, respectively. No associations between PrP haplotypes and conception rate and BW traits were observed. For litter size, the effect of the ARH haplotype was greater than that of the ARQ haplotype. Differences between ARH and ARR haplotypes also suggested an advantage for the ARH. As a whole, our results indicated that the selection favorable to increase litter size in Ripollesa ewes may also increase the ARH haplotype frequency, which contradicts the recommendations of the current European Union legislation aiming to increase the genetic resistance to scrapie. As a consequence, scrapie genotyping needs to be included as a new selection criterion in the breed.     

Effects of inbreeding and heterosis in Hereford females on fertility, calf survival and preweaning growth

Effects of inbreeding and heterosis and the difference between them were estimated by comparing linecross (L), topcross (T), inbred (I) and control line (C) Hereford females for reproductive and preweaning growth traits of their progeny. Inbred females (average inbreeding coefficient = 26.5%) originated from four single-sire inbred lines. Control females (average inbreeding coefficient = 6.9%) were produced by a four-sire, 60-cow line. Linecross females were produced from all possible reciprocal crosses of the I lines. Topcross females were produced by mating I bulls to C cows. Differences in pregnancy rate among these lines were not detected. Effects of maternal heterosis were positive for both prenatal and postnatal survival. The weaning rate by L females exceeded the weaning rate by I females as a result. Prenatal survival was reduced in calves from I females relative to those from C females, resulting in corresponding differences in birth and weaning rates. Differences in the magnitudes of maternal heterosis and inbreeding effects were not detected, except for birth weight. For birth weight the effect of maternal inbreeding was of greater magnitude than the effect of maternal heterosis. Within the I and C lines regressions of pregnancy rate, prenatal survival, birth rate, postnatal survival, weaning rate, weaning weight/cow exposed, birth weight and weaning weight on the inbreeding coefficients of the cows indicated significant inbreeding depression on all traits except pregnancy rate and postnatal survival.     

Population genetic analysis of the new dog breed Elo

The breeding of the dog breed Elo was started in 1987. This dog breed was established by using 16 dogs of nine different breeds. All pedigree information of the dogs from 1987 to 2002 was included for the analysis of the proportion of genes of the different founder breeds, of the inbreeding coefficient, and relationship coefficients. Additionally, the number of died puppies per litter were investigated. The Eurasian dog breed contributed about 48% of the genes in the whole Elo dog population. Old English sheepdog and Chow Chow contributed about 23% and 10% of the genes. The other dog breeds were of minor importance. The mean inbreeding and relationship coefficients of the whole Elo dog population were 12.04% and 19.22%, respectively. With the exception of 3.5% of animals, all Elo dogs were related to each other. The mean litter size was 6.39 puppies. The percentage of stillborn puppies per litter averaged at 9.47%. The inbreeding coefficients of the puppies and of their dams, the age of the sire and the dam at the time of birth of the puppies, the litter size, the puppies' year of birth and the proportion of genes of the Chow Chow showed a significant effect on the number of stillborn puppies per litter. The heritability for the frequency of stillborn puppies was estimated using a linear animal model. After transformation of the linear estimates to the underlying liability scale, the heritability amounted to h2 = 0.15.     

Inbreeding trend and inbreeding depression in the Danish populations of Texel, Shropshire, and Oxford Down

The objective of this study was to analyze the development of inbreeding and estimate inbreeding depression in the Danish populations of 3 major meat type sheep breeds. The pedigrees contained 29,336 Texel, 22,838 Shropshire, and 11,487 Oxford Down. The rate of inbreeding was approximately 1% per generation for all breeds, but the rate of increase in co-ancestry was somewhat lower (0.45 to 0.71), indicating that more inbreeding has been accumulating than would be expected if mating was at random. Inbreeding depression for birth weight, ADG from birth until 2 mo, and litter size was estimated for all 3 breeds using a minimum of 15,000 records per trait and breed. All traits showed depression due to inbreeding of the animal itself. For most combinations of trait and breed, there was also a significant reduction of the phenotype due to inbreeding in the dam. The size of inbreeding depression was 1.2 to 2.6% of the mean, resulting in an increase in the inbreeding coefficient of the individual of 0.10, and estimates were similar for similar increases in maternal inbreeding. The rate of inbreeding in these breeds needs to be reduced in the future to avoid a further decline in birth weight, ADG, and litter size.     

