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Copyright of Revista Cientifica de la Facultade de Veterinaria is the property of Universidad del Zulia, Facultad de Ciencias Veterinarias 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.)

Morphometric parameters and their indices are central to characterization, selection and genetic improvement of farm animals. The present study was conducted to fix multicollinearity among predictors and to fit optimum regression model for prediction of 14-week body weight of 150 un-sexed Sudani ducks from early age (0, 2, 4 and 6 weeks of age) morphometric measurements (body weight, body length, breast circumference and keel length). Pairwise correlation between the 14-week body weight (BWT) and measured variables was the highest with 2-week BWT (r=0.934, P<0.001). Application of multicollinearity diagnostics (variance inflation factor, tolerance, eigenvalues and condition index) revealed collinearity among six variables. Stepwise regression equation identified 2-week BWT as the most important predictor accounting for 87.30% of the total variation of the response variable. However, the optimum regression model for prediction of adult body weight was fitted with 2-week BWT in quadratic model having the highest predictive power (Coefficient of determination/R2/=0.966 and least root mean square error/RMSE/=4.269). This result is applicable under field conditions for both researchers and duck farmers for early selection of 14-week market body weight of Sudani ducks at 2 weeks of age. [ABSTRACT FROM AUTHOR]

Background: Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs identified lncRNAs in specific developmental stages or differentially expressed under specific conditions in a limited number of tissues, more comprehensive identification of lncRNAs in these species is needed. The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs. As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs. Results: Comprehensive lncRNA annotations for the chicken, cattle, and pig genomes were generated by utilizing RNA-seq from eight tissue types from two biological replicates per species at the adult developmental stage. A total of 9393 lncRNAs in chickens, 7235 lncRNAs in cattle, and 14,429 lncRNAs in pigs were identified. Including novel isoforms and lncRNAs from novel loci, 5288 novel lncRNAs were identified in chickens, 3732 in cattle, and 4870 in pigs. These transcripts match previously known patterns of lncRNAs, such as generally lower expression levels than mRNAs and higher tissue specificity. An analysis of lncRNA conservation across species identified a set of conserved lncRNAs with potential functions associated with chromatin structure and gene regulation. Tissue-specific lncRNAs were identified. Genes proximal to tissue-specific lncRNAs were enriched for GO terms associated with the tissue of origin, such as leukocyte activation in spleen. Conclusions: LncRNAs were identified in three important farm animal species using eight tissues from adult individuals. About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species. While lncRNAs are less conserved than protein-coding genes, a set of positionally conserved lncRNAs were identified among chickens, cattle, and pigs with potential functions related to chromatin structure and gene regulation. Tissue-specific lncRNAs have potential regulatory functions on genes enriched for tissue-specific GO terms. Future work will include epigenetic data from ChIP-seq experiments to further refine these annotations. [ABSTRACT FROM AUTHOR]

Abstract: The associations between childhood acute lymphoblastic leukemia (ALL) and several factors related to early stimulation of the immune system, that is, farm residence and regular contacts with farm animals (livestock, poultry) or pets in early childhood, were investigated using data from 13 case–control studies participating in the Childhood Leukemia International Consortium. The sample included 7847 ALL cases and 11,667 controls aged 1–14 years. In all studies, the data were obtained from case and control parents using standardized questionnaires. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by unconditional logistic regression adjusted for age, sex, study, maternal education, and maternal age. Contact with livestock in the first year of life was inversely associated with ALL (OR = 0.65, 95% CI: 0.50, 0.85). Inverse associations were also observed for contact with dogs (OR = 0.92, 95% CI: 0.86, 0.99) and cats (OR = 0.87, 95% CI: 0.80, 0.94) in the first year of life. There was no evidence of a significant association with farm residence in the first year of life. The findings of these large pooled and meta‐analyses add additional evidence to the hypothesis that regular contact with animals in early childhood is inversely associated with childhood ALL occurrence which is consistent with Greaves’ delayed infection hypothesis. [ABSTRACT FROM AUTHOR]

Experiences from international sire evaluation indicate that the multiple-trait across-country evaluation method is sensitive to changes in genetic variance over time. Top bulls from birth year classes with inflated genetic variance will benefit, hampering reliable ranking of bulls. However, none of the methods available today enable countries to validate their national evaluation models for heterogeneity of genetic variance. We describe a new validation method to fill this gap comprising the following steps: estimating withinyear genetic variances using Mendelian sampling and its prediction error variance, fitting a weighted linear regression between the estimates and the years under study, identifying possible outliers, and defining a 95% empirical confidence interval for a possible trend in the estimates. We tested the specificity and sensitivity of the proposed validation method with simulated data using a real data structure. Moderate (M) and small (S) size populations were simulated under 3 scenarios: a control with homogeneous variance and 2 scenarios with yearly increases in phenotypic variance of 2 and 10%, respectively. Results showed that the new method was able to estimate genetic variance accurately enough to detect bias in genetic variance. Under the control scenario, the trend in genetic variance was practically zero in setting M. Testing cows with an average birth year class size of more than 43,000 in setting M showed that tolerance values are needed for both the trend and the outlier tests to detect only cases with a practical effect in larger data sets. Regardless of the magnitude (yearly increases in phenotypic variance of 2 or 10%) of the generated trend, it deviated statistically significantly from zero in all data replicates for both cows and bulls in setting M. In setting S with a mean of 27 bulls in a year class, the sampling error and thus the probability of a false-positive result clearly increased. Still, overall estimated genetic variance was close to the parametric value. Only rather strong trends in genetic variance deviated statistically significantly from zero in setting S. Results also showed that the new method was sensitive to the quality of the approximated reliabilities of breeding values used in calculating the prediction error variance. Thus, we recommend that only animals with a reliability of Mendelian sampling higher than 0.1 be included in the test and that low heritability traits be analyzed using bull data sets only. [ABSTRACT FROM AUTHOR]

