Inheritance of hereditary equine regional dermal asthenia in Quarter Horses

OBJECTIVE: To assess heritability and mode of inheritance for hereditary equine regional dermal asthenia (HERDA) in Quarter Horses. ANIMALS: 1,295 horses with Quarter Horse bloodlines, including 58 horses affected with HERDA. PROCEDURE: Horses were classified as affected or unaffected or as undetermined when data were insufficient to assess phenotype. Pedigree data were analyzed to determine the probable mode of inheritance. Heritability was estimated by use of Bayesian statistical methods. RESULTS: Heritability (mean+/-SD) of HERDA was estimated to be 0.38+/-0.13, with both sexes having an equal probability of being affected. Results for evaluation of the pedigrees were consistent with a single Mendelian autosomal recessive mode of inheritance. CONCLUSIONS AND CLINICAL RELEVANCE: HERDA in Quarter Horses is an inherited disease, and affected horses are more likely to produce affected offspring. An autosomal recessive mode of inheritance should be considered by people making breeding decisions involving Quarter Horses when a first-degree relative has been confirmed with HERDA or has produced affected offspring. In addition, breeders whose horses have produced affected offspring can reduce the likelihood of producing affected horses in the future by avoiding inbreeding.     

A suggested mode of inheritance for wool shedding in sheep

The ability of a sheep to shed its own wool has an attraction in scenarios where the costs of harvesting wool outweigh its value. Certain breeds and composites have the ability to shed their wool in the spring, and these are investigated in this work in an attempt to outline the genetics of wool shedding. One flock from a breeding group in Southern England (UK) containing sheep with wool-shedding characteristics provided shedding scores (1 to 5 scale; no shedding to complete shedding) that were used in a range of genetic analyses. The particular nature of wool shedding suggested that there may be a major gene segregating in these populations that facilitates wool shedding. In addition, there was clearly variation among wool shedders in the speed and extent of shedding, so a polygenic trait was also investigated. The breeding group used a range of shedding breeds and composites in a regular program to introduce wool-shedding genes into their flocks. This allowed the testing of Mendelian ratios for shedders:nonshedders in both first-cross and first-backcross animals. Four modes of inheritance were tested: autosomal recessive, sex-linked recessive, autosomal dominant, and sex-linked dominant. The most likely mode of inheritance was autosomal dominant (P < 0.05), with a low level of incomplete penetrance. In first back-cross animals, this mode of inheritance was confirmed but with complete penetrance. Approximately 11% of shedders did not exhibit the trait as lambs. Mixed-model analyses of shedding scores allowed an investigation of factors that affected wool shedding and also the extent of any genetic and permanent animal variance. Shedding score was found to have a heritability of 0.54 ± 0.07 in lambs and 0.26 ± 0.06 in animals of all ages in one flock using Easycare, Wiltshire Horn, Katahdin, and Dorper shedding animals. Shedding score as a lamb had a genetic correlation of 0.94 ± 0.08 with shedding score as a 2 yr old, but at the phenotypic level this correlation was only 0.39 ± 0.05. No permanent animal effect was found for shedding score. Breeding for increased wool-shedding ability is possible, but improvement of the trait needs to be considered in 2 stages. First, the dominant gene needs to be introduced into the population, and then selection between animals can proceed by using EBV for the polygenic trait (speed or extent of shedding) as the basis for selection.     

Whole genome scan identifies several chromosomal regions linked to equine sarcoids

Despite the evidence for a genetic predisposition to develop equine sarcoids (ES), no whole genome scan for ES has been performed to date. The objective of this explorative study was to identify chromosome regions associated with ES. The studied population was comprised of two half-sibling sire families, involving a total of 222 horses. Twenty-six of these horses were affected with ES. All horses had been previously genotyped with 315 microsatellite markers. Quantitative trait locus (QTL) signals were suggested where the F statistic exceeded chromosome-wide significance at P < 0.05. The QTL analyses revealed significant signals reaching P < 0.05 on equine chromosome (ECA) 20, 23 and 25, suggesting a polygenic character for this trait. The candidate regions identified on ECA 20, 23 and 25 include genes regulating virus replication and host immune response. Further investigation of the chromosome regions associated with ES and of genes potentially responsible for the development of ES could form the basis for early identification of susceptible animals, breeding selection or the development of new therapeutic targets.     