近交对内蒙古白绒山羊体重和产绒量的影响

内蒙古白绒山羊主要是通过本品种选育进行繁育。随着BLUP方法在内蒙古白绒山羊选育上的应用,很大程度上造成了近交的上升。通过对内蒙古白绒山羊近交程度随世代的变化情况、以及近交对生长性状和产绒性状的影响的详细分析,发现随着近交系数的增加,出生重、断奶重、周岁重及产绒量都趋近于正态分布。当近交系数在0.015625～0.03125区间内,各体重值及产绒量均达到最高值。     

Evaluation of Duroc- vs. Pietrain-sired pigs for growth and composition

Accurate evaluations of growth and composition traits enable better management decisions regarding genetic merit, feeding, and marketing. Sires from Duroc and Pietrain populations were used to produce crossbred pigs, which were evaluated for growth and composition traits. All parents were normal for the ryanodine receptor gene. Boars from each breed were mated to either Yorkshire or F1 Yorkshire-Landrace females with 307 offspring evaluated from birth through 26 wk of age. No significant differences between sire breeds were seen for pig BW from birth through 10 wk of age. Body weight, 10th rib backfat (BF10), last rib backfat (LRF), and loin muscle area (LMA) were serially measured at 10, 13, 16, 19, 22, 24, and 26 wk of age. At 26 wk of age, Duroc-sired progeny were heavier (143.4 vs. 132.7 kg, P < 0.001), had more BF10 (27.1 vs. 23.7 mm, P < 0.001) and LRF (21.2 vs. 19.2 mm, P < 0.001), but had similar LMA (46.4 vs. 47.1 cm2) compared with Pietrain-sired progeny. Mean feed efficiency did not differ between breed of sire in any period of the study. Duroc progeny had a greater ADG (980.1 vs. 892.3 g/d, P < 0.001) from 10 to 26 wk of age than Pietrain-sired pigs. Composition traits of fat-free total lean (FFTOLN), total fat tissue (TOFAT), empty body protein (EBPRO), and empty body lipid (EBLIPID) were calculated. Random regression animal models with polynomial regression on week on-test were fitted to BW, BF10, LRF, LMA, FFTOLN, TOFAT, EBPRO, and EBLIPID from 10 to 26 wk of age. Duroc-sired barrows tended to grow faster but with more fat tissue, and Pietrain-sired gilts were slower growing but leaner, whereas Duroc-sired gilts and Pietrain-sired barrows were intermediate for growth and backfat measures. Serial heritability estimates generally increased from 10 to 26 wk of age with ranges as follows: BW (0.05 to 0.39), BF10 (0.13 to 0.76), LRF (0.11 to 0.79), LMA (0.05 to 0.73), FFTOLN (0.07 to 0.16), TOFAT (0.19 to 0.45), EBPRO (0.02 to 0.55), and EBLIPID (0.12 to 0.60). Pigs sired by Duroc and Pietrain boars had similar lean tissue growth but achieved it through different mechanisms.     

Survival analysis from birth to slaughter of Ripollesa lambs under semi-intensive management

The survivability from birth to slaughter of 1,487 Ripollesa lambs with a preslaughter overall mortality of 9.6% was studied under the proportional hazards framework, assuming a Weibull distribution for the baseline hazards function. A sire frailty model was fitted, with the common environment received by the lamb as an additional random source of variation. Common environment was considered time-dependent and was characterized by the dam and the contemporary lamb group during the preweaning and fattening periods, respectively. Only 3 fixed effects were statistically significant: the linear and quadratic effects of birth weight (P < 0.001), the relative position of the delivery within the lambing season (P < 0.001), and the presence of stillbirths or mummified fetuses within the litter (P < 0.05). Birth type and parity of the ewe were significant only when birth weight was removed from the model (P < 0.001 and P < 0.05, respectively). Nevertheless, the model including birth weight became preferable according to the Akaike's information criterion. Survivability dramatically decreased with extreme birth weights, although it reached a survival probability greater than 93.5% within the 3.3 to 5.4 kg range, indicating an optimum birth weight range of Ripollesa lambs for survival purposes. The hazard ratio (HR) increased for births occurring within the last third of the lambing period (HR = 1.70; P < 0.05), as well as for primiparous ewes that lambed in December and January (HR = 5.36; P < 0.001). Survival probability decreased for lambs born from litters with 1 or more stillbirths or mummified fetuses (HR = 1.61; P < 0.05). The variance component estimated for sire variance (0.07) was clearly lower than that of the common environment (1.87), with a heritability estimate of 0.027.     

