Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap

Breeding circles allow genetic management in closed populations without pedigrees. In a breeding circle, breeding is split over sub‐populations. Each sub‐population receives breeding males from a single sub‐population and supplies breeding males to one other sub‐population. Donor‐recipient combinations of sub‐populations remain the same over time. Here, we derive inbreeding levels both mathematically and by computer simulation and compare them to actual inbreeding rates derived from DNA information in a real sheep population. In Veluws Heideschaap, a breeding circle has been in operation for over 30 years. Mathematically, starting with inbreeding levels and kinships set to zero, inbreeding rates per generation (ΔF) initially were 0.29%–0.47% within flocks but later converged to 0.18% in all flocks. When, more realistically, inbreeding levels at the start were high and kinship between flocks low, inbreeding levels immediately dropped to the kinship levels between flocks and rates more gradually converged to 0.18%. In computer simulations with overlapping generations, inbreeding levels and rates followed the same pattern, but converged to a lower ΔF of 0.12%. ΔF was determined in the real population with a 12 K SNP chip in recent generations. ΔF in the real population was 0.29%, based on markers to 0.41% per generation based on heterozygosity levels. This is two to three times the theoretically derived values. These increased rates in the real population are probably due to selection and/or the presence of dominant rams siring a disproportionate number of offspring. When these were simulated, ΔF agreed better: 0.35% for selection, 0.38% for dominant rams and 0.67% for both together. The realized inbreeding rates are a warning that in a real population inbreeding rates in a breeding circle can be higher than theoretically expected due to selection and dominant rams. Without a breeding circle, however, inbreeding rates would have been even higher.     

Population structure of Reyna Creole cattle in Nicaragua

Reyna Creole cattle originated from Bos taurus cattle brought to Latin America during the Spanish colonization in the fifteenth century and are the only remaining local breed in Nicaragua. However, the current genetic status of this breed is unknown. Therefore, the population structure of three recorded Reyna Creole herds in Nicaragua was studied to estimate their level of inbreeding, effective population size, and generation intervals. Data from 2,609 animals born between 1958 and 2007 were analyzed. A pedigree completeness index higher than 0.8 was required to obtain reliable estimates of the level of inbreeding, and this criterion was met for 367 animals (14%) in two herds. The average level of inbreeding was 13.0%, with values ranging from 0% to 43.8% for individual animals. One of the herds had an average inbreeding level of 21.6%, primarily due to long periods in which the same bulls were used for mating, leading to excessive frequencies of matings between closely related animals. The effective population size differed between years and ranged from 28 to 46 animals, showing that the Reyna Creole cattle breed is endangered, close to critical status. The average generation interval was 6.9 years with values as high as 19.1 years for some sires that were used for artificial insemination over a long period of time. Due to the high level of inbreeding and small population size, urgent actions are required for the development of a breeding program to protect the breed and support its sustainable utilization.     

Effective population size and inbreeding depression on litter size in rabbits. A case study

The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47 794 l and a pedigree of 14 622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection.     

Purebreeding of Red Maasai and crossbreeding with Dorper sheep in different environments in Kenya

The aim of this article was to study opportunities for improvement of the indigenous and threatened Red Maasai sheep (RM) in Kenya, by comparing purebreeding with crossbreeding with Dorper sheep (D) as a terminal breed, in two different environments (Env. A and a harsher Env. B), assuming different levels of genotype‐by‐environment interaction (G × E). Breeding goals differed between environments and breeds. Four scenarios of nucleus breeding schemes were stochastically simulated, with the nucleus in Env. A. Overall, results showed an increase in carcass weight produced per ewe by more than 10% over 15 years. Genetic gain in carcass weight was 0.17 genetic SD/year (0.2 kg/year) across scenarios for RM in the less harsh Env. A. For survival and milk yield, the gain was lower (0.04–0.05 genetic SD/year). With stronger G × E, the gain in the commercial tier for RM in the harsher Env. B became increasingly lower. Selection of females also within the commercial tier gave slightly higher genetic gain. The scenario with purebreeding of RM and a subnucleus in Env. B gave the highest total income and quantity of meat. However, quantity of meat in Env. A increased slightly from having crossbreeding with D, whereas that in Env. B decreased. A simple and well‐designed nucleus breeding programme would increase the genetic potential of RM. Crossbreeding of RM with D is not recommended for harsh environmental conditions due to the large breed differences expected in that environment.     

Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP‐derived metrics

Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi‐generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP‐derived metrics of homozygosity (r = 0.814–0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality‐checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.     

Optimization of selection and mating schemes in closed broiler lines

Minimum coancestry mating (MC) is a simple mating system to reduce inbreeding in populations, in which matings are allocated so as to minimize the average inbreeding coefficient of progeny. This system was compared with random mating (RM) in simulated broiler lines. The population structure and genetic parameters were determined on the basis of an existing broiler line. Comparison of mating systems was made under two selection methods. The first method (DIS) was based on selection index for achieving desired genetic gains. In the second method (LPS), a combination of the family index and linear programming technique was applied to obtain the desired genetic gains. The selected traits were body weight at 6 weeks of both sexes and age at sexual maturity of hen. Four schemes by all the possible combinations of selection and mating methods (DIS + RM, DIS + MC, LPS + RM and LPS + MC) were compared in terms of genetic gains and inbreeding during 15 generations of selection and mating. The results obtained are summarized as follows: (i) the four schemes produced similar genetic gains averaged over replicates; (ii) the variations of genetic gains under LPS + RM and LPS + MC schemes were much smaller than under DIS + RM and DIS + MC schemes; (iii) irrespective of the selection methods, MC reduced the average inbreeding coefficients to about 80% of RM and; (iv) the inbreeding coefficients of individuals in the schemes with RM were distributed in a wide range, while the inbreeding coefficients in the schemes with MC showed a high uniformity. From these results, the LPS + MC scheme was recommended as a selection and mating strategy in closed broiler lines.     

Molecular and pedigree analysis applied to conservation of animal genetic resources: the case of Brazilian Somali hair sheep

The first registers of Somali sheep in Brazil are from the beginning of the 1900s. This breed, adapted to the dry climate and scarce food supply, is restricted in the northeast region of the country. Molecular marker technologies, especially those based on genotyping microsatellite and mtDNA loci, can be used in conjunction with breeding (pedigree analysis) and consequently the maintenance of genetic variation in herds. Animals from the Brazilian Somali Conservation Nuclei from Embrapa Sheep and Goats in Ceará State were used to validate genetic monitoring by traditional pedigree methods and molecular markers. Nineteen microsatellite markers and 404 base pairs from the control region of mtDNA were used. For total herd diversity, an average 5.32 alleles were found, with expected heterozygosity of 0.5896, observed heterozygosity of 0.6451, 0.4126 for molecular coancestrality, and coefficient of inbreeding (F _IS) was −0.095. Comparing molecular coancestrality means over the years, there was a consistent increase in this parameter within the herd, increasing from 0.4157 to 0.4769 in 2 years (approx. 12% variation). Sixteen mtDNA haplotypes were identified. Inbreeding and other estimates from genealogical analyses confirm the results from molecular markers. From these results, it is possible to state that microsatellites are useful tools in genetic management of herds, especially when routine herd recording is not carried out, or there were gaps in recent generations. As well as pedigree control, genetic diversity can be optimized. Based on the results, and despite herd recording in the herd of Brazilian Somali of Embrapa Sheep and Goats, additional management measures need to be carried out in this herd to reduce inbreeding and optimize genetic variation.     

Estimation of inbreeding and effective population size of full‐blood wagyu cattle registered with the American Wagyu Cattle Association

The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (F_IT and F_ST) and the effective population size (N_e) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (F_ROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (F_ROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.     

Effects of incomplete pedigree on genetic management of the Dutch Landrace goat

Genetic diversity in the Dutch Landrace goat was investigated based on information from the pedigree with about 6500 animals. Annual inbreeding rate after 1985 was below 0.5% and after 1987 close to 0%. However, pedigree information was incomplete, and 350 animals had unknown parents, while for the majority the real parents must have been in the pedigree. To determine the influence of unknown parents, 20 new pedigrees were created by random assignment of animals, alive at the time of birth, as parents to individuals with unknown parents. Only 12 founders remained for these pedigrees, and inbreeding levels varied considerably between these 20 pedigrees. However, inbreeding rates were remarkably constant. They increased to about 0.2%, indicating that the population is not endangered by inbreeding. The optimal contribution theory was used to evaluate possibilities of decreasing the average relationship in the population and thus to increase the genetic diversity of the breed. Optimal contribution decreased the average relationship in the population whether randomly assigned parents were used or not. However, individuals selected as parents for the resampled pedigrees differed from the original pedigree, and only a few animals were selected for all pedigrees. Candidates for inclusion in the genebank were also selected using optimal contribution. Adding animals to the genebank increased the conserved genetic diversity substantially, but as the lists differed between the analysed pedigrees it was not clear which animals were best added to the genebank.     