Inheritance of hypoadrenocorticism in bearded collies

OBJECTIVE: To assess heritability and mode of inheritance for hypoadrenocorticism in Bearded Collies. ANIMALS: 635 Bearded Collies. PROCEDURES: Dogs were classified as affected by hypoadrenocorticism or unaffected. Phenotypic and pedigree data were analyzed. Heritability was estimated by use of Bayesian statistical methods. Regressive logistic models for complex segregation analyses were used to characterize mode of inheritance. RESULTS: Hypoadrenocorticism was diagnosed in 60 (9.4%) dogs. Heritability of hypoadrenocorticism was estimated to be 0.76 with both sexes affected with equal probability. Evaluation of the pedigrees did not support a Mendelian autosomal dominant mode of inheritance. Evidence from the complex segregation analysis for a single locus of large effect on hypoadrenocorticism was not convincing. CONCLUSIONS AND CLINICAL RELEVANCE: Hypoadrenocorticism in Bearded Collies is highly heritable. Although a precise genetic mechanism responsible for inheritance of the disorder remains undetermined, breeding decisions must include consideration of the genetic likelihood of passing on this deleterious disorder to offspring of affected dams and sires.     

Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM

Genomic selection is based on breeding values that are estimated using genome-wide dense marker maps. The objective of this paper was to investigate the effect of including or ignoring the polygenic effect on the accuracy of total genomic breeding values, when there is coverage of the genome with approximately one SNP per cM. The importance of the polygenic effect might differ for high and low heritability traits, and might depend on the design of the reference dataset. Hence, different scenarios were evaluated using stochastic simulation. Accuracies of the total breeding value of juvenile selection candidates depended on the number of animals included in the reference data. When excluding polygenic effects, those accuracies ranged from 0.38 to 0.55 and from 0.73 to 0.79 for traits with heritabilities of 10 and 50%, respectively. Accuracies were improved by including a polygenic effect in the model for the low heritability trait, when the LD-measure r2 between adjacent markers became smaller than approximately 0.10, while for the high heritability trait there was already a small improvement at r2 between adjacent markers of 0.14. In all situations, the estimated total genetic variance was underestimated, particularly when the polygenic effect was excluded from the model. The haplotype variance was less underestimated when more animals were added in the reference dataset.     

闭锁群体BLUP选择下遗传方差和近交系数的变化

采用计算机随机模拟方法模拟了在一个闭锁群体内连续对单个性状进行 1 5个世代选择的情况。选择过程中世代不重叠 ,每个世代的种畜根据动物模型最佳线性无偏预测 (BLUP)法估计的育种值进行选留 ,并在此基础上系统地比较了不同群体规模、公母比例和性状遗传力对群体遗传方差和近交系数变化的影响。结果表明 ,扩大育种群规模、增加公畜比例以及对低遗传力性状进行选择时 ,群体遗传方差降低的速度和近交系数上升的速度会更慢 ,在长期选择时可望获得更大的持续进展和适宜的近交增量     

比较机器学习等算法对肉鸡产蛋性状育种值估计的准确性

我国白羽肉鸡育种中,通过遗传途径提高产蛋数和控制合适的蛋重是培育优良品系的一个重要方面。为探索适合我国白羽肉鸡育种中的基因组选择模型,本研究以2 474只白羽肉鸡品系的产蛋性状为研究对象,主要分析了机器学习算法KAML、BLUP(包括：PBLUP、GBLUP、SSGBLUP)和Bayes(包括：Bayes A、Bayes B和Bayes Cπ)方法对产蛋数和蛋重性状的预测准确性,准确性以5倍交叉验证进行评估。利用系谱以及基因组信息估计了产蛋数和蛋重性状的遗传力和遗传相关。结果表明,产蛋数性状遗传力为0.061~0.16,属于低遗传力性状;蛋重遗传力为0.28~0.39,属于中等遗传力性状;产蛋数与蛋重是中等遗传负相关(-0.518~-0.184),不同阶段产蛋数之间是强的遗传正相关(0.736~0.998)。不同模型预测43周产蛋数和52周蛋重的育种值估计准确性结果表明,KAML方法对两者的预测准确性分别为0.115和0.266,与GBLUP方法(准确性分别为0.118和0.283)和SSGBLUP方法(准确性分别为0.136和0.259)的准确性差异显著,同时显著低于Bayes方法(准确性分别为0.230~0.239、0.336~0.340)的预测准确性, PBLUP方法预测准确性最低(准确性分别为0.095和0.246)。因此,在白羽肉鸡产蛋数和蛋重性状中应用Bayes方法将获得最高的育种值估计准确性。     

