GxE interactions for growth and carcass leanness: Re-ranking of boars in organic and conventional pig production

The objective of this study was to evaluate genotype by environment interactions for growth rate and carcass leanness in organic and conventional pig production environments. Organic breeding values for fattening traits were estimated for 37 Hampshire AI-boars based on slaughter records registered for 1805 crossbred offspring raised in an organic environment. The offspring were born and raised in herds certified for organic production. The statistical model included the fixed effects of sex, litter size at 2 weeks and herd. It also included the random effects of herd-year-season, birth litter and animal. Conventional breeding values for the same boars were captured from the breeding organization’s genetic evaluation. In the organic environment h² was estimated to 0.30 and 0.37 for growth rate and carcass leanness, respectively (r_g = − 0.11). Spearman rank correlations between organic and conventional breeding values, based on 29 boars with ≥ 20 progenies, were 0.48 for growth rate and 0.42 for carcass leanness. Both correlations were significantly different from 0 and 1. In conclusion, the results of the present study indicate weak genotype by environment interactions for both growth rate and carcass leanness in organic and conventional pig production environments, and there is some re-ranking of boars’ breeding values between environments.     

Genetic relationship among stayability,scrotal circumference and post-weaning weight in Nelore cattle

Improvement of female fertility has become of fundamental importance for profit maximization in the beef cattle herds. Consequently, animal breeding programs in Brazil have applied selection effort to traits related to reproduction as for scrotal circumference (SC), which is already incorporated to the selection routine of the breeders. However, studies have reported no favorable genetic correlation (r_g) of SC with some fertility traits. Recently, stayability (STAY) has been used as means to better indicate and improve female fertility. Values for r_g of STAY with reproductive and productive traits are not available in literature. Therefore, the objectives of the present study are to analyze the r_g between SC and STAY and STAY with weight at 550 days (W550) in Nelore cattle. Data set of 55,682, 28,507 and 59,750 animals for STAY, SC and W550, respectively, were analyzed using two-trait animal model based on Gibbs sampling algorithm. The estimate of posterior r_g between STAY and SC was 0.07 ± 0.03, which can be considered as low and suggesting that STAY does not have sensible relation with SC. The r_g of STAY and W550 was 0.15 ± 0.01, considered low, although positive. It means that selection for W550 should not negatively affect STAY.     

Implications of genetic selection on yolk proportion on the dry matter content of eggs in a White Leghorn population

1. The responses to genetic selection on yolk proportion as a technique for increasing egg dry matter content, an important criterion for the egg-product industry, was investigated in a pedigree flock of White Leghorn hens.

2. Parents were preselected on high and low yolk proportion from a base population. The absolute estimated breeding value for yolk proportion of both groups differed by 3%. The realised selection difference in dry matter content of eggs between groups was more than 1% in the analysed offspring population.

3. Heritability estimates were moderate and dry matter had a lower heritability (h² = 0.39) than yolk proportion (h² = 0.44).

4. The genetic correlation between yolk proportion and dry matter content was highly positive (r_g = 0.91). Genetic correlations with egg weight were negative and would have to be compensated for in a breeding programme (r_g = ?0.76 with yolk proportion and r_g = ?0.64 with dry matter content). The genetic correlation between the laying performance and yolk proportion was r_g = 0.28 and close to zero (r_g = ?0.05) for dry matter content.

5. Easy recording and lower undesirable correlations make yolk proportion more suitable for commercial selection compared with egg dry matter content in layer breeding.     

Comparison of production systems for efficient use of indigenous pig breeds in developing countries

Conserving pig genetic resources and improving their productivity is important to increase returns over investment in developing countries. The purebred, first‐cross, rotational cross and backcross matings representing production systems based on pig breeds indigenous to the country and exotic pig breeds were investigated. The number of pigs in the nucleus and commercial herds necessary to produce a defined quantity of pork was considered. The amount of heterosis between the indigenous and exotic breeds, superiority in meat production, and degree of inferiority in reproductive performance of the exotic breed compared with that of the indigenous breed were investigated. The number of breeding pigs in the whole system was in the following order: pure breeding (PB) > first‐cross (F1) > rotational cross (RC) > backcross (BC) systems. The number of breeding pigs in the nucleus herds of the RC and BC systems was smaller than that in the nucleus herds of the PB and F1 systems. The degree of inferiority in reproductive performance of the exotic breed compared with that of the indigenous breed affected the efficiency of the production system.     