不同来源大白猪总产仔数近交衰退评估

旨在评估两个不同来源大白猪群体经过近8个世代的选育后总产仔数（total number of piglets born，TNB）近交衰退的程度。本研究对1 937头大白猪使用GeneSeek GGP Porcine HD芯片进行分型，其中1 039头来自加系大白猪和898头来自法系大白猪，且两品系均有表型记录和系谱记录，系谱共由3 086头大白猪组成。分别使用系谱、SNP和ROH进行个体近交系数估计，并将近交系数作为协变量利用动物模型对总产仔数进行近交衰退评估。为了精准定位导致总产仔数衰退的基因组片段，又进一步对每条染色体以及显著染色体分段计算近交系数并估计其效应，检测是否能引起总产仔数发生近交衰退现象。对于加系群体，F_ROH、F_GRM和F_PED估计的近交系数均值分别为0.124、0.042和0.013，其中F_ROH和F_PED相关最高，相关系数为0.358；对于法系群体，F_ROH、F_GRM和F_PED均值分别为0.123、0.052和0.007，其中F_ROH和F_GRM相关最高，相关系数为0.371。利用3种不同计算方法所得近交系数用于估计近交衰退时，加系群体的总产仔数均检测到显著的近交衰退，而且当F_ROH、F_GRM和F_PED每增加10%时，总产仔数分别减少0.571、0.341和0.823头；但法系群体仅有F_ROH估计的总产仔数检测到显著近交衰退，F_ROH每增加10%时，总产仔数减少0.690头。为了锁定相关的染色体和基因组区段，首先利用ROH估计每条染色体近交系数并进行近交衰退分析发现，加系群体中检测到第6、7、8和13号染色体产生了显著近的总产仔数交衰退，而法系群体未检测到与近交衰退相关的染色体。然后，又将与加系总产仔数近交衰退显著相关的4条染色体平均分为2、4、6、8个片段进行近交衰退检测，其中平均分成8段后的染色片段的长度范围为15.1~25.8 Mb。在第6、7和8号染色体分别检测到1、2和3个与总产仔数相关的近交衰退染色体片段。这些区域注释到了CUL7、MAPK14和PPARD基因与胎盘发育相关，AREG和EREG基因与卵母细胞成熟有关。本研究利用3种近交系数计算方法对两个不同来源的大白猪总产仔数进行近交衰退评估，在加系大白猪中3种估计方法都能检测到近交衰退的现象，而法系群体中只有F_ROH才能检测到。而且通过ROH方法进一步确定了能引起加系大白猪总产仔数衰退的4条染色体和6个特定的染色体区段，还注释到了与繁殖相关的候选基因。这为揭示近交衰退的遗传机制提供了新的研究手段，也为基因组选种选配提供了参考依据。     

Estimates of direct and maternal (co)variance components as well as genetic parameters of growth traits in Nellore sheep

In the present study, (co)variance components and genetic parameters in Nellore sheep were obtained by restricted maximum likelihood (REML) method using six different animal models with various combinations of direct and maternal genetic effects for birth weight (BW), weaning weight (WW), 6-month weight (6MW), 9-month weight (9MW) and 12-month weight (YW). Evaluated records of 2075 lambs descended from 69 sires and 478 dams over a period of 8 years (2007–2014) were collected from the Livestock Research Station, Palamaner, India. Lambing year, sex of lamb, season of lambing and parity of dam were the fixed effects in the model, and ewe weight was used as a covariate. Best model for each trait was determined by log-likelihood ratio test. Direct heritability for BW, WW, 6MW, 9MW and YW were 0.08, 0.03, 0.12, 0.16 and 0.10, respectively, and their corresponding maternal heritabilities were 0.07, 0.10, 0.09, 0.08 and 0.11. The proportions of maternal permanent environment variance to phenotypic variance (Pe²) were 0.07, 0.10, 0.07, 0.06 and 0.10 for BW, WW, 6MW, 9MW and YW, respectively. The estimates of direct genetic correlations among the growth traits were positive and ranged from 0.44(BW-WW) to 0.96(YW-9MW), and the estimates of phenotypic and environmental correlations were found to be lower than those of genetic correlations. Exclusion of maternal effects in the model resulted in biased estimates of genetic parameters in Nellore sheep. Hence, to implement optimum breeding strategies for improvement of traits in Nellore sheep, maternal effects should be considered.     

Monitoring of genetic diversity in the endangered Martina Franca donkey population