Genetic heterogeneity of variance in production traits of laying hens

Genetic parameters for mean and for environmental variation in egg weight, body weight, age at first egg, and egg production were estimated in eight layer lines. The data were recorded from years 1999-2007, with on average of 6500 birds per line. An iterative mean-variance REML method was applied with a sire-plus-dam model for mean, a sire model for variance, and a fixed effect of hatch within generation for both mean and variance. The estimated heritability of environmental variation averaged about 5% for body weight, 3% for egg weight, and 11% for age at first egg, but was inconsistent among the lines for egg production (0-15%). Correlations between means and variances were slightly positive for body weight, egg weight, and age at first egg; and strongly negative for egg production. Age at first egg had the highest heritability of environmental variation; and favourable correlations with egg production and with variation in other production traits indicate that reducing variation in this trait may have potential benefits for the breeding industry.     

Heritability and complex segregation analysis of hypoadrenocorticism in the standard poodle

The heritability of hypoadrenocorticism (Addison's disease) was evaluated in 778 standard poodles with known Addisonian phenotypes. Addisonian status was confirmed clinically by adrenocorticotropic hormone (ACTH) challenge and 8.6 per cent of the poodles enrolled in the study were classified as being Addisonian. Hypoadrenocorticism affected both sexes with equal probability (P > 0.1). The most common coat colours had a negligible effect on the incidence of hypoadrenocorticism (P > 0.09), although red coat colour had a significant impact on the disease, probably due to the relatively small numbers of dogs with that coat colour. The heritability of hypoadrenocorticism in the standard poodle was estimated to be 0.75. Complex segregation analyses suggested that hypoadrenocorticism in the breed is influenced by an autosomal recessive locus. Clarification of both the heritability and mode of inheritance of hypoadrenocorticism in the standard poodle allows for better-informed breeding decisions.     

性别比例和性状遗传力对闭锁群体BLUP选择效果的影响

采用MonteCarlo方法模拟研究了性别比例和性状遗传力对闭锁群体动物模型BLUP选择效果的影响 ,选育过程中世代不重叠 ,共进行了 1 5个世代的选择。结果表明性别比例对群体育种值和近交系数的变化都有明显的影响。在育种值达到最大值以前 ,群体平均育种值提高的速度随着公畜比例的增加而有所减慢 ,但会使育种值达到最大值的时间后移 ,在育种值达到最大值后 ,其下降的速度则随着公畜比例的降低而加快。随着公畜比例的增加 ,群体近交系数的上升速度会明显变慢。高遗传力性状的选择效果要优于低遗传力性状     

Equine hospital data as a source for study of prevalence and heritability of osteochondrosis and palmar/plantar osseous fragments of Swedish Warmblood horses