Rates of inbreeding and genetic adaptation for populations managed as herds in zoos with a rotational mating system or with optimized contribution of parents

This study compares two genetic management scenarios for species kept in herds, such as deer. The simulations were designed so that their results can be extended to a wide range of zoo populations. In the first scenario, the simulated populations of size 3 × 20, 6 × 40 or 20 × 60 (herds × animals in herd) were managed with a rotational mating (RM) scheme in which 10%, 20% or 50% of males were selected for breeding and moved between herds in a circular fashion. The second scenario was based on optimal contribution theory (OC). OC requires an accurate pedigree to calculate kinship; males were selected and assigned numbers of offspring to minimize kinship in the next generation. RM was efficient in restriction of inbreeding and produced results comparable with OC. However, RM can result in genetic adaptation of the population to the zoo environment, in particular when 20% or less males are selected for rotation and selection of animals is not random. Lowest rates of inbreeding were obtained by combining OC with rotation of males as in the RM scheme. RM is easy to implement in practice and does not require pedigree data. When full pedigree is available, OC management is preferable.     

Differences in Antibiotic Resistance in Escherichia coli,Isolated from East‐European Swine Herds With or Without Prophylactic Use of Antibiotics

The aim of the study was to compare the resistance patterns of Escherichia coli isolates from pig herds with or without prophylactic use of anti‐microbial substances. The presented pig units received either antibiotics or oregano as preventive feed additives. The trial was performed from April to October 2001, in the large ‘country‐corner’, Hungary–Rumania–Serbia. Thirty of 39 evaluated herds suffered E. coli O139 K88 ac or ad LT STb caused losses, the remaining were negative for E. coli O139. Thirteen of the selected 30 herds produced with oregano feed supplementation (Oregpig^® Pecs, Hungary) antibiotic‐free pigs. These units had no history of prophylactic antibiotic use since 1995. The remaining 17 herds routinely used prophylactic antibiotic feed supplementation. In each herd, pigs of four different age groups (suckling piglets, weaners, fattening swine and breeding sows), showing the clinical symptoms of wasting, were investigated. E. coli O139 K88 ac or ad LT STb were tested for their resistance to antibiotics, available in this region. Oregano‐fed herds demonstrated high significantly (P < 0.001) lower MICs (μg/ml) for ampicillin, doxycyclin, enrofloxacin, gentamycin, oxytetracyclin and sulfamethacin compared to herds with prophylactic use of antibiotics. Resistance to ceftiofur revealed significant (P < 0.05) differences between the antibiotic‐ or oregano‐treated units. The present results confirm literature data, that prophylactic use of antibiotics likely plays a role in inducing resistance of E. coli and other intestinal bacteria. Thus, imposing greater restrictions on antibiotic use in animal agriculture is likely to reduce but not eliminate the occurrence of resistant isolates.     

Detailed genetic analysis of feeding behaviour in Romane lambs and links with residual feed intake