Extension of the concept of kinship, relationship, and inbreeding to account for linked epistatic complexes

Although epistatic effects are well defined and, in principle, can be exploited in quantitative-genetic selection theory, they often are ignored or even treated as nuisance parameters in practical applications. Traditionally, epistasis is considered as an interaction between genes at unspecified loci. Inspired by the observation that functional genes are often organised in physical clusters, we developed a model to combine additive effects and additive × additive interactions in linked gene clusters of defined length. Malécot's kinship concept is extended to identity by descent probabilities for chromosome segments of a given length in Morgan units, called epistatic kinship. Using the analogy of Malécot's kinship and Wright's relationship and inbreeding coefficients, epistatic relationship coefficients and epistatic inbreeding coefficients are defined. Simple rules are given to set up the epistatic numerator relationship matrix and its inverse directly from a pedigree list. The well-known single locus parameters and algorithms to set up the additive numerator relationship matrix and its inverse are a special case of the suggested methodology for a chromosome segment length of null Morgan. A proof of concept of the suggested method is given with a small simulation study. Assuming additive, linked epistatic and residual variance components, 100 replicated data sets for 1000 individuals are generated. From these data, residual maximum likelihood estimates of the variance components and of the chromosome segment size are obtained. Potential applications of the methodology are discussed. Given that a substantial variance component is attributed to this effect, the expected genetic gain can be increased on the short term if selection is on additive and epistatic effects, the latter comprising additive × additive interaction effect of loci in linkage disequilibrium. This extra benefit, however, will diminish through crossing over in subsequent generations. Despite some practical problems yet to be solved, the suggested model and algorithms open new perspectives to use a higher proportion of genetic variability in selection and breeding.     

Implementation of genetic evaluation and mating designs for the endangered local pig breed ‘Bunte Bentheimer’

A pedigree including 1538 individuals of the endangered pig breed ‘Bunte Bentheimer’ and 3008 records of the fertility traits ‘number of piglets born alive’ (NBA) and ‘number of piglets weaned’ (NW) were used to i) characterize the population structure, ii) to estimate genetic (co)variance components and estimated breeding values (EBVs) and iii) to use EBVs for the application of the concept of optimal genetic contributions. The average coefficient of inbreeding increased from F = 0.103 to F = 0.121 within the two recent cohorts. Average rate of inbreeding amounted to 1.66%, which resulted in an effective population size of N_e = 30 animals in the recent cohort. Average generation interval was 3.07 years considering the whole pedigree, and in total, only 612 sows and boars generated offspring. Estimated heritabilities for both traits NBA and NW were 0.12, and the estimated genetic correlation between both traits was 0.96. The variance component due to the service sire was higher than in commercial pig breeds, presumably due to the widespread use of natural service boars. The EBVs for NBA from 333 selection candidates (63 boars and 270 sows) were used to determine optimal genetic contributions. Based on selected animals and their optimal genetic contributions, specific mating designs were evaluated to minimize inbreeding in the next generation. Best results were achieved when using a simulated annealing algorithm and allowing artificial insemination.     

Factors affecting reproductive performance in dromedary camel herds in Saudi Arabia