Llama, the most numerous domestic camelid in Argentina, has good fiber-production ability. Although a few genes related to other productive traits have been characterized, the molecular genetic basis of fiber growth control in camelids is still poorly understood. Fibroblast growth factor 5 ( FGF5) is a secreted signaling protein that controls hair growth in humans and other mammals. Mutations in the FGF5 gene have been associated with long-hair phenotypes in several species. Here, we sequenced the llama FGF5 gene, which consists of three exons encoding 813 bp. cDNA analysis from hair follicles revealed the expression of two FGF5 alternative spliced transcripts, in one of which exon 2 is absent. DNA variation analysis showed four polymorphisms in the coding region: a synonymous SNP (c.210A>G), a single base deletion (c.348delA), a 12-bp insertion (c.351_352ins CATATAACATAG) and a non-sense mutation (c.499C>T). The deletion was always found together with the insertion forming a haplotype and producing a putative truncated protein of 123 amino acids. The c.499C>T mutation also leads to a premature stop codon at position 168. In both cases, critical functional domains of FGF5, including one heparin binding site, are lost. All animals analyzed were homozygous for one of the deleterious mutations or compound heterozygous for both (i.e. c.348delA, c.351_352ins CATATAACATAG/c.499T). Sequencing of guanaco samples showed that the FGF5 gene encodes a full-length 270-amino acid protein. These results suggest that FGF5 is likely functional in short-haired wild species and non-functional in the domestic fiber-producing species, the llama. [ABSTRACT FROM AUTHOR]

In the past few years, new technologies have arisen that enable higher efficiency of gene editing. With the increase ease of using gene editing technologies, it is important to consider the best method for transferring new genetic material to livestock animals. Microinjection is a technique that has proven to be effective in mice but is less efficient in large livestock animals. Over the years, a variety of methods have been used for cloning as well as gene transfer including; nuclear transfer, sperm mediated gene transfer (SMGT), and liposome-mediated DNA transfer. This review looks at the different success rate of these methods and how they have evolved to become more efficient. As well as gene editing technologies, including Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the most recent clustered regulatory interspaced short palindromic repeats (CRISPRs). Through the advancements in gene-editing technologies, generating transgenic animals is now more accessible and affordable. The goals of producing transgenic animals are to 1) increase our understanding of biology and biomedical science; 2) increase our ability to produce more efficient animals; and 3) produce disease resistant animals. ZFNs, TALENs, and CRISPRs combined with gene transfer methods increase the possibility of achieving these goals. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace backcross population and study their association with fatty acid composition and growth-related traits. A total of 1,279 CNVs, including duplications and deletions, were detected, ranging from 106 to 235 CNVs across samples, with an average of 183 CNVs per sample. Moreover, we detected 540 CNV regions (CNVRs) containing 245 genes. Functional annotation suggested that these genes possess a great variety of molecular functions and may play a role in production traits in commercial breeds. Some of the identified CNVRs contained relevant functional genes (e.g., CLCA4, CYP4X1, GPAT2, MOGAT2, PLA2G2A and PRKG1, among others). The variation in copy number of four of them (CLCA4, GPAT2, MOGAT2 and PRKG1) was validated in 150 BC1_LD (25% Iberian and 75% Landrace) animals by qPCR. Additionally, their contribution regarding backfat and intramuscular fatty acid composition and growth–related traits was analyzed. Statistically significant associations were obtained for CNVR112 (GPAT2) for the C18:2(n-6)/C18:3(n-3) ratio in backfat and carcass length, among others. Notably, GPATs are enzymes that catalyze the first step in the biosynthesis of both triglycerides and glycerophospholipids, suggesting that this CNVR may contribute to genetic variation in fatty acid composition and growth traits. These findings provide useful genomic information to facilitate the further identification of trait-related CNVRs affecting economically important traits in pigs. [ABSTRACT FROM AUTHOR]