Breeding strategies based on feed efficiency are now implemented in most animal species using residual feed intake (RFI) criteria. Although relevant, the correlated responses of feeding behaviour traits resulting from such selection on RFI are poorly documented. We report the estimated feeding behaviour at three time levels (visit, meal and day) and genetic parameters between the feeding behaviour traits and their links with RFI and its components. Feed intake, feeding duration at three time levels (per visit, meal and day), feeding rate, number of visits and time‐between‐visits were estimated for 951 Romane lambs fed via automatic concentrate feeders. Heritability estimates of feeding behaviour traits ranged from 0.19 to 0.54 with higher estimates for the day level than the visit level. Daily feed intake was not genetically linked to feed intake at the visit level, whereas feeding duration between visit and day levels was moderately correlated (R_g = +0.41 ± 0.12). RFI was not significantly correlated with feeding rate, but was positively linked to feed intake and feeding duration at the day level (+0.73 ± 0.09 and +0.41 ± 0.13, respectively) and negatively at the visit level (?0.33 ± 0.14 and ?0.22 ± 0.17, respectively). Selecting animals with lower RFI values might modify their feeding behaviour by increasing feed intake and feeding duration at the visit level but decrease the number of visits per day (+0.51 ± 0.14).     

Prevalence and consequence of subacute ruminal acidosis in Polish dairy herds

The aim of this study was to estimate the prevalence of subacute ruminal acidosis (SARA) in Polish high‐yielding dairy herds. Also, the relationships between the chemical composition of the diet and the feed particle size, ruminal pH and the occurrence of this metabolic disease and the fermentation profile were determined. Rumen fluid samples were obtained from a total of 213 cows from nine dairy herds (≥20 cows per herd) via rumenocentesis. Almost 14% (30/213) of cows as acidotic (pH<5.6) were found, which is indicative of SARA. Moreover, 44% of the herds were classified as SARA‐positive and 56% as SARA‐negative. Results of the current study suggested that the physically effective NDF (NDF_>1.18 mm)‐to‐starch ratio could be better indices than peNDF_>1.18 mm to preventing the occurrence of SARA, and their level should not be lower than 1.00. Also, linear negative relationships between rumen fluid pH and concentration of propionate, valerate and total VFA were determined. According to the herd's SARA status and rumen fluid biochemical indices, there were significant differences between the pH of rumen fluid (p ≤ 0.01), concentrations of acetate (p ≤ 0.05), propionate (p ≤ 0.05), n‐butyrate (p ≤ 0.01), n‐valerate (p ≤ 0.01), the sum of VFA (p ≤ 0.01) and ammonia (p ≤ 0.05) in SARA‐positive herds compared to SARA‐negative herds. The better understanding the strategy of ruminant nutrition to coordinate energy conversion and the role of the ruminal pH in regulating N‐NH₃ production, absorption through rumen mucosa, urea secretion, the more successfully we can utilize these processes with due recognition of animal needs and welfare, as well as prevention of SARA occurrence.     

Genetic evaluation of calf and heifer survival in Iranian Holstein cattle using linear and threshold models

Calf and heifer survival are important traits in dairy cattle affecting profitability. This study was carried out to estimate genetic parameters of survival traits in female calves at different age periods, until nearly the first calving. Records of 49 583 female calves born during 1998 and 2009 were considered in five age periods as days 1–30, 31–180, 181–365, 366–760 and full period (day 1–760). Genetic components were estimated based on linear and threshold sire models and linear animal models. The models included both fixed effects (month of birth, dam's parity number, calving ease and twin/single) and random effects (herd‐year, genetic effect of sire or animal and residual). Rates of death were 2.21, 3.37, 1.97, 4.14 and 12.4% for the above periods, respectively. Heritability estimates were very low ranging from 0.48 to 3.04, 0.62 to 3.51 and 0.50 to 4.24% for linear sire model, animal model and threshold sire model, respectively. Rank correlations between random effects of sires obtained with linear and threshold sire models and with linear animal and sire models were 0.82–0.95 and 0.61–0.83, respectively. The estimated genetic correlations between the five different periods were moderate and only significant for 31–180 and 181–365 (r_g = 0.59), 31–180 and 366–760 (r_g = 0.52), and 181–365 and 366–760 (r_g = 0.42). The low genetic correlations in current study would suggest that survival at different periods may be affected by the same genes with different expression or by different genes. Even though the additive genetic variations of survival traits were small, it might be possible to improve these traits by traditional or genomic selection.     

