Search

Summary: Local breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome‐wide SNP genotypes. Twenty pedigree‐recorded non‐closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (UHE = 0.341, HO = 0.368), and the highest heterozygote excess (UFIS = −0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST‐based Neighbor‐Net tree and Admixture clustering, clearly distinguished the Belarusian Red cattle from the other European cattle breeds. Moreover, the presence of ancestral genomic components of Danish Red and Brown Swiss breeds were clearly visible, which agrees with the breed's history and its recent development. Our study highlights the importance of maintaining the specific genomic components, which makes a significant contribution to the global genetic diversity in the modern population of Belarusian Red cattle, allowing us to consider them a valuable national genetic resource. Our research results will be useful for the development of conservation programs for this local cattle breed. [ABSTRACT FROM AUTHOR]

A morphometric characterization study was conducted using purebred Baoulé cattle and two crossbreds' populations in the southwestern region of Burkina-Faso. A total of 421 cattle, including 266 crossbreds from the department of Kampti and Loropeni and 155 purebred Baoulé, from the department of Bouroum-Bouroum were measured for quantitative and qualitative traits. The quantitative traits were analyzed by fitting the linear model including genotype-location, sex, age and all two-way interactions. The chi square test was performed for qualitative traits. The results provide evidence for difference between purebred and crossbred populations, and among crossbreds for all traits. The genotype-location effect showed that facial length, distance between horn tips, ear length and chest width differed between purebred and crossbred populations. For qualitative traits, coat color and horn shape showed large variation between Baoulé and crossbreds. These results will serve as basis for further characterization, conservation and improvement strategies for purebred and crossbred populations. [ABSTRACT FROM AUTHOR]

Context: The productivity of Ethiopian smallholder farms is considered to be low owing to different factors such as feed shortage, lack of breeding strategies, disease prevalence and missing marketing strategies. Aim: The main objective of the study was to develop a dynamic, stochastic herd model by adopting system dynamic modelling methodology for evaluation of the effect of increased feed availability (forage production) in combination with different fattening strategies on herd dynamics and profitability of an Ethiopian sheep population. Methods: Forage production utilising part of smallholder farmers' cropland was built into a dynamic simulation model. Two alternative feed-supply systems were evaluated: turning 25% and 50% of the current cropland into area used for forage production. The simulation period was 20 years, the first 10 years representing the baseline fattening scenario (culled rams fattened). For the last 10 years, genetic selection was introduced and two scenarios were evaluated: fattening of culled rams (Scenario I) and fattening of young rams (Scenario II). Key results: Increasing the feed supply resulted in an increase to the herd size when the model balanced dry matter supply and demand of the herd. Fattening of young rams (Scenario II) with genetic selection was significantly more profitable than the baseline and Scenario I in both of the simulated alternative feed-supply systems. This can be used for regular cash generation, which might reduce disposal of animals at lower price in cases of need for emergency cash. Conclusions: Overall, the simulation model demonstrates that production of improved forage crops should be combined with selective breeding and an appropriate finishing strategy. The competition for resources (land and labour) with crop production, forage seed shortage and extended family size are other challenges raised by smallholder farmers for the feasibility of the two alternative feed-supply systems. Feed shortage is a critical problem for the livestock sector in Ethiopia; therefore, development and evaluation of alternative feed-supply systems that enhance feed supply are needed. The alternative feed supply systems should be combined with selective breeding and appropriate finishing strategy. Support of farmers by extension service and development agents is crucial to helping farmers adopt this alternative feed supply system. [ABSTRACT FROM AUTHOR]

Cattle production is an essential livelihood strategy in south-western Burkina Faso. Although having a distinct cultural role and known to be resistant against African animal trypanosomosis, the Lobi taurine cattle breed is endangered due to its low market value. As the first step in preservation efforts, our study aimed to develop a typology of production systems at the farm level. We used a structured questionnaire and focus group discussions for collecting data on household characteristics, socioeconomic activities, livestock, and access to services. The sample comprised 169 households in three communities. The analytical strategy included factor analysis of mixed data and hierarchical clustering. We identified four distinct types of cattle production systems: (1) sedentary Lobi farms, (2) sedentary crossbreed farms, (3) semi-transhumant Fulani zebu farms, and (4) transhumant Fulani zebu farms. Significant factors in developing this typology were the farmers' ethnic group, crop diversity, cattle herd size, cattle herd composition, number of small ruminants, and livestock management strategies. Across all production systems, men were considered being primary decision-makers in cattle production, with women, herders, and children being responsible for specific tasks. All identified production systems are increasingly confronting disease pressure and scarcity of water and land. Future efforts in preservation and breeding will need to respond to these trends in the agroecosystem, integrate risk management measures, and resonate with the specific needs of the different household members involved in cattle rearing. [ABSTRACT FROM AUTHOR]