Production environments are expected to change, mostly to a hotter climate but also possibly more extreme and drier. Can the current generation of farm animals cope with the changes or should it be specifically selected for changing conditions? In general, genetic selection produces animals with a smaller environmental footprint but also with smaller environmental flexibility. Some answers are coming from heat-stress research across species, with heat tolerance partly understood as a greater environmental flexibility. Specific studies in various species show the complexities of defining and selecting for heat tolerance. In Holsteins, the genetic component for effect of heat stress on production approximately doubles in second and quadruples in third parity. Cows with elevated body temperature have the greatest production under heat stress but probably are at risk for increased mortality. In hot but less intensive environments, the effect of heat stress on production is minimal, although the negative effect on fertility remains. Mortality peaks under heat stress and increases with parity. In Angus, the effect of heat stress is stronger only in selected regions, probably because of adaptation of calving seasons to local conditions and crossbreeding. Genetically, the direct effect shows variability because of heat stress, but the maternal effect does not, probably because dams shield calves from environmental challenges. In pigs, the effect of heat stress is strong for commercial farms but almost nothing for nucleus farms, which have lower pig density and better heat abatement. Under intensive management, heat stress is less evident in drier environments because of more efficient cooling. A genetic component of heat stress exists, but it is partly masked by improving management and selection based on data from elite farms. Genetic selection may provide superior identification of heat-tolerant animals, but a few cycles may be needed for clear results. Also, simple traits exist that are strongly related to heat stress (e.g., slick hair in dairy cattle and shedding intensity in Angus). Defining resilience may be difficult, especially when masked by improving environment. Under climate change, the current selection strategies may be adequate if they 1) are accompanied by constantly improving management, 2) use commercial data, and 3) include traits important under climate change (e.g., mortality). [ABSTRACT FROM AUTHOR]

Four-horned sheep are an ideal animal model for illuminating the genetic basis of horn development. The objective of this study was to locate the genetic region responsible for the four-horned phenotype and to verify a previously reported polled locus in three Chinese breeds. A genome-wide association study ( GWAS) was performed using 34 two-horned and 32 four-horned sheep from three Chinese indigenous breeds: Altay, Mongolian and Sishui Fur sheep. The top two significant single nucleotide polymorphisms ( SNPs) associated with the four-horned phenotype were both located in a region spanning positions 132.6 to 132.7 Mb on sheep chromosome 2. Similar locations for the four-horned trait were previously identified in Jacob, Navajo-Churro, Damara and Sishui Fur sheep, suggesting a common genetic component underlying the four-horned phenotype. The two identified SNPs were both downstream of the metaxin 2 ( MTX2) gene and the HOXD gene cluster. For the top SNP- OAR2:g.132619300G>A-the strong associations of the AA and AG genotypes with the four-horned phenotype and the GG genotype with the two-horned phenotype indicated the dominant inheritance of the four-horned trait. No significant SNPs for the polled phenotype were identified in the GWAS analysis, and a PCR analysis for the detection of the 1.8-kb insertion associated with polled sheep in other breeds failed to verify the association with polledness in the three Chinese breeds. This study supports the hypothesis that two different loci are responsible for horn existence and number. This study contributes to the understanding of the molecular regulation of horn development and enriches the knowledge of qualitative traits in domestic animals. [ABSTRACT FROM AUTHOR]

The principles of genomic selection are described, with the main factors affecting its efficiency and the assumptions underlying the different models proposed. The reasons of its fast adoption in dairy cattle are explained and the conditions of its application to other species are discussed. Perspectives of development include: selection for new traits and new breeding objectives; adoption of more robust approaches based on information on causal variants; predictions of genotype × environment interactions. [ABSTRACT FROM AUTHOR]

In recent years, molecular genetic technologies allowed to identify genetic structure in farm animals have great advantages for animal breeding. Especially, in developed countries these methods began to be widely used to assist animal breeding studies. It can be said that there are various molecular genetic markers. These markers can be classified by taking into consideration a number of factors such as the principle of the detection technique, type of polymorphism. Although old type molecular genetic markers such as RFLP, AFLP, microsatellites are widely used today, the information obtained from them is more limited than modern molecular genetic markers. SNP chip technologies, which known as modern molecular markers and are one of the most important developments in the molecular genetics field, have provided genomic breeding value estimation and genomic selection in farm animals. In this review, old and new types of molecular markers were compared and their usage in animal breeding were discussed. [ABSTRACT FROM AUTHOR]

Domestic animals show considerable genetic diversity. Previous studies suggested that animal phenotypes were affected by mi RNA- mRNA interplay, but these studies focused mainly on the analysis of one or several mi RNA- mRNA interactions. However, in this study, we investigated mi RNA- mRNA and mi RNA-lnc RNA interactions on a genomic scale using miranda and targetscan algorithms. There has been strong directional artificial selection practiced during the domestication of animals. Thus, we investigated SNPs that were located in mi RNAs and mi RNA binding sites and found that several SNPs located in 3′- UTRs of mRNAs had the potential to affect mi RNA- mRNA interactions. In addition, a database, named mi RBond, was developed to provide visualization, analysis and downloading of the resulting datasets. Our results open the way to further experimental verification of mi RNA- mRNA and mi RNA-lnc RNA interactions as well as the influence of SNPs upon such interplay. [ABSTRACT FROM AUTHOR]

An introduction is presented in which the editor discusses various reports within the issue on topics including methods to genomic and bioinformatics approaches for characterization of farm animal genetic resources, livestock genetic resources in Africa, and farm animal genomics.

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that the genetic diversity of farmed and domesticated animals and of wild relatives is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity. However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development. [ABSTRACT FROM AUTHOR]

Objective. To assess the population structure and genetic diversity in populations of domestic horse (Equus caballus) in the municipality Cienaga de Oro-Córdoba (Colombia). Materials and methods. Random sampling were conducted between August and October 2013, in adult animals on farms seven districts, which was carried out phenotypic characterization of each animal, based on autosomal markers encoding morphological Extension (E), Agouti (A), Cream (C), White (W), Gray (G), Tobiano (TO), Overo (O) and Roan (RN). Population genetic parameters: allele frequency, genetic diversity, gene flow, Hardy-Weinberg equilibrium and genetic distance were calculated through the program POPGENE 1.31; the genetic structure was assessed using the program FSTAT v. 2.9.3.2. Results. 341 individuals were analyzed in the seven populations studied, where the Extension gene Was the MOST faq frequently as the Overo and Tobiano genes showed the lowest values. Insignificant values of genetic variability and population recorded a global level, likewise, low genetic differentiation among populations, accompanied by a high gene flow was obtained; an excess of heterozygotes at population and global level was observed; to this is added the presence of Hardy-Weinberg equilibrium in all populations relative to the markers studied and low genetic distance values were reported. Conclusions. The populations are highly genetically related, a situation that may result from the existing geographical proximity between them, favoring genetic exchange and the establishment of a metapopulation. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mt DNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mt DNA variants. Herein, we provide the most up-to-date mt DNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mt DNA haplogroup trees based on 1240 complete or near-complete mt DNA genome sequences are available in open resource DomeTree (). In addition, we offer the software MitoToolPy () to facilitate the mt DNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy. [ABSTRACT FROM AUTHOR]

Background: For most domestic animal species, including bovines, it is difficult to identify causative genetic variants involved in economically relevant traits. The candidate gene approach is efficient because it investigates genes that are expected to be associated with the expression of a trait and defines whether the genetic variation present in a population is associated with phenotypic diversity. A potential limitation of this approach is the identification of candidates. This study used a bioinformatics approach to identify candidate genes via a search guided by a functional interaction network. Results: A functional interaction network tool, BosNet, was constructed for Bos taurus. Predictions for candidate genes were performed using the guilt-by-association principle in BosNet. Association analyses identified five novel markers within BosNet-prioritized genes that had significant effects on different growth traits in Charolais and Brahman cattle. Conclusions: BosNet is an excellent tool for the identification of single nucleotide polymorphisms that are potentially associated with complex traits. [ABSTRACT FROM AUTHOR]

Background: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs. Results: The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs. Conclusions: ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from . [ABSTRACT FROM AUTHOR]

AIM: To use estimated breeding value (EBV) analysis to investigate the genetic trend of the total hip score (to assess canine hip dysplasia) in four populous breeds of dogs using the records from the New Zealand Veterinary Association (NZVA) Canine Hip Dysplasia Scheme database (1991 to 2011). METHODS: Estimates of heritability and EBV for the NZVA total hip score of individual dogs from the German Shepherd, Labrador Retriever, Golden Retriever and Rottweiler breeds were obtained using restricted maximum likelihood procedures with a within-breed linear animal model. The model included the fixed effects of gender, birth year, birth season, age at scoring and the random effect of animal. The pedigree file included animals recorded between 1990 and 2011. A total of 2,983 NZVA hip score records, from a pedigree of 3,172 animals, were available for genetic evaluation. Genetic trends of the NZVA total hip score were calculated as the regression coefficient of the EBV (weighted by reliabilities) on year of birth. RESULTS: The estimates of heritability for hip score were 0.32 (SE 0.08) in German Shepherd, 0.37 (SE 0.08) in Labrador Retriever, 0.29 (SE 0.08) in Golden Retriever and 0.52 (SE 0.18) in Rottweiler breeds. Genetic trend analysis revealed that only the German Shepherd breed exhibited a genetic trend towards better hip conformation over time, with a decline of 0.13 (SE 0.04) NZVA total hip score units per year (p<0.001). The genetic trends of total hip score for the remaining three breeds were not significantly different from zero (p>0.1). CONCLUSIONS: Despite moderate heritability of the NZVA total hip score, there has not been substantial improvement of this trait for the four breeds analysed in the study period. CLINICAL RELEVANCE: Greater improvement in reducing the prevalence of canine hip dysplasia may be possible if screening were to be compulsory as a requirement for registration of pedigree breeding stock, greater selection pressure were to be applied and selection of breeding stock made on the basis on an individual's EBV rather than the NZVA total hip score alone. [ABSTRACT FROM PUBLISHER]

Sustainable intensification (SI) is a multifaceted concept incorporating the ambition to increase or maintain the current level of agricultural yields while reduce negative ecological and environmental impacts. Decision-support systems (DSS) that use integrated analytical methods are often used to support decision making processes in agriculture. However, DSS often consist of set of values, objectives, and assumptions that may be inconsistent or in conflict with merits and objectives of SI. These potential conflicts will have consequences for adoption and up-take of agricultural research, technologies and related policies and regulations such as genetic technology in pursuit of SI. This perspective paper aimed at comparing a number of frequently used socio-economic DSS with respect to their capacity in incorporating various dimensions of SI, and discussing their application to analyzing farm animal genetic resources (FAnGR) policies. The case of FAnGR policies was chosen because of its great potential in delivering merits of SI. It was concluded that flexible DSS, with great integration capacity with various natural and social sciences, are needed to provide guidance on feasibility, practicality, and policy implementation for SI. [ABSTRACT FROM AUTHOR]

Advances in animal genome data and in genetic analysis, next to the increasing use of artificial reproductive technology resulted in progress into the animal sciences area, transposing the applied technologies into the omics field. This paper provides a brief overview related to some aspects of the population genetics characterization, as well as on the animal population genetic improvement and on the main molecular tools available for farm animals, highlighting at the same time the perspectives and priorities in terms of the advanced genetic methods, that can be considered for farm animal genetic resources (FAnGR) breeding, improvement and conservation programmes in Romania. [ABSTRACT FROM AUTHOR]

Background Phlebotomus orientalis feeds on a variety of wild and domestic animals and transmits Leishmania donovani from hitherto unknown reservoir hosts to humans in extra-domestic habitats in the Metema - Humera lowlands. The aim of this study was to determine the nocturnal activities of P. orientalis and its preferred blood meal hosts. Methods Collections of Phlebotomus orientalis were made by using CDC light traps to determine the density as P. orientalis/hour CDC trap and preference to rodents by using Turner’s traps in agricultural fields, animal shelters and thickets of Acacia seyal in Baeker site-1 and Gelanzeraf site-2. The blood meal sources were detected by Reverse Line Blot (RLB) of cytochrome b polymerase chain reaction (PCR) amplification in August, 2012 from collections of sand flies in thickets of A. seyal (March 2011) and dense mixed forest (July 2011) in Baeker site 1. RLB PCR involved first amplification of animal specific sequences of cytochrome b using PCR techniques. Then the amplified sequence was hybridized with 11 species-specific probes for domestic animals adsorbed on nitrocellulose membrane for calorimetric color detection. Results A total of 6,083 P. orientalis (2,702 males and 3,381 females) were collected at hourly intervals using 22 CDC traps from January to May 2013. The peak activities of P. orientalis were at 1.00 a.m (134.0 ± 7.21) near animal shelters, 3.00 a.m (66.33 ± 46.40) in agricultural fields and 21:00 pm (40.6 ± 30.06) in thickets of A. seyal. This species was not attracted to the different species of rodents in trials carried out in March and April 2013. RLB PCR identified 7 human (28%), 9 mixed (human and cattle) (36%) and 2 cattle (8%) blood meals while 7 were unknown (28%). Conclusion Female P. orientalis can bite humans in extra-domestic habitats of Kafta-Humera lowlands at any hour of the night with peak biting after midnight. [ABSTRACT FROM AUTHOR]

Anatolia has been an important region for civilizations and agricultural revolution as a major domestication centre for livestock species. Goats ( Capra hircus) were among the earliest domesticated animals in this region. In this study, genetic diversity of Anatolian goat breeds was characterized by comparison of mitochondrial DNA hypervariable region 1. A total of 295 individuals, including 99 Anatolian Black goats, 96 Angora goats and 100 Kilis goats, were used. Haplogroup A was found to be the dominant haplogroup in all three breeds. The highest haplogroup diversity, including haplogroups A, B2, C and G, was observed in the Anatolian Black breed. Haplogroup D was only observed in Kilis and Angora goats. Haplogroup G was found in Angora and Anatolian Black breeds. The Anatolian goat breeds had high genetic diversity values and a weak phylogeographical structure. The nucleotide diversity values were found to be higher than those in previously studied goat breeds. The fact that Anatolia is a domestication centre and its geographical position as a junction of trade routes may have caused the higher genetic diversity of Anatolian goat breeds. [ABSTRACT FROM AUTHOR]

More than 1000 complete or near-complete mitochondrial DNA (mt DNA) sequences have been deposited in GenBank for eight common domestic animals (cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives, as well. Nevertheless, few efforts have been performed to evaluate the sequence data quality. Herein, we conducted a phylogenetic survey of these complete or near-complete mt DNA sequences based on mt DNA haplogroup trees for the eight animals. We show that errors due to artificial recombination, surplus of mutations and phantom mutations do exist in 14.5% (194/1342) of mt DNA sequences and all of them should be treated with wide caution. We propose some caveats for future mt DNA studies of domestic animals. [ABSTRACT FROM AUTHOR]

The yak is one of the few animals that can thrive in the harsh environment of the Qinghai-Tibetan Plateau and adjacent Alpine regions. Yak provides essential resources allowing Tibetans to live at high altitudes. However, genetic variation within and between wild and domestic yak remain unknown. Here, we present a genome-wide study of the genetic variation within and between wild and domestic yak. Using next-generation sequencing technology, we resequenced three wild and three domestic yak with a mean of fivefold coverage using our published domestic yak genome as a reference. We identified a total of 8.38 million SNPs (7.14 million novel), 383 241 InDels and 126 352 structural variants between the six yak. We observed higher linkage disequilibrium in domestic yak than in wild yak and a modest but distinct genetic divergence between these two groups. We further identified more than a thousand of potential selected regions ( PSRs) for the three domestic yak by scanning the whole genome. These genomic resources can be further used to study genetic diversity and select superior breeds of yak and other bovid species. [ABSTRACT FROM AUTHOR]