Reasons for performing study: Disturbances in skeletal development, primarily osteochondrosis (OC) and palmar/plantar osseous fragments (POF), have been commonly reported as problems in young horses. However, there are few reports of such findings for epidemiological analyses or breeding purposes. Objectives: To evaluate equine hospital data as a possible source of information for genetic evaluations by estimating prevalence and heritability of OC in the stifle, hock and fetlock joints and of POF in the fetlock. Methods: Data on Swedish Warmblood (SWB) horses were obtained from a large equine hospital in south Sweden. Prevalences were based on radiographic examinations of 879 screened horses, mainly evaluated as part of a prepurchase examination and 3639 horses with a reported history of orthopaedic problems. For the heritability study the 2 data sources were pooled and 3199 examined horses with pedigree information were considered for the linear animal model analyses. Results: The overall prevalence of OC was 13% (stifle 9%, hock 6% and dorsal osseous fragments in fetlock [DOF] 10%) and POF 10%. The overall heritability of OC was 0.05 on the visible binomial scale. The corresponding heritabilities for OC in the stifle were 0.03, hock 0.08, DOF 0.10 and POF 0.13. These values correspond to heritabilities of 0.09–0.38 on the underlying quantitative scale. Conclusions and potential relevance: Obtained prevalences and heritabilities were in accordance with other studies, supporting the hypothesis that data regularly obtained from equine hospitals may be a valuable source in studies of inherited disorders such as OC and POF. There is a need for more standardised documentation of diagnoses and consistent recording of identity of examined horses using passports or breed databases. Compilation of results from major clinics is desired in order to cover most progenies of stallions used in a region or nation.     

Genetic evaluation of carcass yield using ultrasound measures on young replacement beef cattle

Live weight and ultrasound measures of fat thickness and longissimus muscle area were available on 404 yearling bulls and 514 heifers, and carcass measures of weight, longissimus muscle area, and fat thickness were available on 235 steers. Breeding values were initially estimated for carcass weight, longissimus muscle area, and fat thickness using only steer carcass data. Breeding values were also estimated for weight and ultrasound muscle area and fat thickness using live animal data from bulls and heifers, with traits considered sex-specific. The combination of live animal and carcass data were also used to estimate breeding values in a full animal model. Breeding values from the carcass model were less accurate and distributed more closely around zero than those from the live data model, which could at least partially be explained by differences in relative amounts of data and in phenotypic mean and heritability. Adding live animal data to evaluation models increased the average accuracy of carcass trait breeding values 91, 75, and 51% for carcass weight, longissimus muscle area, and fat thickness, respectively. Rank correlations between breeding values estimated with carcass vs live animal data were low to moderate, ranging from 0.16 to 0.43. Significant rank changes were noted when breeding values for similar traits were estimated exclusively with live animal vs carcass data. Carcass trait breeding values estimated with both live animal and carcass data were most accurate, and rank correlations reflected the relative contribution of carcass data and their live animal indicators. The addition of live animal data to genetic evaluation of carcass traits resulted in the most significant carcass trait breeding value accuracy increases for young replacements that had not yet produced progeny with carcass data.     

MicroRNA fingerprints in serum and whole blood of sarcoid‐affected horses as potential non‐invasive diagnostic biomarkers

Serum and whole blood microRNA (miRNA) fingerprints have been proposed as a new class of non‐invasive human cancer biomarkers. In this study, we compared equine sarcoid (ES) disease‐specific serum and whole blood miRNA fingerprints and correlated them to miRNA expression in sarcoid tissue. After high throughput sequencing, miRNA differential expression analysis between six ES‐affected and five control horses was carried out in serum and whole blood using a DESeq algorithm, accounting for the influence of hemolysis and the white blood cell count. Target gene, pathway prediction and enrichment analyses were conducted using TarBase, mirPath and GeneCodis. After exclusion of 4 hemolyzed out of a total of 11 serum samples, 9 miRNAs were found to be differentially expressed in serum of ES vs control horses. In whole blood, all 11 samples showed normal white blood cell counts and 19 miRNAs were found to be differentially expressed. A total of 2/9 serum and 7/19 whole blood differentially expressed miRNAs were also highly expressed at the tissue level and their predicted target genes were associated with cancer pathways. Serum and whole blood miRNA expression allowed discrimination between ES and control horses and merits further validation in a larger study cohort. The use of whole blood might be superior because it has higher miRNA content and is less influenced by pre‐analytical variables compared to serum. Concurrent dysregulation of single miRNAs in tissue and blood suggests a possible biological function of circulating miRNAs.     