Summary: In the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single‐step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (−0.75 ± 0.22 puppies per litter). The variant was further predicted to cause a proline to serine substitution. The affected residue was immediately followed by a six‐residue deletion that is fixed in the canine species but absent in non‐canids. We further confirmed that the deletion is prevalent in the Canidae family by sequencing three species of wild canids. Since canids uniquely ovulate oocytes at the prophase stage of the first meiotic division, requiring maturation in the oviduct, we conjecture that the amino acid substitution and the six‐residue deletion of GDF9 may serve as a model for insights into the dynamics of oocyte maturation in canids. [ABSTRACT FROM AUTHOR]

Summary: A specific white spotting phenotype, termed finching or line‐backed spotting, is known for all Pinzgauer cattle and occurs occasionally in Tux‐Zillertaler cattle, two Austrian breeds. The so‐called Pinzgauer spotting is inherited as an autosomal incompletely dominant trait. A genome‐wide association study using 27 white spotted and 16 solid‐coloured Tux‐Zillertaler cattle, based on 777k SNP data, revealed a strong signal on chromosome 6 at the KIT locus. Haplotype analyses defined a critical interval of 122 kb downstream of the KIT coding region. Whole‐genome sequencing of a Pinzgauer cattle and comparison to 338 control genomes revealed a complex structural variant consisting of a 9.4‐kb deletion and an inversely inserted duplication of 1.5 kb fused to a 310‐kb duplicated segment from chromosome 4. A diagnostic PCR was developed for straightforward genotyping of carriers for this structural variant (KITPINZ) and confirmed that the variant allele was present in all Pinzgauer and most of the white spotted Tux‐Zillertaler cattle. In addition, we detected the variant in all Slovenian Cika, British Gloucester and Spanish Berrenda en negro cattle with similar spotting patterns. Interestingly, the KITPINZ variant occurs in some white spotted animals of the Swiss breeds Evolèner and Eringer. The introgression of the KITPINZ variant confirms admixture and the reported historical relationship of these short‐headed breeds with Austrian Tux‐Zillertaler and suggests a mutation event, occurring before breed formation. [ABSTRACT FROM AUTHOR]

Summary: Background: Vitiligo and melanoma are relatively common disorders in grey Pura Raza Español horses and other horse breeds with grey‐coloured coats. Objectives: To determine the breed prevalence, environmental risks factors and estimate the genetic parameters for vitiligo and melanoma in Pura Raza Español horses. Study design: Retrospective cohort study. Methods: We analysed data from a large worldwide population of Pura Raza Español horses. The database included the vitiligo and melanoma scores, on either a four‐ or six‐point linear scale, of 11,436 horses. Genetic parameters were estimated using a Bayesian genetic animal model including the four associated environmental risk factors as systematic effects. Inbreeding was used as a covariate, and animal and residual effects were included as random effects. Results: Of the horses included in the study, 2.8 and 20.5% showed some traces of vitiligo around the eyes and mouth, respectively, while 1.6% showed varying degrees of melanoma. Age, coat colour and inbreeding were significantly associated with the three outcomes studied. The estimated heritability for the whole population was 0.09 (s.d. +0.019), 0.44 (s.d. +0.031) and 0.13 (s.d. +0.037), for eye vitiligo score, nostril vitiligo score and melanoma scores respectively. The genetic correlations ranged from 0.42 (s.d. +0.084) between eye and nostril vitiligo score to 0.15 (s.d. +0.096) between nostril vitiligo and melanoma. Main limitations: Vitiligo scores for the perianal regions were not collected. The veterinarian responsible for each assessment was not recorded. Conclusions: Vitiligo and melanoma are prevalent in this population and those environmental risk factors and genetics both have an effect on the clinical expression of the diseases. These findings may help to reduce prevalence through breeding programmes. [ABSTRACT FROM AUTHOR]

Summary: An ectopic ureter is a congenital anomaly which may lead to urinary incontinence and without a surgical intervention even to end‐stage kidney disease. A genetic component contributes to the development of this anomaly in Entlebucher mountain dogs (EMD); however, its nature remains unclear. Using the Illumina CanineHD bead chip, a case–control genome‐wide association study was performed to identify SNPs associated with the trait. Six loci on canine chromosomes 3, 17, 27 and 30 were identified with 16 significantly associated SNPs. There was no single outstanding SNP associated with the phenotype, and the association signals were not close to known genes involved in human congenital anomalies of the kidney or lower urinary tract. Additional research will be necessary to elucidate the potential role of the associated genes in the development of ectopic ureters in the EMD breed. [ABSTRACT FROM AUTHOR]

Summary: The aim of this study was to estimate the non‐additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross‐bred progeny over the mid‐purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus‐specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible. [ABSTRACT FROM AUTHOR]