In contrast to other farm animals, the matrilineal structure of domestic goose has remained an open question. In this study, we analyzed mitochondrial DNA control region sequence variation of 245 domestic geese to discern the main matrilineal components and their phylogeneticrelationships. The result of phylogeneticanalysis indicated the distinct lineage of clade II and the result of network analysis further suggested the major group of Chinese native goose breeds (subclade S) and introgressive goose breeds (subclade G). Except Yili geese, all Chinese domestic goose breeds were clustered in S, whereas clade II were widely distributed in 2 European breeds, Yili geese as well as 3 domesticGraylag geese. The results support that Chinese domesticgoose breeds (except the Yili breed) originated from Swan goose (Anser cygnoides) while European goose breeds originated from Graylag goose (Anser anser). In total, 17 Landoise and 16 White Roman geese were clustered in subclade G together with 1 domestic goose (A. anser, AY112966), which supported the previous finding that European geese originated from Graylag goose (A. anser). But 9 unanticipated samples of two Chinese domestic goose breeds including 7 Lion-head geese and 1 ZhedongWhite goose in haplotype H9 were also clustered in subclade G as well as 3 Lion-head geese in haplotypes H13, H15 and H16 and 2 Zhedong White geese in haplotypes H18 and H19, which may be caused by the potential gene introgressions between swan goose breeds and graylag breeds with a directional contribution towards graylag geese. [ABSTRACT FROM AUTHOR]

The Albanian National Action Plan for FANGR considers the ex-situ conservation of local/native animal breeds as one of the main priorities. The law "On Livestock Breeding" serves as a legal base to implement actions that are foreseen in the National Action Plan. It provides the implementation and establishment of the genebank for cryoconservation and/or ex-situ in vivo conservation of local breeds at risk of extinction. Meanwhile it should be noted that, the Albanian legislation does not cover issues related to property rights and use of the materials that are stored in the Cryobank and ex-situ in vivo Genebank. Yet, they are treated and considered as a public asset. The establishment and the administration of the Cryobank and ex-situ in vivo Conservation bank, are defined as a public institutions right/duty. The Albanian legislation lacks the necessary legal framework in order to regulate the relations between stakeholders and other actors, also misses the specific legal framework in order to develop the transboundary and/or regional issues regarding the exchange of genetic material. The legal and regulatory framework concerning the entirety of the storage conditions and documentations (storage facilities and rules, data management and documentations, genebank security, special sanitary arrangement and legal issues related to the genetic material and data, ownership and IP, collecting new materials and access to genebank) should be developed. Given the lack of necessary infrastructure and human capacities to enable collection, management and administration of semen, oocytes and embryos, the establishment of the Genetic Bank for somatic cells conservation should be a priority. Drafting of the necessary legal framework for the establishment of somatic cells genebank, its management, ownership rights and veterinary rules that should be implemented during collection, handling and storage of biologic materials, has to be elaborated, as an important part of the legal framework. [ABSTRACT FROM AUTHOR]

Studies aiming the identification of DNA variations are one of the most important research areas in farm animal genetics. New techniques are being developed for the determination of DNA variations and especially genome-wide studies to understand the biology of quantitative characters in farm animals are gaining momentum. Copy Number Variations (CNV) are studied widely and associated with various characters that are economically important. This review is intended to explain the importance of copy number variation (CNV) in cattle and to provide information on the determination methods of CNVs in cattle genome. [ABSTRACT FROM AUTHOR]

Highlights: [•] Coat colour variability unlikely to be a pleiotropic effect of selection for tameness. [•] Coat colour variation appeared soon after domestication. [•] Selection for novelty led to proliferation of coat colour genetic variability. [Copyright &y& Elsevier]

Our aim was to identify elements useful in designing policies and programmes for conservation of farm animal genetic resources, taking as case study a group of European local cattle breeds. We first investigated the implications of differences among countries in the policies and programmes to be developed. Secondly, we analysed key elements common to countries, which may affect local breed viability. We used the herd size trend expected by the farmer in the near future as an indicator of breed viability. Fifteen breeds, for a total of 355 farms, were surveyed. To take into account the multiple factors influencing breeds' demographic trends, the questionnaire included economical, technical and social aspects. Among the major differences across countries was the perception of the farmer on the value attributed to the local breed by society. Concerning the elements common to countries and their association to breed viability, the greater the collaboration among farmers and the stakeholders' appreciation as perceived by the farmer, the greater the viability of the farm. An opposite trend was observed for the age of the farmer. Older farmers generally planned to soon cease farming or decrease herd size, whereas young farmers planned to increase the size of their herds. Implications of including these elements in conservation polices are discussed. [ABSTRACT FROM AUTHOR]

General pedigrees are very common in farm animals, and the recent availability of large panels of SNPs in domestic species has given new momentum to the search for the mutations underlying variation in quantitative traits. In this paper, we proposed a new transmission disequilibrium test approach, called the pedigree transmission disequilibrium test, which deals with general pedigrees and quantitative traits in farm animals. Compared with the existing pedigree disequilibrium test (PDT) and general linear model-based method QTDT, our approach performed better with higher power and lower type I error, especially in scenarios where the quantitative trait locus (QTL) effect was small. We also investigated the application of our approach in selective genotyping design. Our simulation studies indicated that it was plausible to implement a selective genotyping strategy in the proposed pedigree transmission disequilibrium test. We found that our approach performed equally well or better when only some proportion of the individuals in the two tails were genotyped compared with its performance when all the individuals in the pedigree were genotyped. [ABSTRACT FROM AUTHOR]

Copy number variation ( CNV) might be one of the main contributors to phenotypic diversity and evolutionary adaptation in animals and plants, employing a wide variety of mechanisms, such as gene dosage and transcript structure alterations, to modulate organismal plasticity. In the past 4 years, considerable advances have been made in the characterization of the genomic architecture of CNV in domestic species. First, low-resolution CNV maps were produced for cattle, goat, sheep, pig, dog, chicken, duck and turkey, showing that these structural polymorphisms comprise a significant part of these genomes. Furthermore, CNVs have been associated with several pigmentation (white coat in horse, pig and sheep) and morphological (late feathering and pea comb in chicken) traits, as well as with susceptibility to a wide array of diseases and developmental disorders, for example osteopetrosis, anhidrotic ectodermal dysplasia, copper toxicosis, intersexuality, cone degeneration, periodic fever and dermoid sinus, among others. In the future, development of high-resolution tools for CNV detection and typing combined with the implementation of databases integrating CNV, QTL and gene expression data will be essential to identify and measure the impact of this source of structural variation on the many phenotypes that are relevant to animal breeders and veterinary practitioners. [ABSTRACT FROM AUTHOR]

Bio-techniques such as genetic manipulation, marker-assisted selection, and identity test have largely facilitated the modern animal production practices. In the present study, we established a reliable and cost-effective molecular method of species identification for common farm animals. We first (re-)analyzed 179 mitochondrial 12S rRNA gene sequences of ten farm animal species to determine the intra-species and species-specific variations. The PCR-RFLP method was subsequently designed to identify these species by using endonucleases BshNI, ScaI, AluI, and BfaI. The poultry and livestock species were first discriminated by one double-digestion of both BshNI and ScaI, which generated different fragment patterns (325 bp and 115 bp for poultry vs. 364 bp and 76 bp for livestock). The ten species could be further discerned according to species-specific restriction pattern by subjecting to digestion of AluI and BfaI, respectively. Our approach would be more reliable by taking the intra-species variations into consideration and could be applied to species identity test, commercial fraud, and wildlife crime. [ABSTRACT FROM PUBLISHER]

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Global mitochondrial DNA (mtDNA) data indicates that the dog originates from domestication of wolf in Asia South of Yangtze River (ASY), with minor genetic contributions from dog-wolf hybridisation elsewhere. Archaeological data and autosomal single nucleotide polymorphism data have instead suggested that dogs originate from Europe and/or South West Asia but, because these datasets lack data from ASY, evidence pointing to ASY may have been overlooked. Analyses of additional markers for global datasets, including ASY, are therefore necessary to test if mtDNA phylogeography reflects the actual dog history and not merely stochastic events or selection. Here, we analyse 14 437 bp of Y-chromosome DNA sequence in 151 dogs sampled worldwide. We found 28 haplotypes distributed in five haplogroups. Two haplogroups were universally shared and included three haplotypes carried by 46% of all dogs, but two other haplogroups were primarily restricted to East Asia. Highest genetic diversity and virtually complete phylogenetic coverage was found within ASY. The 151 dogs were estimated to originate from 13-24 wolf founders, but there was no indication of post-domestication dog-wolf hybridisations. Thus, Y-chromosome and mtDNA data give strikingly similar pictures of dog phylogeography, most importantly that roughly 50% of the gene pools are shared universally but only ASY has nearly the full range of genetic diversity, such that the gene pools in all other regions may derive from ASY. This corroborates that ASY was the principal, and possibly sole region of wolf domestication, that a large number of wolves were domesticated, and that subsequent dog-wolf hybridisation contributed modestly to the dog gene pool. [ABSTRACT FROM AUTHOR]

The management of domestic animal genetic resources is a topic of pressing concern given developing trends such as the liberalization of genetic resources markets, the increasing number of patents and intellectual property rights and the withdrawal of governments from the organization and control of breeding activities. Managing territorialized common goods of this nature calls for cooperative mechanisms involving a wider range of actors than so far. How to steer these mechanisms and handle crises in cooperation that can impede them, is crucial to maintaining biodiversity. This article proposes an analytical framework to analyze and facilitate cooperation in distributed breeding organizations. This framework is the result of an intervention research into breeding organizations for three local breeds of milk sheep in the Western-Pyrenees. By investigating the design and uses of scientific, technical and management instruments on which breeding activities and organization rely, we identified three dimensions to be considered in the analysis of cooperation for animal resources management: a) tensions between the design and uses of scientific instruments for genetic gain achievement; b) tensions between the evaluation of animals using scientific instruments and the evaluation of animals based on breeder know-how in qualifying animal common resources; c) diversity of farmer strategies and functioning of the market for breeding goods and services resulting from the activities conducted in the two previous dimensions (production of genetic gain, qualification of the common resources). [ABSTRACT FROM AUTHOR]

The standard view of modern human infectious diseases is that many of them arose during the Neolithic when animals were first domesticated, or afterwards. Here we review recent genetic and molecular clock estimates that point to a much older Paleolithic origin (2.5 million years ago to 10,000 years ago) of some of these diseases. During part of this ancient period our early human ancestors were still isolated in Africa. We also discuss the need for investigations of the origin of these diseases in African primates and other animals that have been the original source of many neglected tropical diseases. [ABSTRACT FROM AUTHOR]

The article reports on advances in canine genetic testing and also presents a chart giving information on disease, causative gene and breeds affected based on data from testing laboratories in the U.S. Single gene mutations have been identified as the cause of most of these diseases. Most of the causative genes identified are inherited in an autosomal recessive manner.