The Martina Franca (MF) donkey, an ancient native breed of Apulia, was mostly famous for mule production. The breed was at serious risk of extinction in the 1980s following the decrease in demand for draft animals because they were increasingly replaced by agricultural machinery. Much has been done in the last few decades to safeguard the existing donkey breeds, but the situation remains critical. Successful implementation of conservation measures includes an evaluation of the present degree of breed endangerment, so the aim of this work was to analyze the demographic and genetic parameters of this breed to suggest effective conservation strategies. With a current breed register counting less than 500 recorded animals, the pedigree data set included 1,658 MF donkeys born between 1929 and 2006. Analyses were carried out on the whole data set as well as on a smaller one consisting of 422 living animals. Demographic and genetic variability parameters were evaluated using the ENDOG (v4.6) software. The pedigree completeness level was evaluated as well as the generation length, which was calculated for each of the 4 gametic pathways. This information was obtained from animal birth date records together with those of their fathers and mothers. The effective number of founders (f(e)), the effective number of ancestors (f(a)), the founder genome (f(g)), individual inbreeding (F), average relatedness (AR), and the rate of inbreeding per generation were analyzed to describe the genetic variability of the population. Because pedigree depth and completeness were appropriate, especially regarding the current population, the parameters defining genetic variability, namely, f(e), f(a), f(g), F, and AR, could be reliably estimated. Analysis of these parameters highlighted the endangerment status of the MF donkey. Our special concern was with the increased percentage of males and females exhibiting increased AR values. Moreover, the effective size of the current population, 48.08, is slightly less than the range of the minimum effective size, and the rates of inbreeding per generation found in the current MF population exceed the maximum recommended level of 1%. Such a scenario heightens concerns over the endangered status of the MF breed and calls for proper conservation measures and breeding strategies, such as selecting individuals for mating when relationships are below 12.5%.     

Inbreeding effects on the parameters of the growth function in three strains of Iberian pigs

The growth performance of inbred pigs coming from full-sib matings was compared to that of contemporary animals coming from the same sires mated to control dams. The animals belong to three strains of Iberian pigs with different histories of previous inbreeding. The data consisted of 1,615 weight records between 50 and 250 d of age from 229 pigs. The statistical model assumed the two parameters that describe the linear growth function (a = intercept, b = slope) as different traits (weight at 120 d and daily gain) and the analysis was carried out in a Bayesian framework via Gibbs sampling. The means of the posterior distribution of heritabilities, common litter environmental coefficients, and genetic correlation were 0.328 (h(2)a), 0.332 (h2b), 0.084 (c(2)a), 0.060 (c(2)b) and 0.973 (rhoG). Inbreeding depression, expressed as the performance decrease relative to the mean, per 10% increase of the inbreeding coefficient, was -3.18, -2.31 and -5.37% for weight at 120 d (a), and -3.16, -2.08 and -6.49% for daily gain (b) in each of the three strains. The results indicate that the inbreeding effects are dependent on the level of previous inbreeding, the more previous inbreeding, the less inbreeding depression.     

Bayes factor analysis for the genetic background of physiological and vitality variables of F2 Iberian x Meishan newborn piglets

The Bayes factor (BF) procedure was applied to examine the additive genetic component of several physiological and vitality variables for newborn pigs. Nine variables were studied: heart rate, arterial oxygen saturation, rectal temperature (all at birth and 60 min later), birth weight, interval between birth and first teats contact, and interval between birth and first colostrum intake. The available numbers of data ranged from 288 (heart rate at 60 min) to 839 records (birth weight) from F(2) Iberian x Meishan newborn pigs. We compared a model with zero heritability (nonheritable) with the one where the additive genetic background was included. The BF was used to discriminate between both candidate models. Very strong evidence of genetic background was detected for heart rate 60 min after birth (BF = 48.90), and strong evidence was detected for rectal temperature at birth (BF = 13.82). Posterior modes (means) of heritabilities were 0.29 (0.32) and 0.40 (0.39), respectively. In addition, substantial evidence of absence of genetic background was detected for arterial oxygen saturation at birth.     

Rates of inbreeding and genetic diversity in Iranian Holstein Cattle

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1 048 572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non‐founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non‐founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co‐ancestry and inbreeding, which would lead to better handling of the effective population size.     

Inbreeding depression in Zebu cattle traits

The productivity of herds may be negatively affected by inbreeding depression, and it is important to know how intense is this effect on the livestock performance. We performed a comprehensive analysis involving five Zebu breeds reared in Brazil to estimate inbreeding depression in productive and reproductive traits. Inbreeding depression was estimated for 13 traits by including the individual inbreeding rate as a linear covariate in the standard genetic evaluation models. For all breeds and for almost all traits (no effect was observed on gestation length), the performance of the animals was compromised by an increase in inbreeding. The average inbreeding depression was ?0.222% and ?0.859% per 1% of inbreeding for linear regression coefficients scaled on the percentage of mean (β_m) and standard deviation (β_σ), respectively. The means for β_m (and β_σ) were ?0.269% (?1.202%) for weight/growth traits and ?0.174% (?0.546%) for reproductive traits. Hence, inbreeding depression is more pronounced in weight/growth traits than in reproductive traits. These findings highlight the need for the management of inbreeding in the respective breeding programmes of the breeds studied here.