A comprehensive dynamic simulation model was developed to describe a community-based breeding program for the Menz sheep population of Ethiopia. Selection of male and female animals based on their own and maternal performance was simulated. The breeding goal traits were 6-mo weight, preweaning survival, and fertility rate. The model input data were obtained from the flock book, questionnaires, and references. The simulation model used a mix of deterministic and stochastic procedures to model the complex system. In the baseline scenario, the proportion of selected male and female animals varied between 20 and 30% and between 70 and 80%, respectively. A reasonable annual genetic gain was predicted for the breeding goal traits at the village level. For 6-mo weight and preweaning survival rate, the annual genetic gain varied from 0.213 to 0.214 kg and 0.255 to 0.256%, respectively. For fertility rate, an annual genetic gain of 0.063% was obtained. The predicted rate of inbreeding per year was between 0.094 and 0.116%. Furthermore, a scenario analysis was conducted by varying the proportions of selected animals. Annual genetic gains of 0.230 kg, 0.277%, and 0.069% were obtained for 6-mo weight, preweaning survival rate, and fertility rate, respectively, when the proportion of selected male and female animals decreased by 10%. The annual genetic gains decreased to 0.198 kg, 0.236%, and 0.059%, respectively, when the selection proportion of male and female animals increased by 10%. The lowest rate of inbreeding per year, ranging from 0.065 to 0.079%, was achieved when the selection proportion of selected male and female animals increased. The model is relevant for the step-by-step evaluation of more than one round of selection. It is flexible and usage driven. The model is a valuable tool to design different population structures and can be easily expanded to adopt different breeding strategies. Hence, the system dynamics modeling approach is a potential tool to describe complex breeding programs. [ABSTRACT FROM AUTHOR]

Background Longevity/durability is a relevant trait in racehorses. Genetic analysis and knowledge of factors that influence number of harness race starts would be advantageous for both horse welfare and the equine industry. Objectives To perform a genetic analysis on harness racing using number of races as a measure of longevity/durability and to identify factors associated with career length in Spanish Trotter Horses ( STH). Study design Longitudinal study. Methods Performance data (n = 331,970) on the STH population for harness racing at national level between 1990 and 2014 were used. A grouped data model was fitted to assess factors influencing the risk of ending harness racing career and to estimate the heritability and breeding values for total number of harness races starts as an indicator of horses' longevity and durability. The model included sex, age at first race and first start earnings as time-independent effects, and the calendar year, driver, trainer, racetrack category and season of competition as time-dependent effects. Results Across the whole dataset, the average number of harness races horses achieved in Spain was 54.7 races, and this was associated with the horses' sex, age at first race and first start earnings, calendar year, driver, racetrack category, and season. The heritability estimated (0.17 ± 0.01) for number of harness race starts indicates that a beneficial response to direct genetic selection can be expected. Main limitations Data on horses' health status were not available. Conclusions Horses' total number of harness race starts is a promising tool for genetic analysis and the evaluation of racing longevity and durability. The estimated heritability provides evidence to support the application of genetic selection of total career number of races to improve longevity/durability of STH. [ABSTRACT FROM AUTHOR]

Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental ( SI) and Red Holstein Friesian ( RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3-47.3 Mb) and 18 (18.7-25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within ( iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6-24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI ( Fst), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and Fst was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions. [ABSTRACT FROM AUTHOR]

We have evaluated the use of genomic coancestry coefficients based on shared segments for the maintenance of genetic diversity through optimal contributions methodology for populations of three different Austrian cattle breeds. This coancestry measure has been compared with the genomic coancestry coefficient calculated on a SNP-by- SNP basis and with pedigree-based coancestry. The regressions of the shared segments coancestry on the other two coefficients suggest that the former mainly reflect Identity By Descent but with the advantage over pedigree-based coancestry of providing the realized Identity By Descent rather than an expectation. The effective population size estimated from the rate of coancestry based on shared segments was very similar to those obtained with the other coefficients and of small magnitude (from 26.24 to 111.90). This result highlights the importance of implementing active management strategies to control the increase of inbreeding and the loss of genetic diversity in livestock breeds, even when the population size is reasonably large. One problem for the implementation of coancestry based on shared segments is the need of estimating the gametic phases of the SNPs which, given the techniques used to obtain the genotypes, are a priori unknown. This study shows, through computer simulations, that using estimates of gametic phases for computing coancestry based on shared segments does not lead to a significant loss in the diversity maintained. This has been shown to be true even when the size of the population is very small as it is usually the case in populations subjected to conservation programmes. [ABSTRACT FROM AUTHOR]

Covariance components and genetic parameters were estimated for birth weight (BiW); adjusted weights at 4, 7, 12, and 18 mo; and ADG between 0 and 4 mo, between 4 and 7 mo, between 7 and 12 mo, and between 12 and 18 mo. Additionally, reproductive traits, calving interval, and age at first calving were analyzed, together with traits measured by ultrasound: loin eye area, deep fat mean, back fat, and rump fat. Analyses were performed using an animal model, considering the fixed effects of the farm (n = 37), year and month of birth, sex, calving number (1 to 7), season (dry and rainy seasons), region (North Coast, Andean Region, and Oriental Savannas), and conception (natural mating or AI), whereas the age of the cows at calving was considered a polynomial covariate with linear and quadratic effects. Three different models were used to find the one with the best fit for each trait: a single-trait model with an additive direct genetic effect, a single-trait model with additive direct and maternal genetic effects, and finally, a multitrait model with an additive direct genetic effect. For the growth traits, the heritability was between 0.24 and 0.47, with the lowest value for weight at 7 mo and the greatest value for BiW, and the maternal heritability was found to be between 0.15 and 0.21 but did not decrease later on. The correlation between direct and maternal effects was high and negative (-0.59 to -0.76). With ultrasound traits, a model with only direct effects was used. The heritability was between 0.13 and 0.28 for back fat and loin eye area, respectively. The heritabilities for deep fat mean and rump fat were similar, being 0.19 and 0.21, respectively. The reproductive traits showed high residual variance. In particular, the heritability of calving interval was low (0.06). The results showed that the growth traits have an important genetic component, which is a favorable indicator for obtaining improvement progress in the zebu Brahman breed for beef production in tropical regions of Colombia. The maternal effects influenced the weight performance from 4 to 18 mo and should be taken into account in genetic analyses. In general, the direct heritability of medium magnitude estimated for growth and traits measured by ultrasound suggests that individual selection for these traits will be effective. [ABSTRACT FROM AUTHOR]

This is the first report performing the whole genome SNP scanning of snow sheep ( Ovis nivicola). Samples of snow sheep ( n = 18) collected in six different regions of the Republic of Sakha (Yakutia) from 64° to 71° N. For SNP genotyping, we applied Ovine 50K SNP BeadChip (Illumina, United States), designed for domestic sheep. The total number of genotyped SNPs (call rate 90%) was 47796 (88.1% of total SNPs), wherein 1006 SNPs were polymorphic (2.1%). Principal component analysis (PCA) showed the clear differentiation within the species O. nivicola: studied individuals were distributed among five distinct arrays corresponding to the geographical locations of sampling points. Our results demonstrate that the DNA chip designed for domestic sheep can be successfully used to study the allele pool and the genetic structure of snow sheep populations. [ABSTRACT FROM AUTHOR]

An introduction to the journal is presented in which the author discusses various reports within the issue on topics including alternate breeding objectives, livestock breeding, and genetics.

GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the 'classical' inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient ( AHC), defined here for the first time. AHC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients. [ABSTRACT FROM AUTHOR]

Breeding programmes described as community-based ( CBBP) typically relate to low-input systems with farmers having a common interest to improve and share their genetic resources. CBBPs are more frequent with keepers of small ruminants, in particular smallholders of local breeds, than with cattle, pigs or chickens with which farmers may have easier access to alternative programmes. Constraints that limit the adoption of conventional breeding technologies in low-input systems cover a range of organizational and technical aspects. The analysis of 8 CBBPs located in countries of Latin-America, Africa and Asia highlights the importance of bottom-up approaches and involvement of local institutions in the planning and implementation stages. The analysis also reveals a high dependence of these programmes on organizational, technical and financial support. Completely self-sustained CBBPs seem to be difficult to realize. There is a need to implement and document formal socio-economic evaluations of CBBPs to provide governments and other development agencies with the information necessary for creating sustainable CBBPs at larger scales. [ABSTRACT FROM AUTHOR]

Crossbreeding of indigenous tropical and improved western dairy cattle breeds as tool to improve dairy cattle performance on smallholder farms has been widely advocated, criticised and yet applied. The government of Ethiopia supported this technology for decades but adoption rate is low. Constraints are documented but there is little information about farm level introduction and development of crossbreeding. A total 122 smallholders with mixed crop livestock farms and at least 8 years of successful crossbreeding were interviewed using a pre-tested questionnaire in two contexts in Amhara Regional state in north-western Ethiopia. Crossbreeding initiator was either uncoordinated government extension or a coordinated development project, also implemented with governmental support. Qualitative and quantitative data on farmers’ motivations, crossbreeding introduction, initiator support, breeding adaptation and impacts at farm level were analysed. Results show that even though motives vary between contexts the underlying reason to introduce crossbreeding was economic profit. To be able to introduce crossbreeding support of initiators (e.g. extension) and other farmers was essential. The crossbreeding introduction context had some influence. Governmental actors were the main source of support and supplier of exotic genetics but the farmer network acted as safety net filling gaps of government support. Breeding strategies focused on performance increase. A lack of basic understanding of crossbreeding has been identified. A surprising, probably biased, result was general satisfaction with initiator support and with breeding services. It was challenged by the high proportion of farmers unable to follow a breeding strategy due to insufficient bull and/or semen supply. Crossbreeding changed the smallholder production system to a high input – high output system. Except for crossbred adaptation problems, challenges were ranked context specific and influenced by the initiator. Farmers perceived crossbreeding as success and recommended it. We conclude that farmers can realize income increase with crossbreeding. The complexity of this technology, high initial investment and the need for support services and external production inputs are probable reasons why crossbreeding uptake is low. Improving the availability of semen and/or bulls must be the top priority for breeding service providers to enable farmers to follow a breeding strategy and reach a suitable and sustainable herd performance. Access to investment capital, input supply, strong technical support and market linkages are crucial for successful crossbreeding. [ABSTRACT FROM PUBLISHER]

Copyright of Animal Genetic Resources is the property of Cambridge University Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Using genome-wide SNP data, we calculated genomic inbreeding coefficients ( FROH > 1 Mb, FROH > 2 Mb, FROH > 8 Mb and FROH > 16 Mb) derived from runs of homozygosity ( ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity ( FHOM). We compared these values of inbreeding coefficients with those calculated from pedigrees ( FPED) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh ( FPED = 0.014, FROH > 8 Mb = 0.019 and FROH > 16 Mb = 0.008); the highest, for Brown Swiss ( FPED = 0.048, FROH > 8 Mb = 0.074 and FROH > 16 Mb = 0.037). In contrast, inbreeding estimates based on the genomic coefficients FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3-1.7-fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors. [ABSTRACT FROM AUTHOR]

Copyright of Animal Genetic Resources is the property of Cambridge University Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Swiss Fleckvieh was established in 1970 as a composite of Simmental ( SI) and Red Holstein Friesian ( RHF) cattle. Breed composition is currently reported based on pedigree information. Information on a large number of molecular markers potentially provides more accurate information. For the analysis, we used Illumina Bovine SNP50 Genotyping Beadchip data for 90 pure SI, 100 pure RHF and 305 admixed bulls. The scope of the study was to compare the performance of hidden Markov models, as implemented in structure software, with methods conventionally used in genomic selection [BayesB, partial least squares regression ( PLSR), least absolute shrinkage and selection operator ( LASSO) variable selection)] for predicting breed composition. We checked the performance of algorithms for a set of 40 492 single nucleotide polymorphisms ( SNPs), subsets of evenly distributed SNPs and subsets with different allele frequencies in the pure populations, using FST as an indicator. Key results are correlations of admixture levels estimated with the various algorithms with admixture based on pedigree information. For the full set, PLSR, BayesB and structure performed in a very similar manner (correlations of 0.97), whereas the correlation of LASSO and pedigree admixture was lower (0.93). With decreasing number of SNPs, correlations decreased substantially only for 5% or 1% of all SNPs. With SNPs chosen according to FST, results were similar to results obtained with the full set. Only when using 96 and 48 SNPs with the highest FST, correlations dropped to 0.92 and 0.90 respectively. Reducing the number of pure animals in training sets to 50, 20 and 10 each did not cause a drop in the correlation with pedigree admixture. [ABSTRACT FROM AUTHOR]

Genetic studies of livestock populations focus on questions of domestication, within- and among-breed diversity, breed history and adaptive variation. In this review, we describe the use of different molecular markers and methods for data analysis used to address these questions. There is a clear trend towards the use of single nucleotide polymorphisms and whole-genome sequence information, the application of Bayesian or Approximate Bayesian analysis and the use of adaptive next to neutral diversity to support decisions on conservation. [ABSTRACT FROM AUTHOR]

We report on a complete genome scan for quantitative trait loci ( QTL) affecting milk protein percentage ( PP) in the Italian Holstein- Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein- Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinucleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes ( BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes ( ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candidate genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long-term selection for high PP. [ABSTRACT FROM AUTHOR]

The Bahima ethnic group have been crossbreeding autochthonous Ankole with Holstein-Friesian cattle. Separate herds (pure Ankole and crossbreds) are common. A survey was conducted to characterize pasture utilization and management in the Ankole region to gain a better understanding of current and emerging practices. Herds are largely grazed by continuous stocking although there are efforts to establish paddocks. Factors considered for pasture allocation to cattle genotypes were high-quality feed, limited shrubs/weeds and close proximity to homestead for 80, 80 and 30% of farmers, respectively. Cross-bred cattle were kept on medium/high-quality, and Ankole cattle on medium/low-quality pastures. Pastures for cross-bred cattle yielded 0·17 t ha−1 more dry matter than pastures allocated to Ankole cattle. Crude protein (CP) content of Ankole pasture was significantly ( P < 0·05) lower than CP of cross-bred pasture (6·3% compared with 7·3%). Neutral detergent fibre content was similar (72·8% vs. 69·8%) for both pasture types. Farmers' perceptions of indicator plant species were important for allocation of pasture. Hyparrhenia rufa, Brachiaria spp., Themeda triandra and Chloris gayana were identified as the preferred pasture species. Sporobolus pyramidalis and Cymbopogon afronardus were the most undesirable pasture species. Brachiaria spp. offers an opportunity for utilization as hay for dry season supplementation. [ABSTRACT FROM AUTHOR]

Identification of breeding objective traits pertinent to specific production environments with the involvement of target beneficiaries is crucial to the success of a breed improvement program. A choice experiment was conducted in four locations representing different production systems and agro-ecologies that are habitat to four indigenous sheep breeds (Afar, Bonga, Horro and Menz) of Ethiopia with the objective of identifying farmers’/pastoralists’ preferences for sheep breeding traits. Following a synthesis of secondary information and diagnostic surveys, two communities per location consisting of 60 households each having at least four breeding ewes were identified. Producers’ priority attributes used in the choice sets were identified through in-depth production system studies conducted from December 2007 to March 2008. On the basis of prior information, four to seven attributes were used to design choice sets with different profiles in order to capture results that mimic real life of the different communities. The attributes and levels chosen for the sheep profile were as follows: body size (large/small), coat color (brown/white/black), tail type (good/bad) for both rams and ewes; horn (polled/horned) and libido (active/poor) for rams; and lambing interval (three lambings in 2 years/two lambings in 2 years time), mothering ability (good mother/bad mother), twinning rate (twin bearer/single bearer) and milk yield (two cups per milking/one cup per milking) for ewes. A fractional factorial design was implemented to construct the alternatives included in the choice sets. The design resulted in a randomized selection of 48 sheep profiles (24 sets) for both sexes, which were grouped into four blocks with six choice sets each. An individual respondent was presented with one of the four blocks to make his/her choices. Results indicate that producers’ trait preferences were heterogeneous except for body size in rams and mothering ability in ewes where nearly homogeneous preferences were investigated. In the pastoral production system, attention was given to coat color of both breeding rams and ewes, favoring brown and white colors over black. Ram libido influenced producers’ decisions in Bonga, Horro and Menz areas. The influence of milk yield and twinning on respondents’ decision making was high in Afar and Horro, respectively. Breeders in all areas attempt to combine production and reproduction traits as well as they can in order to maximize benefits from their sheep. The elicited measurable objective traits were used to design alternative community-based sheep breeding plans for the four indigenous sheep breeds in their production environments that have been implemented since. [ABSTRACT FROM AUTHOR]

In this study, we show how Y-specific interspersed multilocus microsatellites, which are loci that yield several amplified bands differing in size from the same male individual and PCR reaction, are a powerful source of information for tracing the history of cattle. Our results confirm the existence of three main groups of sires, which are separated by evolutionary time and clearly predate domestication. These three groups are consistent with the haplogroups previously identified by Götherström et al. (2005) using five Y-specific segregating sites: Y1 and Y2 in taurine (Bos taurus) cattle and Y3 in zebu (Bos indicus) cattle. The zebu cattle cluster clearly originates from a domestication process that was geographically and temporally separated from that of taurine clusters. Our analyses further suggest that: (i) introgression of wild sire genetic material into domesticated herds may have a significant role in the formation of modern cattle, including the formation of the Y1 haplogroup; (ii) a putative domestication event in Africa probably included local Y2-like wild sires; (iii) the West African zebu cattle Y-chromosome may have partially originated from an ancient introgression of humped cattle into Africa; and (iv) the high genetic similarity among Asian zebu sires is consistent with a single domestication process. [ABSTRACT FROM AUTHOR]

The article describes the case of a 2.5-month-old female Tyrolean Grey calf that developed degenerative axonopathy. Results of clinical tests revealed that the calf was normally developed for its age and breed. The calf manifested mild ambulatory paraparesis along with moderate-to-severe ataxia of the pelvic limbs and a tendency to drop to both sides.

Five cattle Y-specific microsatellites, totalling six loci, were selected from a set of 44 markers and genotyped on 608 Bos taurus males belonging to 45 cattle populations from Europe and Africa. A total of 38 haplotypes were identified. Haplogroups (Y1 and Y2) previously defined using single nucleotide polymorphisms did not share haplotypes. Nine of the 27 Y2-haplotypes were only present in African cattle. Network and correspondence analyses showed that this African-specific subfamily clustered separately from the main Y2-subfamily and the Y1 haplotypes. Within-breed genetic variability was generally low, with most breeds (78%) showing haplotypes belonging to a single haplogroup.amova analysis showed that partitioning of genetic variation among breeds can be mainly explained by their geographical and haplogroup assignment. Between-breed genetic variability summarized via Principal Component Analysis allowed the identification of three principal components explaining 94.2% of the available information. Projection of principal components on geographical maps illustrated that cattle populations located in mainland Europe, the three European Peninsulas and Mediterranean Africa presented similar genetic variation, whereas those breeds from Atlantic Europe and British Islands (mainly carrying Y1 haplotypes) and those from Sub-Saharan Africa (belonging to Y2-haplogroup) showed genetic variation of a different origin. Our study confirmed the existence of two large Y-chromosome lineages (Y1 and Y2) in taurine cattle. However, Y-specific microsatellites increased analytical resolution and allowed at least two different Y2-haplotypic subfamilies to be distinguished, one of them restricted to the African continent. [ABSTRACT FROM AUTHOR]

The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average coancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed. [ABSTRACT FROM AUTHOR]

No national breeding programme for llamas is in place in Bolivia. Initiatives for genetic improvement are rarely found and are usually carried out by NGOs working in rural development or improvement of livestock production or research stations. Farmers in the Province of Ayopaya in the District of Cochabamba have formed a breeders’ organization with the aim of improving fibre production. In this study, a detailed outline of a breeding programme with a focus on organizational and technical details is described. Facing constraints like illiteracy of farmers, bad infrastructure and lack of finances, a simple breeding programme is set up. The breeding goal is a higher fleece weight while keeping the fleece quality at the current high level. Greasy fleece weight and fibre diameter are identified as main selection criteria. Mass selection of males is carried out. Selected males are either exchanged between farmers and used in the herds or are kept during the mating season in a central mating station owned by the breeders’ organization. Model calculations were carried out with the programzplan, which is based on a deterministic approach.zplan evaluates the genetic and economic efficiency of breeding strategies considering one cycle of selection. Scenarios with only intra-herd use, using only the central mating station or combinations of those were compared in terms of expected genetic gain and expected increase of inbreeding. Fastest genetic progress is achieved when the males are kept in a central mating station as the selection intensity is on a high level. Rates of inbreeding vary between 0.08 and 0.32% per generation. [ABSTRACT FROM AUTHOR]

All over Europe, the number of draught horses has decreased drastically during the last 50 years. As a prerequisite for efficient management decisions, we analysed the conservation status in Austrian (Noriker Carinthia – NC, Noriker Salzburg – NS), Croatian (Croatian Coldblood – C, Posavina horse – P) and German (Altmaerkisch Coldblood – A, Black Forest horse – BF, Mecklenburg Coldblood – M, Rhenish German Draught horse – R, Saxon Thuringa Coldblood – ST, Schleswig Draught horse – Sch, South German Coldblood – SG) draught horses (434) using multilocus genotypic information from 30 (effectively 27) microsatellite loci. Populations located in areas with less intensive agricultural production (C, NC, NS, P and SG) had greater diversity within the population and estimated effective population size than A, BF, Sch, M, R and ST populations. The PCA plots revealed that populations form five separate groups. The ‘Noriker’ group (NC, NS and SG) and the ‘Rhenish’ group (A, M, R and ST) were the most distinctive (pairwise FST values ranged from 0.078 to 0.094). The ‘Croatian’ group (C and P) was in the centre, while the BF and Sch populations formed two out-groups. A posterior Bayesian analysis detected further differentiation, mainly caused by political and geographical factors. Thus, it was possible to separate the South German Coldblood from the Austrian Noriker population where no subpopulation structure was detected. The admixture analysis revealed imprecise classification between C and P populations. A small but notable separation of R from A, M and ST populations was detected, while Sch and BF populations remained as out-groups. The information obtained should aid in making efficient conservation decisions.Heredity (2007) 98, 114–122. doi:10.1038/sj.hdy.6800910; published online 11 October 2006 [ABSTRACT FROM AUTHOR]

The aim of this study was to estimate genetic parameters for coat color in horses. Besides defining coat color classes (gray, chestnut, bay, and black), the phenotypes were also measured quantitatively according to standardized international procedures (Commission Internationale de l'Eclairage L*, a*, b*), where L* describes lightness, a* describes color saturation from red to green, and b* describes color saturation from yellow to blue. The total color saturation was derived from a* and b* and referred to as Chroma. A total of 294 horses from the breeds Lipizzan, Nonius, Arabian Pure Bred, Shagya Arabian, and Gidran were measured at neck, shoulder, and belly. Heritabilities (within and between breeds or color classes) and repeatabilities were estimated using REML from univariate animal models defined separately for gray and nongray horses. For gray horses, the estimated within-breed heritabilities for L* ranged from 0.45 to 0.49 and for a*, b*, and Chroma from 0.09 to 0.52, indicating moderate polygenic effect. For nongray horses, between-color class heritabilities were high (0.70 to 0.85) and within-color class heritabilities were negligible (except for L* measured on neck and belly, 0.21 and 0.34, respectively). Additionally, the importance of L* was described by the relation with the total melanin content of horse coat hair; for gray and nongray horses, a strong negative linear relationship was detected (P < 0.01). The spectrometric measures and the results of this study demonstrate a possible approach to the estimation of the polygenic component involved in coat color inheritance. [ABSTRACT FROM AUTHOR]

Samples from 717 sheep of 11 Austrian sheep breeds were genotyped for 25 microsatellite loci. Twenty-one loci showing no deviation from Hardy–Weinberg equilibrium were used to calculate pairwise genetic distances (Nei's minimum distance and Reynolds’ distance). All breeds could be clearly distinguished through these genetic distances. The shortest genetic distance was found between Alpines Steinschaf (AS) and Waldschaf (WS). Within the so-called ‘Steinschaf’ group [AS, Montafoner Steinschaf (MS), Krainer Steinschaf (KS) and Tiroler Steinschaf (TS)] the MS adopted an extreme status with the largest distance to the other breeds in the group. This finding resulted in the decision to consider the MS no longer as subpopulation of Alpines Steinschaf but as an independent breed. A correct breed assignment using a Bayesian approach was possible for only 66% of all individuals belonging to Alpines Steinschaf, but for at least 90% of individuals for all other breeds investigated. [ABSTRACT FROM AUTHOR]

Blood samples of 561 Lipizzan horses from subpopulations (studs) of seven European countries representing a large fraction of the breed's population were used to examine the genetic diversity, population subdivision and gene flow in the breed. DNA analysis based on 18 microsatellite loci revealed that genetic diversity (observed heterozygosity = 0.663, gene diversity = 0.675 and the mean number of alleles = 7.056) in the Lipizzan horse is similar to other horse breeds as well as to other domestic animal species. The genetic differentiation between Lipizzan horses from different studs, although moderate, was apparent (pairwise FST coefficients ranged from 0.021 to 0.080). Complementary findings explaining the genetic relationship among studs were revealed by genetic distance and principal component analysis. One genetic cluster consisted of the subpopulations of Austria, Italy and Slovenia, which represent the classical pool of Lipizzan horse breeding. A second cluster was formed by the Croatian, Hungarian and Slovakian subpopulations. The Romanian subpopulation formed a separate unit. The largest genetic differentiation was found between the Romanian and Italian subpopulation. Genetic results are consistent with the known breeding history of the Lipizzan horse. Correct stud assignment was obtained for 80.9% and 92.1% of Lipizzan horses depending on the inclusion or exclusion of migrant horses, respectively. The results of the present study will be useful for the development of breeding strategies, which consider classical horse breeding as well as recent achievements of population and conservation genetics. [ABSTRACT FROM AUTHOR]

Summary Reasons for performing study: Equine melanomas occur most commonly in grey horses at age 5 years or more. Generally, benign and malignant melanomas are distinguished by microscopy, but a more distinct classification would be helpful. Objectives: The objectives of this study were to gain further evidence concerning the occurrence of melanotic tumours, and to evaluate the impact of heredity on melanoma development. Methods: A clinical study was conducted on a defined population of 296 grey horses of Lipizzaner breed. Individuals were classified according to theirstage of disease using a 0-5 scale. Heritability was estimated on a sample of 296 grey horses with pedigrees traced back as far as 32 generations. Results: Of the 296 horses, dermal melanomas were present in 148 horses (50%), 68 of which were more than age 15 years; 51 of these were melanoma-bearing. In 75.6% of cases, melanotic tumours were detected underneath the tail. Although melanoma-bearing grey horses were encountered up to stage 4, none of the affected individuals suffered any severe clinical effect or was handicapped in performance. Statistical analysis revealed highly significant effects of stud and age (P<0.0001), explaining 28% of the total variability. Conclusions: In contrast to melanomas in solid-coloured horses characterised by early metastases, melanomas in grey horses showed less malignancy. Affected individuals often had encapsulated nodules or structures similar to human blue nevi. Grey horse-specific genetic factors inhibiting metastatic processes may be responsible for this phenomenon. Potential clinical relevance: Although the obtained heritability estimate of 0.36 with a standard error of 0.11 indicates a strong genetic impact on the development of melanoma in ageing grey horses, a possible influence of the genes with large effects was also suggested. Therefore, further analysis is required of melanoma development in the ageing grey horse. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Animal Breeding & Genetics is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The most common goal of animal conservation programmes is to maintain genetic diversity. Various measures for genetic variability based on pedigree information can be used, but most of them are very sensitive to completeness of pedigree information. Different criteria based on probability of identity-by-descent (effective population size via increase in inbreeding Ne ) or probability of gene origin (effective number of founders fe , ancestors fa and founder genomes Ng ) were used to describe the genetic variability of three Austrian cattle breeds [Original Pinzgau (PI), Tux-Zillertal (TZ), Carinthian Blond (CB)]. Reference populations for PI were defined by animals born between 1993 and 1997 and for TZ and CB by all living animals, irrespective of birth year. The numbers of animals in the reference populations were 9706, 471 and 230 for PI, TZ and CB, respectively. The average complete generation equivalent showed the different quality of pedigree information: 5.33 for PI, 2.52 for TZ and 1.73 for CB. The following Ne s were calculated: 76 for PI and CB and 43 for TZ. For PI, TZ and CB a fe -value of 65.4, 21.0 and 29.9, a fa -value of 32.1, 14.2 and 29.0 and a Ng -value of 19.5, 9.7 and 22.6, respectively, were calculated. In particular, the results for TZ demonstrate the urgent need for a well-planned conservation programme. [ABSTRACT FROM AUTHOR]

Focuses on the importance of the study of the aetiology of retained placenta in animal anatomy. Risks of infectious disorders; Effects of overfeeding during dry period; Levels of placenta expulsion.

A method is presented to treat gametes as homozygous diploid individuals allowing their inclusion into the relationship matrix between animals. In this way standard techniques developed for the analysis of individual genetic variation may be used to analyze gametic variation. An example is given for maternal gametic imprinting and equivalence is shown to a gametic model. The method may also be adopted for the analysis of species (like the honey bee) with one haploid sex. [ABSTRACT FROM AUTHOR]

Parameters based on probabilities of gene origin were used to evaluate the genetic variability of four Austrian cattle breeds. Effective numbers of founders, ancestors and remaining founder genomes showed that all four populations investigated are rather small genetically. Effective numbers of remaining founder genomes were 94 for Simmental, 41 for Braunvieh (Brown Swiss), 32 for Pinzgauer and 21 for Grauvieh (Grey cattle, a small mountain breed). As the value of 94 for Simmental was rather large in comparison with estimates from other populations in previous studies, the effect of population structure was investigated. A cosine measure of similarity based on differences in individual founder contributions to different subpopulations was defined and used for analysis. Subpopulations defined by regions were clearly more distinct for Simmental than for Braunvieh. The size of the cosine values depended on the method of calculating founder contributions and was overestimated when choosing the method not accounting for drift and bottlenecks (effective number of founders). [ABSTRACT FROM PUBLISHER]