A survey of 7122 dromedary camels in 115 herds in Saudi Arabia was used to estimate the effects of herd size (HZ; <?25 vs. 25–49 vs. 50–100 vs. >?100 camels), herder/camels ratio (H/C; 1:<?25 vs. 1:25–50 vs. 1:>?50), manager experience (ME; <?5 vs. 5–10 vs. >?10 years), male/females ratio (M/F), housing system (HS; free vs. closed vs. mixed), length of the breeding season (winter vs. winter and spring vs. fall, winter and spring), age at first mating (3 vs. >?3 years), and time of mating after parturition (≤?3 vs. >?3 months) and their interactions on the overall pregnancy rate. Barren females of these herds (n?=?886) were examined for the causes of infertility. Results showed that herds with H/C of 1:<?25 had higher overall pregnancy rate (95.29%) than herds with H/C of 1:25–50 (79.84%) and those with H/C of 1:>?50 (72.79%) (p?=?0.003). Herds having ME of >?10 years revealed greater overall pregnancy rate (94.89%) than herds with ME of 5–10 years (80.54%) and those with ME of <?5 years (72.5%) (p?=?0.001). There were significant interactions between H/C × HZ (p?=?0.003), H/C × HS (p?=?0.006), and ME × HS (p?=?0.02). The overall pregnancy rate did not significantly differ between herds bred females by age of 3 years and those bred females by age >?3 years and in females bred within 3 months after parturition and in those bred after 3 months. The mean calving interval was shorter (p?=?0.008) in camels mated within 3 months of parturition (15.25?±?2.8 months) than in those mated after that time (24.33?±?6.5 months). Clinical endometritis, ovarian hydrobursitis, and vaginal adhesions were the common clinical findings in barren females. Thus, efforts to reduce the age at first mating and the interval after calving, increase the number of herders/camels, and control reproductive disorders could improve the reproductive performance and quality of camel herds in Saudi Arabia.

     

Epistatic kinship a new measure of genetic diversity for short-term phylogenetic structures – theoretical investigations

The epistatic kinship describes the probability that chromosomal segments of length x in Morgan are identical by descent. It is an extension from the single locus consideration of the kinship coefficient to chromosomal segments. The parameter reflects the number of meioses separating individuals or populations. Hence it is suggested as a measure to quantify the genetic distance of subpopulations that have been separated only few generations ago. Algorithms for the epistatic kinship and the extension of the rules to set up the rectangular relationship matrix are presented. The properties of the epistatic kinship based on pedigree information were investigated theoretically. Pedigree data are often missing for small livestock populations. Therefore, an approach to estimate epistatic kinship based on molecular marker data are suggested. For the epistatic kinship based on marker information haplotypes are relevant. An easy and fast method that derives haplotypes and the respective frequencies without pedigree information was derived based on sampled full‐sib pairs. Different parameters of the sampling scheme were tested in a simulation study. The power of the method decreases with increasing segment length and with increasing number of segments genotyped. Further, it is shown that the efficiency of the approach is influenced by the number of animals genotyped and the polymorphism of the markers. It is discussed that the suggested method has a considerable potential to allow a phylogenetic differentiation between close populations, where small sample size can be balanced by the number, the length, and the degree of polymorphism of the chromosome segments considered.     

近交对狼山鸡繁殖性状影响的研究

利用RAD-seq简化基因组测序鉴定狼山鸡保种群个体基因组SNP标记,计算个体(间)分子近交系数和分子亲缘系数,结合系谱信息组建高、低近交两个试验组。分析后代繁殖性状近交衰退系数,评价近交对繁殖性状的影响。结果显示:利用FROH、FGRM、FHOM和FUNI四种分子近交系数结合亲缘系数kin估算的后代分子近交系数较为一致。低近交组后代的平均分子近交系数小于0.04,高近交组(6个家系)后代的平均分子近交系数介于0.14~0.25。近交对各繁殖性状的效应表现并不一致。高近交组后代母鸡开产日龄、300日龄产蛋数发生显著衰退(P<0.05,P<0.01),且与分子近交系数呈显著相关(P<0.05,P<0.01);开产体重和开产蛋重未发生显著性衰退(P>0.05)。研究结果为进一步探讨狼山鸡繁殖性状近交衰退分子机制提供了基础。     

Indicators of genetic erosion in an endangered population: the Alentejana cattle breed in Portugal

A study was conducted to characterize genetic diversity in the Alentejana breed of cattle based on its demographic trends and to investigate the major factors affecting genetic erosion in this breed. Herdbook information collected between 1940 and 2004, including pedigree records on 100,562 animals in 155 herds, was used to estimate demographic parameters. The mean generation intervals were 6.0 +/- 2.4 yr and 6.8 +/- 3.2 yr for sires and dams of calves, respectively. Average inbreeding increased steadily over the period analyzed, with an annual rate of inbreeding of 0.33 +/- 0.004% (P < 0.01) and an effective population size of 23.3. In the reference population (28,531 calves born between 2000 and 2003) the average inbreeding was 8.35 +/- 9.02% and nearly 80% of the calves were inbred, whereas the average relationship among all animals was 0.026 +/- 0.040. Nevertheless, the mean relationship was 0.328 +/- 0.264 and 0.022 +/- 0.026 for animals born in the same and in different herds, respectively. The computed genetic contributions to the reference population resulted in estimates for the effective number of founders, ancestors, founding herds, and herds supplying sires of 121.6, 55.0, 17.1, and 26.9, respectively, the 2 most influential herds and ancestors contributing 24.2 and 15.1%, respectively, of the current genetic pool. Of the 671 founding sires, only 24 Y-chromosomes are currently represented, but 1 sire alone contributes nearly 60% of this representation, such that the effective number of Y-chromosomes is only 2.73. The observed inbreeding per herd was, on average, 0.053 +/- 0.071 lower than expected from the relationship among the generation of parents of calves in the reference population, indicating that producers have followed breeding strategies that have kept inbreeding at lower levels than anticipated with random selection and mating. When compared with other cattle breeds, Alentejana has some of the highest levels of mean inbreeding and annual rate of inbreeding, and an effective population size that is nearly half of the minimum recommended for maintenance of genetic variability. These critical indicators demonstrate the need to adopt strategies aimed at minimizing inbreeding to avoid further losses of genetic diversity.     

Phenotypic characteristics of upright and pendulous comb among chicken breeds and association with growth rate and egg production

Upright and pendulous combs commonly exist in most single‐comb chicken breeds. Here, the phenotypic characteristics of upright and pendulous combs in chickens and association with growth rate and egg production were analyzed. Phenotypic frequencies of upright and pendulous comb were investigated in five chicken breeds; the phenotypic frequencies of complete pendulous comb (CPC) and partial pendulous comb (PPC) ranged from 10.1% to 29.0% and 21.8% to 65.3%, respectively. CPC hens produced more eggs than PPC hens (P < 0.05) in Nongda‐3, Huainan and Wenchang breeds. In Huainan breed, CPC males were heavier than PPC males at 12 and 16 weeks of age, while CPC females were heavier at 24 weeks of age. PPC and CPC chickens have greater (P < 0.05) comb length, comb height and comb index than upright comb (UC) chickens. There was no significant difference in comb phenotypic frequency distribution between the offspring from UC(♂) × CPC(♀) and CPC(♂) × UC(♀); however, it differed (χ² = 45.12, P < 0.01) between offspring from UC(♂) × UC(♀) and CPC(♂) × CPC(♀). These results suggested that the comb phenotype does not appear to be Z‐linked; the effective loci influencing the trait could be estimated in a further study.     

Birth weight,reproduction traits and effects of inbreeding in Nicaraguan Reyna Creole cattle

Reyna Creole cattle in Nicaragua comprise about 650 purebred animals, and the breed has been shown to have a high level of inbreeding. To characterize the breed, as basis for a conservation program, information from two herds on birth weight (BW, n = 1097), age at first calving (AFC, n = 449) and calving interval (CI, n = 1,347) was analysed. Overall averages were 27.8 kg for BW, 37.4 months for AFC and 424 days for CI. Large differences between the herds were observed for all traits. Thus, there would be opportunities for management interventions to improve reproduction results. The heritability for BW was 0.34. For CI, the heritability of 0.20 and the additive genetic standard deviation of 36 days were comparatively high values. No genetic variation was found in AFC. Estimated inbreeding effects were associated with large standard errors due to the small size of the data and incompleteness of pedigrees. Nevertheless, significant effects were shown of dam inbreeding level on all traits. For each percentage of increased inbreeding, BW decreased by 0.06 kg, AFC increased by 3.5 days and CI increased by 1.4 days. The effects of the inbreeding level of the individual itself were not significant. The relatively good reproduction traits of Reyna Creole cattle shown in this study, despite high inbreeding levels, will be supplemented with a characterization of milk production traits.     