Genetic variation of in vivo muscle glycerol,glycogen, and pigment in Danish purebred pigs

Heritability values of glycerol, glycogen and pigment concentrations measured on muscle biopsy samples from longissimus dorsi obtained from 85?kg boars of Danish purebred pigs (Landrace, Yorkshire, and Duroc) and their genetic correlations to performance and meat quality traits were calculated. The heritability values of glycogen, pigment, and glycerol were 0.38±0.02, 0.17±0.02, and 0.065±0.016, respectively. Glycogen was negatively related to the feed conversion ratio (FCR) (r _g =?0.25±0.06) and ultimate meat pH (r _g =?0.41±0.04), and positively to the carcass meat percentage (r _g =0.35±0.04), L* (lightness of meat, r _g =0.32±0.04) and a* (redness of meat, r _g =0.12±0.03). Pigment was positively related to the FCR (r _g =0.12±0.05), the meat percentage (r _g =0.28±0.05), and a* (r _g =0.59±0.04), and negatively to the L* (r _g =?0.46±0.06). The concentrations of pigment and glycogen (r _g =0.27±0.05) were interrelated. Based on the heritability values and the signs of the genetic correlations the present data suggest that it is possible to select for higher ultimate pH and improved colour by selection for either lower muscle glycogen or higher pigment concentration, respectively. However, the positive genetic correlation between these two traits may restrict the efficiency of simultaneous selection for lower glycogen and higher pigment. All genetic parameter estimates presented are calculated across three purebreds. Values for each breed are warranted for use in pig production. However, this requires more animals per breed.     

Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight

Linkage disequilibrium (LD) plays an important role in genomic selection and mapping of quantitative trait loci (QTL). This study investigated the pattern of LD and effective population size (N_e) in Gir cattle selected for yearling weight. For this purpose, 173 animals with imputed genotypes (from 18 animals genotyped with the Illumina BovineHD BeadChip and 155 animals genotyped with the Bovine LDv4 panel) were analysed. The LD was evaluated at distances of 25–50 kb, 50–100 kb, 100–500 kb and 0.5–1 Mb. The N_e was estimated based on 5 past generations. The r² values (a measure of LD) were, respectively, .35, .29, .18 and .032 for the distances evaluated. The LD estimates decreased with increasing distance of SNP pairs and LD persisted up to a distance of 100 kb (r² = .29). The N_e was greater in generations 4 and 5 (24 and 30 animals, respectively) and declined drastically after the last generation (12 animals). The results showed high levels of LD and low N_e, which were probably due to the loss of genetic variability as a consequence of the structure of the Gir population studied.     

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.     

Genetic association between leg conformation in young pigs and sow longevity

Longevity is important in pig production with respect to both economic and ethical aspects. Direct selection for longevity might be ineffective because ‘true’ longevity can only be recorded when a sow has been culled or died. Thus, indirect selection for longevity using information from other traits that can be recorded early in life and are genetically correlated with longevity might be an alternative. Leg conformation has been included in many breeding schemes for a number of years. However, proving that leg conformation traits are good early indicators for longevity still remains. Our aim was to study genetic associations between leg conformation traits of young (5 months; 100 kg) Swedish Yorkshire pigs in nucleus herds and longevity traits of sows in nucleus and multiplier herds. Data included 97 533 animals with information on conformation (Movement and Overall score) recorded at performance testing and 26 962 sows with information on longevity. The longevity traits were as follows: stayability from 1st to 2nd parity, lifetime number of litters and lifetime number of born alive piglets. Genetic analyses were performed with both linear models using REML and linear‐threshold models using Bayesian methods. Heritabilities estimated using the Bayesian method were higher than those estimated using REML, ranging from 0.10 to 0.24 and 0.07 to 0.20, respectively. All estimated genetic correlations between conformation and longevity traits were significant and favourable. Heritabilities and genetic correlations between conformation and longevity indicate that selection on leg conformation should improve sow longevity.     

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.     