Analysis of new temperament traits to better understand the trait spirit assessed in breeding field tests for Icelandic horses

This study investigated different aspects of the trait spirit that is routinely recorded in breeding field tests (BFTs) for Icelandic horses. Genetic parameters were estimated for spirit and six newly introduced temperament suppleness traits assessed by judges and riders in Icelandic BFTs, and for everyday life temperament traits assessed by owners of breeding horses in 2014 and 2015. The findings suggested moderate heritability for some temperament traits assessed by riders in BFTs and showed that the assessment method needs to be improved in order for judges to discern the variation in these traits. Furthermore, according to estimated correlations the score for spirit described only part of the general temperament of the horse, where aspects of general nerve strength was not well covered. Nevertheless, no clearly unfavourable correlations with spirit were found and the majority of horse owners surveyed in this study were satisfied with the assessment for spirit.     

Efficient selection against categorically scored hip dysplasia in dogs is possible using best linear unbiased prediction and optimum contribution selection: a simulation study

Breeding to reduce the prevalence of categorically scored hip dysplasia (HD), based on phenotypic assessment of radiographic hip status, has had limited success. The aim of this study was to evaluate two selection strategies for improved hip status: truncation selection based on phenotypic record versus best linear unbiased prediction (BLUP), using stochastic simulation and selection scenarios resembling those in real dog populations. In addition, optimum contribution selection (OCS) was evaluated. Two traits were considered: HD (as a categorical trait with five classes and a heritability of 0.45 on the liability scale) and a continuous trait (with a heritability of 0.25) intended to represent other characteristics in the breeding goal. A population structure mimicking that in real dog populations was modelled. The categorical nature of HD caused a considerably lower genetic gain compared to simulating HD as a continuous trait. Genetic gain was larger for BLUP selection than for phenotypic selection in all scenarios. However, BLUP selection resulted in higher rates of inbreeding. By applying OCS, the rate of inbreeding was lowered to about the same level as phenotypic selection but with increased genetic improvement. For efficient selection against HD, use of BLUP breeding values should be prioritized. In small populations, BLUP should be used together with OCS or similar strategy to maintain genetic variation.     

Breeding for better eye health in Finnish blue fox (Vulpes lagopus)

The frequency of eye infections in the Finnish blue fox population has increased during the past decade. Eye infection may incur economic losses to producers due to reduced selection intensity, but ethical aspects need to be considered as well because eye infection can be quite painful and reduce animal well‐being. The purpose of this study was to determine the potential for genetic selection against susceptibility to eye infection. The data were collected from 2076 blue foxes at the MTT fur animal research station. Genetic parameters were estimated using single‐ and multiple‐trait animal models. The heritability estimate for eye infection was analysed as a binary trait (EYE) and was moderate (0.24 ± 0.07). EYE had a moderate antagonistic genetic correlation (–0.49 ± 0.20) with grading density (thick underfur). The genetic correlation of EYE with grading size or body condition score was estimated without precision, but all size traits had a low antagonistic phenotypic correlation with EYE. Our results suggest that there is genetic variance in susceptibility to EYE, indicating that eye health can be improved through selection. The current recommendation is that the sick animals should be culled immediately. If more efficient selection is needed, the selection index and multiple‐trait animal models can be applied in breeding for better eye health.     

中国肉用西门塔尔牛场间遗传联系分析

旨在加快中国肉用西门塔尔牛的遗传进展，实现全国范围内的联合育种。本研究利用全国38家育种场和公牛站在2000—2019年出生的3 991头肉用西门塔尔牛初生重性状，使用DMU软件对场间关联率进行计算。对各场站划分关联组，并比较单场和关联组内的遗传力和估计育种值（estimated breeding value，EBV）的预测准确性。结果表明，中国肉用西门塔尔牛全国平均关联率为1.91%，大部分场间关联率处于较低水平。依据关联率可划分出两个关联组，分别包括6个和8个场，组内平均关联率分别为11.23%和12.54%。对两个关联组分别进行单场和联合估计，单场估计初生重的遗传力范围为0.32~0.44，关联组1的初生重遗传力为0.47，关联组2的初生重遗传力为0.43。两个关联组单场估计EBV的平均准确性分别为0.47和0.45，联合估计EBV的平均准确性分别为0.61和0.56。联合估计较单场估计EBV的准确性有明显提高。依据关联率划分关联组进行联合育种有利于加快中国肉用西门塔尔牛的育种进程。为推进中国肉用西门塔尔牛的育种进程，应先形成区域性联合育种，再逐步加强遗传联系，形成全国范围内的遗传关联体系。     