Genomic prediction of growth traits for pigs in the presence of genotype by environment interactions using single-step genomic reaction norm model

Economically important traits are usually complex traits influenced by genes, environment and genotype-by-environment (G × E) interactions. Ignoring G × E interaction could lead to bias in the estimation of breeding values and selection decisions. A total of 1,778 pigs were genotyped using the PorcineSNP80 BeadChip. The existence of G × E interactions was investigated using a single-step reaction norm model for growth traits of days to 100 kg (AGE) and backfat thickness adjusted to 100 kg (BFT), based on a pedigree-based relationship matrix (A) or a genomic–pedigree joint relationship matrix (H). In the reaction norm model, the herd-year-season effect was measured as the environmental variable (EV). Our results showed no G × E interactions for AGE, but for BFT. For both AGE and BFT, the genomic reaction norm model (H) produced more accurate predictions than the conventional reaction norm model (A). For BFT, the accuracies were greater based on the reaction norm model than those based on the reduced model without exploiting G × E interaction, with EV ranging from 0.5 to 1, and accuracy increasing by 3.9% and 4.6% in the reaction norm model based on A and H matrices, respectively, while reaction norm model yielded approximately 8.4% and 7.9% lower accuracy for EVs ranging from 0 to 0.4, based on A and H matrices, respectively. In addition, for BFT, the highest accuracy was obtained in the BJLM6 farm for realizing directional selection. This study will help to apply G × E interactions to practical genomic selection.     

Inbreeding and fertility in Irish Wolfhounds in Sweden: 1976 to 2007

Background

Given that no influence of inbreeding on life expectancy could be demonstrated in Irish Wolfhounds in a previous study, it was decided to test the influence of inbreeding and other parameters on fertility in this breed.

Methods

The study was based on all Irish Wolfhound litters registered in Sweden between 1976 and 2007 (n = 822 litters) as provided by the Swedish Kennel Club (SKK) and combined with a pedigree database going back to 1862. Analyses were performed using linear regression in a Generalised Linear Model and other tests in the SAS system^®.

Results

Mean number of pups per litter was 6.01 ± 2.65, with a maximum of 13. There were no significant differences in either the number of litters or the number of pups between years of birth. Males were used for breeding at a significantly earlier age than females. Mean number of litters per parent was 2.96 ± 3.14 for males and 1.59 ± 0.87 for females. No influence of Wright''s inbreeding coefficients over 5, 10, 20 and 30 generations and/or Meuwissen''s inbreeding coefficients on litter size was detected. In the Generalised Linear Model, highly significant, but weak (coefficient of determination (R²) = 0.0341) influences were found for maternal age at mating as well as maternal inbreeding measured by Wright''s inbreeding coefficient over 30 generations and Meuwissen''s inbreeding coefficient. Paternal inbreeding coefficients over 5, 10, 20 and 30 generations and calculated after Meuwissen, as well as maternal inbreeding coefficients over 5, 10 and 20 generations did not have significant effects on litter size.

Conclusion

The low coefficient of determination (R²) value of the Generalised Linear Model indicates that inbreeding does not have a strong influence on fertility in Irish Wolfhounds, which is consistent with earlier results and the breed''s genetic history. These results likely reflect the aforementioned genetic history and should not be extrapolated to other breeds without prior breed-specific research.     

The Effect of Scours on Calf Weaning Weight

Beef cattle health and performance records of 3637 calves from inbred and outbred populations were evaluated to determine the effect of scours on weaning BW (WW). Animals were maintained under similar environmental conditions at the Northern Agricultural Research Center near Havre, Montana. Inbred animals were linebred Hereford cattle with an average inbreeding coefficient of 0.20. Outbred animals were Hereford, Angus × Hereford, Simmental × Hereford crosses and backcrosses, and Tarentaise × Hereford crosses and backcrosses. Weaning BW was analyzed by least squares ANOVA. Model included year, age of dam, line (inbred or outbred), scours, and date of birth as a covariate. When zero WW were included for calves that died of scours (1%), all main effects were important. The least squares mean WW were 208 and 217 kg for scouring and non-scouring groups, respectively. Interactions between year × age of dam (P < 0.01) and year × line (P < 0.01) were detected. Incidence of scours was analyzed by the CATMOD procedure of SAS. The model included year, age of dam, and line (inbred or outbred). All main effects were important (P < 0.01). Incidence of scours ranged from 13% in 1982 to 64% in 1991. Incidence of scours was greatest in calves born to 2-yr-old dams with probabilities of 47% and 33% in inbred and outbred dams, respectively. These results indicate that scours negatively influenced WW. Incidence of scours was greater in calves born to younger dams and for inbred cattle.