Estimates of genetic parameters for milkability from automatic milking

Genetic parameters were estimated by restricted maximum likelihood with a multi-trait animal model for three milkability traits with serial data from an automatic milking system from a research farm (401 dairy cows) collected between September 2000 and June 2003 (320834 milkings). Furthermore, daily values for milk yield and milkability were formed from all single milkings resulting in 104 132 records and, subsequently, an estimation of genetic parameters was carried out based on these daily values.The resulting estimated heritability coefficients (based on daily values) are h² = 0.55, h² = 0.55 and h² = 0.39 for average milk flow, maximum milk flow and milking time, respectively. The heritabilities are at a high level and thus breeding for good milkability makes sense. The genetic correlations between the three milkability traits are near unity with r_g = 0.98 between average and maximum milk flow, r_g = − 0.89 between average milk flow and milking time and r_g = − 0.86 between maximum milk flow and milking time. Thus it may be sufficient to record only one of these traits in performance tests. The genetic correlations between milk yield and average milk flow, maximum milk flow and milking time are r_g = 0.51, r_g = 0.44 and r_g = − 0.23, respectively.In future, serial data on milkability, already existing on many farms with automatic milk yield recording, should be used to greater extent for selective breeding with the aim of achieving good milkability.     

Genetic variation and genetic trends in hip and elbow dysplasia in Swedish Rottweiler and Bernese Mountain Dog

The aim of this study was to estimate genetic parameters and genetic trends for hip (HD) and elbow dysplasia (ED) in Swedish Rottweiler (RW) and Bernese Mountain Dog (BMD). Analyses were based on screening results of hip status for 14 693 RW and 8221 BMD and elbow status for 11 891 RW and 7963 BMD, as well as pedigree data for 16 614 RW and 9835 BMD, recorded by the Swedish Kennel Club. Components of (co)variance and breeding values were obtained with a mixed linear animal model. The model included the fixed effects of sex, birth month, age at screening and a combined random effect of clinic and year of examination. The need to include genetic groups for phantom parents in the model was evaluated by comparison of two different models: with and without genetic groups. Estimated heritabilities for HD and ED were between 0.34 and 0.42. The genetic correlation between the traits was weak and positive for RW (r_g = 0.23 ± 0.05) and not different from zero for BMD (r_g = 0.06 ± 0.06). F‐statistics of the genetic group effects were not significant, implying that genetic groups do not need to be included in the model. Genetic trends indicated a genetic improvement in both traits. However, a faster genetic progress is expected if selection is based on predicted breeding values rather than phenotype. Based on the results, a statistical model for routine prediction of breeding values for HD and ED in Swedish dogs was suggested.     

Effects of Dietary Contamination by Zearalenone and Its Metabolites on Serum Anti‐Müllerian Hormone: Impact on the Reproductive Performance of Breeding Cows

We investigated the effects of in vivo exposure to low zearalenone levels on the anti‐Müllerian hormone endocrine levels and the reproductive performance of cattle. Urine and blood samples and reproductive records were collected from two Japanese Black breeding female cattle herds with dietary zearalenone contamination below the threshold levels (<1 ppm) at 30 days after calving. Urinary zearalenone, α‐zearalenol and β‐zearalenol concentrations were measured by chromatography‐tandem mass spectrometry, and serum anti‐Müllerian hormone concentrations were determined along with serum biochemical parameters. Urinary concentrations of α‐zearalenol were significantly higher (p < 0.05) in cattle in Herd 1 than in cattle in Herd 2, reflecting the different amounts of zearalenone in the diet of the two herds. Although the number of 5‐mm and 10‐mm follicles of the herds and their fertility after artificial insemination were similar, the serum anti‐Müllerian hormone concentrations in herds 1 and 2 were 438.9 ± 48.6 pg/ml and 618.9 ± 80.0 pg/ml, respectively, with a trend towards a significant difference (p = 0.053), which may indicate differences in the antral follicle populations between herds. Thus, zearalenone intake from dietary feed, even when below the threshold zearalenone contamination level permitted in Japan, may affect the ovarian antral follicle populations, but not the fertility, of post‐partum cows.     