China is particularly rich in goose genetic resources. Systematic study of the genetic diversity and origin of Chinese domestic geese will provide an important scientific basis for the conservation and utilization of these resources and for human history. The 521-bp control region (D-loop) of mitochondrial DNA from 26 goose breeds and 6 Landaise geese were sequenced. The results showed that the average haplotype diversity and nucleotide diversity of Chinese domestic geese were 0.1384 and 0.00029, respectively. Shared haplotype analysis and systematic evolution analysis revealed that Chinese domestic geese had 2 maternal origins. The Yili goose breed originated from the Greylag goose (Anser anser), and the other 25 domestic goose breeds originated from the swan goose (Anser cygnoides). An interesting finding was that 1 Linxian white goose and 1 Wanxi white goose shared the same H4 haplotype with the Rhine goose and the Landaise goose, which originated from the Greylag goose (A. anser). Further research on this finding is planned. [ABSTRACT FROM AUTHOR]

Siberian chipmunks, Tamias sibiricus, are one of several popular companion animals found in the pet shops of South Korea. At present, however, there have been no studies done in South Korea examining their origin even though they could be potential carriers of zoonotic diseases, and are a species of concern for efficient conservation and management strategies. Sequences of the mitochondrial cytochrome b gene (1140 bp) were determined to investigate the origin of Siberian chipmunks sold in four South Korean pet shops through comparison with sequence data from animals of known locality. Nine Siberian chipmunks were collected from pet shops in South Korea, which resulted in nine haplotypes. One (AR) of these coincided with the haplotype previously described. Phylogenetic and network analyses using 53 haplotypes including 45 haplotypes from GenBank showed three phylogenetic groups in South Korea, almost concordant to locality, designated as northern, central, and southern parts as described in a previous study. Of the nine individuals examined from the pet shops, eight were clustered into the northern phylogroup but one (cgrb9153) was grouped with the southern phylogroup, implying that at least the Siberian chipmunks examined in this study did not originate from other countries. It is likely that most individuals sold in the pet shops of Seoul were caught in the wild in Gyeonggi-do and Gangwon-do, or are maternal descendants of captive-bred individuals originating from the northern part of South Korea. It is recommended that conservation and management units of Korean chipmunks should be examined in further detail. [ABSTRACT FROM AUTHOR]

Recently developed Bayesian genotypic clustering methods for analysing genetic data offer a powerful tool to evaluate the genetic structure of domestic farm animal breeds. The unit of study with these approaches is the individual instead of the population. We aimed to empirically evaluate various individual-based population genetic statistical methods for characterization of genetic diversity and structure of livestock breeds. Eighteen British pig populations, comprising 819 individuals, were genotyped at 46 microsatellite markers. Three Bayesian genotypic clustering approaches, principle component analysis (PCA) and phylogenetic reconstruction were applied to individual multilocus genotypes to infer the genetic structure and diversity of the British pig breeds. Comparisons of the three Bayesian genotypic clustering methods (, BAPS and STRUCTURAMA) revealed some broad similarities but also some notable differences. Overall, the methods agreed that majority of the British pig breeds are independent genetic units with little evidence of admixture. The three Bayesian genotypic clustering methods provided complementary, biologically credible clustering solutions but at different levels of resolution. BAPS detected finer genetic differentiation and in some cases, populations within breeds. Consequently, it estimated a greater number of underlying genetic populations (K, in the notation of Bayesian clustering methods). Two of the Bayesian methods (STRUCTURE and BAPS) and phylogenetic reconstruction provided similar success in assignment of individuals, supporting the use of these methods for breed assignment. [ABSTRACT FROM AUTHOR]

Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication. [ABSTRACT FROM AUTHOR]

Until recently, the construction of a reference genome was performed using Sanger sequencing alone. The emergence of next-generation sequencing platforms now means reference genomes may incorporate sequence data generated from a range of sequencing platforms, each of which have different read length, systematic biases and mate-pair characteristics. The objective of this review is to inform the mammalian genomics community about the experimental strategy being pursued by the International Sheep Genomics Consortium (ISGC) to construct the draft reference genome of sheep ( Ovis aries). Component activities such as data generation, sequence assembly and annotation are described, along with information concerning the key researchers performing the work. This aims to foster future participation from across the research community through the coordinated activities of the consortium. The review also serves as a ‘marker paper’ by providing information concerning the pre-publication release of the reference genome. This ensures the ISGC adheres to the framework for data sharing established at the recent Toronto International Data Release Workshop and provides guidelines for data users. [ABSTRACT FROM AUTHOR]

We recently showed that genes at 3 loci account for the majority of variation in canine fur. Allelic variation at genes controlling length of fur, texture, and curl is responsible for the striking phenotypic variety observed among purebred dogs in the United States today. In this paper, we investigate the phenomenon of “improper coat” (IC) or a coat that is not typical of the breed. IC is occasionally observed among specific breeds, such as the Portuguese Water Dog (PWD), and is characterized by short hair on the head, face, and lower legs, rather than a thick and even coat covering the whole body. The IC is reminiscent of that observed on the curly or flat-coated retriever, thus making such dogs unable to compete effectively in conformation events. We have found that the presence of the wild-type allele, rather than the expected variant allele at the R-spondin 2 (RSPO2) gene, accounts for this phenotype. The development of a genetic test that distinguishes these 2 allelic types would allow breeders to easily avoid producing PWD with ICs. [ABSTRACT FROM PUBLISHER]