Validation of alternative models in genetic evaluation of racing performance in North Swedish and Norwegian cold-blooded trotters

There have been several approaches to the estimation of breeding values of performance in trotters, and the objective of this study was to validate different alternatives for genetic evaluation of racing performance in the North Swedish and Norwegian cold-blooded trotters. The current bivariate approach with the traits racing status (RACE) and earnings (EARN) was compared with a threshold-linear animal model and the univariate alternative with the performance trait only. The models were compared based on cross-validation of standardized earnings, using mean-squared errors of prediction (MSEP) and the correlation between the phenotype (Y) and the estimated breeding value (EBV). Despite possible effects of selection, a rather high estimate of heritability of EARN was found in our univariate analysis. The genetic trend estimate for EARN was clearly higher in the bivariate specification than in the univariate model, as a consequence of the considerable size of estimated heritability of RACE and its high correlation with EARN (approximately 0.8). RACE is highly influenced by ancestry rather than the on-farm performance of the horse itself. Consequently, the use of RACE in the genetic analysis may inflate the genetic trend of EARN because of a double counting of pedigree information. Although, because of the higher predictive ability of the bivariate specification, the improved ranking of animals within a year-class and the inability to discriminate between models for genetic trend, we propose to base prediction of breeding values on the current bivariate model.     

Inheritance of rupture of the cranial cruciate ligament in Newfoundlands

OBJECTIVE: To determine prevalence, level of inbreeding, heritability, and mode of inheritance for rupture of the cranial cruciate ligament (RCCL) in Newfoundlands. DESIGN: Retrospective and recruitment study. ANIMALS: 574 client-owned Newfoundlands. PROCEDURE: Medical records from January 1, 1996, to December 31, 2002, were evaluated for prevalence of RCCL. A pedigree was constructed by use of recruited Newfoundlands with RCCL status based on results of veterinary examination; level of inbreeding, heritability, and mode of inheritance were calculated. RESULTS: Hospital prevalence for RCCL was 22%; dogs in the pedigree from the recruitment study had a mean level of inbreeding of 1.19 x 10(4), heritability of 0.27, and a possible recessive mode of inheritance with 51% penetrance for RCCL. CONCLUSIONS AND CLINICAL RELEVANCE: Identification of a genetic basis for RCCL in Newfoundlands provided evidence that investigators can now focus on developing methods to identify carriers to reduce the prevalence of RCCL.     

Estimation of genome-wide haplotype effects in half-sib designs

Genome-wide estimated breeding values can be computed from the simultaneous estimates of the effects of small intervals of DNA throughout the genome on a trait or traits of interest. Small intervals or segments of DNA can be created by the use of thousands of single nucleotide polymorphisms (SNP) available in panels of 10, 25 and 50 thousand SNP. A simulation study was conducted to compare factors that could influence the accuracy of genome-wide selection. Factors studied were the heritability of the trait, dispersion of quantitative trait loci (QTL) across the genome and size of the QTL effects. A 100-cM genome was assumed with 100 equally spaced SNP markers and 10 QTL. A granddaughter design was constructed with 20 sires and 100 sons per sire. Population-wide linkage disequilibrium was assumed to be sufficient after 25 generations of random mating starting with 30 sires and 400 dams. Best linear unbiased prediction was used to simultaneously estimate the effects of 99 SNP intervals, based on determining the SNP haplotype of each son inherited from the sire. Indicator variables were used in the model to indicate haplotype transmission. A genome-wide estimated breeding value was calculated as the sum of the appropriate haplotype interval estimates for each son. Correlations between estimated and true breeding values ranged from 0.60 to 0.79. Situations with unequally sized QTL effects and randomly dispersed QTL gave higher correlations. QTL positions could be estimated to within 2 cM or less.