ImmuneDEX: a strategy for the genetic improvement of immune competence in Australian Angus cattle

In animal breeding and genetics, the ability to cope with disease, here defined as immune competence (IC), with minimal detriment to growth and fertility is a desired objective which addresses both animal production and welfare considerations. However, defining and objectively measuring IC phenotypes using testing methods which are practical to apply on-farm has been challenging. Based on previously described protocols, we measured both cell-mediated immune response (Cell-IR) and antibody-mediated immune response (Ab-IR) and combined these measures to determine an animal’s IC. Using a population of 2,853 Australian Angus steers and heifers, we compared 2 alternative methods to combine both metrics into a single phenotype to be used as a tool for the genetic improvement of IC. The first method, named Z_MEAN, is obtained by taking the average of the individual metrics after subjecting each to a Z-score standardization. The second, ImmuneDEX (IDEX), is a weighted average that considers the correlation between Cell-IR and Ab-IR, as well as the difference in ranking of individuals by each metric, and uses these as weights in the averaging. Both simulation and real data were used to understand the behavior of Z_MEAN and IDEX. To further ascertain the relationship between IDEX and other traits of economic importance, we evaluated a range of traits related to growth, feedlot performance, and carcass characteristics. We report estimates of heritability of 0.31 ± 0.06 for Cell-IR, 0.42 ± 0.06 for Ab-IR, 0.42 ± 0.06 for Z_MEAN and 0.370 ± 0.06 for IDEX, as well as a unity genetic correlation (r_g) between Z_MEAN and IDEX. While a moderately positive r_g was estimated between Cell-IR and Ab-IR (r_g = 0.33 ± 0.12), strongly positive estimates were obtained between IDEX and Cell-IR (r_g = 0.80 ± 0.05) and between IDEX and Ab-IR (r_g = 0.85 ± 0.04). We obtained a moderately negative r_g between IC traits and growth including an r_g = −0.38 ± 0.14 between IDEX and weaning weight, and negligible with carcass fat measurements, including an r_g = −0.03 ± 0.12 between IDEX and marbling. Given that breeding with a sole focus on production might inadvertently increase susceptibility to disease and associated antibiotic use, our analyses suggest that ImmuneDEX will provide a basis to breed animals that are both highly productive and with an enhanced ability to resist disease.     

Genetic diversity,structure and individual assignment of Casta Navarra cattle: a well‐differentiated fighting bull population

The Casta Navarra lineage was one of the populations used to establish the fighting bull (FB) breed, and it has also been reproductively isolated from the others FBs. A total of 1284 individuals from two generations of 16 Casta Navarra herds were sampled to analyse their diversity, their genetic structure and the ability of 28 microsatellite markers to assign individuals to closely related populations. These animals were compared with closely related phylogenetic (FB) or geographical (Pirenaica and Monchina) populations. Hardy–Weinberg equilibrium analysis showed that 82% of the loci had a significant heterozygote deficit as a consequence of the Wahlund effect. The average proportion of genetic variation explained by farm differences was 9% by Wright's F_ST index. A phylogenetic tree constructed with a neighbour‐joining method based on Reynolds genetic distances and a Bayesian Markov chain Monte Carlo clustering approach revealed clear differences between farm groups that generally corresponded to historical information and could unambiguously differentiate Casta Navarra cattle from the other populations. The percentage of animals correctly assigned to the Casta Navarra population was 91.78% for a q threshold of >0.9. Admixture was only detected in 4.45% (q < 0.8) of the cattle. These results are relevant for the maintenance and development of diversity and conservation in the Casta Navarra population.     

Founder representation and effective population size in old versus young breeds—genetic diversity of Finnish and Nordic Spitz

Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (f_a) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis () is 168, whereas the genetic effective population size (N_eg) computed the decay of linkage disequilibrium (r²) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had f_a of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz ( = 98 and N_eg = 49). Interestingly, the r² data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed.