European Breeds Research Articles

Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent

Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1–13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.

Whole-genome resequencing reveals the genomic diversity and signatures of selection in Romanov sheep.

Romanov sheep are adapted to the extremely cold and harsh environment and display a distinctive grey color. Herein, we analyzed the population structure, genetic diversity, and selection signatures of Romanov sheep based on whole-genome sequencing data of 17 Romanov sheep, 114 individuals from other 10 European breeds. The results of PCA, ADMIXTURE, and NJ-tree showed that the Romanov sheep was closely related to other northern European breeds. A relative high level of genetic diversity, low inbreeding coefficient, and large effective population size was observed in Romanov sheep when compared with other European breeds. We then screened the genomic selection signatures of Romanov sheep using FST, XP-XLP, and XP-EHH methods. The most significant region under selection (CHR14:14.2 to 14.3 Mb) harbored a haplotype that contained MC1R gene. Furthermore, this haplotype was also found in other grey-body breeds including Gotland sheep, Grey Tronder Sheep, and German grey heath sheep, suggesting that it was associated with the unique coat color of these breeds. We also found one region (CHR10:40.8Mb- 41.0Mb) harboring PCDH9 gene which was potentially associated with cold environmental adaptation. In summary, this study identified candidate genes that were associated with the unique grey color and environmental adaptation in Romanov sheep, which provided a basis for understanding the genetic background and utilization of this breed.

Effects of dairy cow temperament on milk yield: a systematic review and meta-analysis.

The temperament of dairy cows interferes in milk yield and quality, but there is a lack of consensus throughout the literature. Thus, systematic review (SR) and meta-analysis (MA) methodologies were used to assess the effects of dairy cow temperament on milk yield. Our literature search included four electronic databases (CABI Abstracts, Web of Science, PubMed, and Scopus) and bibliographies of the publications included on MA. As inclusion criteria, we considered publications about the temperament of lactating cows and its effect on daily milk yield and total milk yield (whole lactation). A random effect-MA was carried out separately for daily milk yield and total milk yield related to each class of cows' temperament, 'low' (low reactivity, calm animals), 'intermediate' (intermediate reactivity), and 'high' (high reactivity, reactive animals). A total of eight publications reporting 75 trials were included in the analyses for daily milk yield, and three publications reporting nine trials for total milk yield. For daily and total milk yield the heterogeneity between publications was high (I2 = 99.9%). Cows of European breeds with intermediate temperament produced less milk daily than the calm (P = 0.020) and reactive ones (P < 0.001). In the case of primiparous cows, those with intermediate temperament produced less milk daily (P < 0.001) than the reactive ones, while for multiparous, the intermediate produced less than calm (P = 0.032) and reactive cows (P < 0.001). Regarding the stage of lactation, cows evaluated throughout lactation with a calm temperament tended (P = 0.081) to produce more milk than the intermediate ones, but less than the reactive ones (P < 0.001). For total milk yield, reactive cows tended to produce more than the calm (P = 0.082) and intermediate (P = 0.001) ones. Among European and primiparous cows, reactive cows produced more than the intermediate (P = 0.001). According to our results, we cannot confirm what we expected, that calmer cows would be the most productive for both daily and total yield.

Infestação natural por carrapatos como causa de morte em bovinos de corte

ABSTRACT: Although infestation by Rhipicephalus microplus is mentioned as the cause of death among cattle, there are only studies with artificial infestations in which intense parasitism led to the death of cattle due to severe anemia. This study seems to be the first to describe the epidemiology, clinical-pathological condition, and diagnostic conduct of infestation by R. microplus as the cause of death of European breed calves introduced in shady, enclosed pastures in regions with rainfall prior to the onset of the outbreak. The affected calves presented apathy, anorexia, and anemia and were severely infested by R. microplus. The lethality rate of the outbreak was 36.5%. After the rainy period, the dry season facilitated a decrease in the nutritional status of the affected cattle. The delay in the definitive diagnosis contributed to the economic loss of the farm due to the cost of erroneous treatments and the number of dead cattle. The main factors that contributed to the deaths were climatic, environmental, and individual. This study demonstrates that severe infestations by R. microplus in low-quality pasture-raised calves are fatal and emphasizes the importance of diagnostic tools to reduce the economic loss caused by death due to infestation by ticks.

Prevalence of feline cardiomyopathy phenotypes and arterial thromboembolism

The aim: To investigate the prevalence of cardiomyopathy (CMP) phenotypes and the weight of cardiogenic arterial thromboembolism (ATE) as a complication in cats. To determine the influence of age, breed and sex on the frequency of detection of CMP and ATE. Animals: One hundred and seventeen cats with various phenotypes of cardiomyopathies.&#x0D; Materials and methods: the database of the veterinary center was analyzed. From 1066 studied cats, 117 stories of animal diseases were selected, in which the diagnosis of cardiomyopathy was established.&#x0D; Results: In the experimental group, the prevalence of CMP was 11 % (HCMP - 94 %; DCMP - 3.4 %; RCMP - 2.6 %). Males were affected more often and had a more severe course. As the age of the animals increased, the relative frequency of heart failure increased slightly, but CMP was diagnosed more often in young animals. The Scottish Straight, Scottish Fold, European Shorthaired, European Longhaired, British Longhaired, and Canadian Sphynx can be considered susceptible breeds in Vinnytsia. There have been no cases of cardiomyopathy in Maine Coons. 57 % of cats with HCMP phenotype were asymptomatic. Arterial thromboembolism occurred in 14.5 % of animals with various CMP phenotypes. The lethality of ATE before discharge was 17.6 %, euthanized (different time period after the incident) 29 %.&#x0D; Conclusion: HCMP phenotype is the most common. Probably, genetic factors related to sex and breed have a significant influence on the development of cardiomyopathy. More often, CMP phenotypes were diagnosed in younger animals. Heart failure develops more often in older animals. The number of animals with ATE and HCMP phenotype is high, but relative to the number of animals with heart failure, cats with DCMP were more prone. ATE occurred more often in females. Thromboembolism is more common in the European Longhair breed.

Reconstruction of the origin of the ukrainian population of vietnamese pigs

Pigs of the Vietnamese breed, which were imported from Vietnam to the countries of Eastern Europe and Canada, have a high percentage of muscle mass, so the improvement of this breed is currently ongoing and active breeding work is being conducted in many countries, in particular in Ukraine. These animals are precocious, have high immunity, sows have high milk productivity, well-developed maternal instinct. These animals belong to the bacon line of the production. The body is wide, stout, the chest is wide. Up to 50 % roughage can be included in the fattening ration (taking into account the breed specifics of the digestive system). This breed adapts well to both hot and humid climates. In Ukraine, this breed appeared thanks to the Transcarpathian entrepreneur M. N. Popovych In 2004, the Vietnamese breed of pigs conquered all the western and central regions of Ukraine, and in 2005, young animals began to be sold in the eastern regions of Ukraine. Two breeds called Vietnamese are grown on the territory of Ukraine: actually Vietnamese and Korean. These breeds have differences in phenotype. Aim. Solving the question of the origin of the Vietnamese breed of pigs in Ukraine by using mtDNA polymorphism. Methods. To identify the origin of the genome of the Vietnamese breed of pigs, the method of determining the mitochondrial DNA is used, which allows to study the origin of the ancestral maternal form and thus to solve its origin. The methods used for the study involved the use of mitochondrial DNA polymorphism in the maternal line of the Vietnamese pig population in Ukraine. For the study, blood samples were taken from 4 boars and 6 gilts of the Vietnamese breed in a private farm in the village Takhtaulove, Poltava district. DNA isolation was performed using Chelex 100 ion exchange resin. DNA amplification was performed using Thermo Fisher Scientific reagents according to the manufacturer's conditions. The results. A study of 29 aboriginal Chinese, European breeds and subspecies of wild boar identified a distinct difference in the mtDNA of Asian and European pig breeds. Phylogenetic studies of relationships among domestic Euro-American, Asian breeds and wild boar populations also revealed a clear division of mitochondrial haplotypes into Asian and European ones. Using this approach, it is possible to determine 10 European and 8 Asian mitochondrial haplotypes. Conclusions. Mitochondrial haplotypes A and C belonging to the European group have been identified among Vietnamese pigs. A contribution to the creation of the Ukrainian population of Vietnamese pigs may have been made by sows of the Durok, Mangalitsa or Hampshire breeds. Key words: pigs, Vietnamese breed, polymorphism, mitochondrial DNA, haplotypes, phenotypic difference, origin, genome, population, genetic variability

Haplogroup of the modern lines of hybrid pigs

The aim. The study was conducted to characterize the genetic diversity of hybrid pigs (Large White×Landrace)×Maxgro in Ukraine. Method. DNA isolation was performed from bristle samples using Chelex-100 ion exchange resin and epithelial tissue from the ear of pigs by the sorbent method. The results. The results of DNA typing of hybrid pigs (Large White×Landrace)×Maxgro from LLC "Hlobynskyi Svynocomplex" are presented. Using PCR-RFLP analysis of the polymorphism of the D-loop section, 7 mitochondrial haplotypes were determined – N, C, O, G, D, E, K. In the studied sample of pigs (n=50), the concentration of haplotypes as a percentage is determined. It was found that mitochondrial haplotypes C (24 %) were found to be characteristic of Landrace pigs, Hampshire, Wales, a wild pig (Ukraine, Poland, France); haplotype O (12%) – inherent in a wild pig and Landrace breed (Sweden); haplotype G (12 %) – peculiar to Wales breed, a wild pig (Italy, France); haplotype N (28%) is characteristic of the Large White breed of pigs, representatives are carriers of the Asian type. It is worth noting that the Asian haplotype N is characteristic of the Asian wild pig and Berkshire breed. The presented data on the hybridization of mitochondrial genomes of Asian and European origin are the basis for the creation of modern lines of hybrid pigs along the maternal line. Haplotype N refers to haplogroup A(D), and haplotypes C, O, G belong to haplogroup E. It is completely uncertain that haplotypes D (10 %), E (6 %), K (8 %) belong to haplogroup A(D). According to the results obtained, haplogroup E in hybrid pigs is dominant, however, it is haplogroup A that is the predecessor of haplogroup E. We assume opinions that pigs of the Large White breed with haplotype N, D, E, K – contain aboriginal genetic resources. Pigs with haplotype D, E, K – are the result of hybridization with European wild boars. Over time, this led to the almost complete disappearance of the primary Middle Eastern ancestors in the nuclear genomes of European domesticated pigs. The speculation that traditional seasonal cattle breeding, annual long-distance migrations that have occurred in the past, and commercial trade in nucleuses explain the observatory pattern of favorable gene flow among hybrid pigs. Conclusions. The results obtained during the study of the mitochondrial genome of hybrid pigs improved the understanding of matrilineal origin and phylogeographic model of distribution of genetic diversity of cross-border pig breeds (Large White×Landrace)×Maxgro in Ukraine. We came to the conclusion that natural selection acts very weakly on the single nucleotide polymorphism that led to the formation of the haplogroup of cross-border breeds of pigs that are found today. The obtained results of the study are evidence that European pig breeds consist of pigs with Asian and non-Asian mitochondria, some of which were formed from closely related maternal ancestors. The work was carried out with the support of the National Academy of Agrarian Sciences of Ukraine 31.01.00.07.F. "To study the pleiotropic effect of genes whose SNPs are used in markerassociated selection of pigs." SR No. 0121U109838. Key words: hybrid pigs, (Large White×Landrace)×Maxgro, mtDNA, D-loop, haplotype, haplogroup, PCR-PDRF.

Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.

Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.

Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms

Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from −0.04 to 0.16 in Sumava and from −0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.

Mitochondrial DNAD-loop hyper-variable region 1 variability in Kurdish horse breed.

Kurdish horse is one of the most valuable horse genetic resources in the Middle East. To assess the genetic diversity of Kurdish horses, Mitochondrial DNA D-loop hyper-variable region1 (HVR1) was sequenced in 29 non-related Kurdish horses which were sampled from diverse geographic regions of Iran. Total DNA was extracted from the collected blood samples by modified salting out method. The HVR1 was amplified by PCR and then sequenced using ABI PRISM BigDyeTM Terminator Cycle Sequencing Ready Reaction Kit. Consequently, the sequences were trimmed to 294bp using BIOEDIT to become comparable with other reported HVR1 sequences in GeneBank. Sequence alignment was performed using CLUSTALW package. Haplotype and nucleotide diversity were estimated using DNASP5.10 and phylogenetic tree was constructed by neighbour joining method. Fourteen different haplotypes and 22 polymorphic sites were detected. Haplotype diversity, nucleotide diversity and Tajima D values were 0.901 ± 0.001, 0.01153 ± 0.0020 and -1.378, respectively. Kurdish horse showed a high haplotype and low nucleotide diversity. The compositional frequency of consensus sequences for base A was the highest (29.93%) compared to other three nucleotides (C = 28.91%, T = 26.53% and G = 14.63%). As expected, all of the detected Kurdish horse haplotypes belonged to haplogroup K (i.e., Kurdish horses). According to the phylogenetic analysis, Kurdish horses were genetically more closely related to Tibetan, Chinese, Bulgarian and Iranian native horse breeds, compared to other Asian horse breeds, but some traces of European horse breeds were detected in their maternal lines.

The ancestral origin of the critically endangered Quadricorna sheep as revealed by genome-wide analysis.

Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds’ biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Among primitive breeds, aside from sharing common ancestral genomic components, they also show several traits such as the policeraty, large horns in the ram, short tail, and a moulting fleece, considered as ancestral. Although most of the primitive breeds characterized by these traits are confined on the very edge of Northern Europe, several residual populations are also scattered in the Mediterranean region. In fact, although in Italy a large number of local breeds are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterized by several ancestral traits. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 33 primitive traits-related, Mediterranean and Middle-East breeds, with the specific aim to reconstruct its origin. After retaining 35,680 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds’ distances and by the maximum likelihood tree as implemented in treemix. Multiple convergent evidence from all our population genetics analyses, indicated that the two Quadricorna populations differ from all the other Italian breeds, while they resulted to be very close to the Middle Eastern and primitive European breeds. In addition, the genetic diversity indices highlighted values comparable with those of most of the other analyzed breeds, despite the two populations exhibit slightly different genetic indices suggesting different levels of genomic inbreeding and drift (FIS and FROH). The admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of the two populations, while on the other hand the treemix analysis seems to suggest an ancient admixture with other primitive European breeds. Finally, all these evidences seem to trace back the residual Quadricorna sheep to an early Neolithic spread, probably following a Mediterranean route and that urgent conservation actions are needed in order to keep the breed and all related cultural products alive.

Lost pigs of Angola: Whole genome sequencing reveals unique regions of selection with emphasis on metabolism and feed efficiency.

Angola, in the western coast of Africa, has been through dramatic social events that have led to the near-disappearance of native swine populations, and the recent introduction of European exotic breeds has also contributed to the erosion of this native swine repertoire. In an effort to investigate the genetic basis of native pigs in Angola (ANG) we have generated whole genomes from animals of a remote local pig population in Huambo province, which we have compared with 78 genomes of European and Asian pig breeds as well as European and Asian wild boars that are currently in public domain. Analyses of population structure showed that ANG pigs grouped within the European cluster and were clearly separated from Asian pig breeds. Pairwise F ST ranged from 0.14 to 0.26, ANG pigs display lower levels of genetic differentiation towards European breeds. Finally, we have identified candidate regions for selection using a complementary approach based on various methods. All results suggest that selection towards feed efficiency and metabolism has occurred. Moreover, all analysis identified CDKAL1 gene, which is related with insulin and cholesterol metabolism, as a candidate gene overlapping signatures of selection unique to ANG pigs. This study presents the first assessment of the genetic relationship between ANG pigs and other world breeds and uncovers selection signatures that may indicate adaptation features unique to this important genetic resource.

Inbreeding and pedigree analysis of the European red dairy cattle

BackgroundRed dairy cattle breeds have an important role in the European dairy sector because of their functional characteristics and good health. Extensive pedigree information is available for these breeds and provides a unique opportunity to examine their population structure, such as effective population size, depth of the pedigree, and effective number of founders and ancestors, and inbreeding levels. Animals with the highest genetic contributions were identified. Pedigree data included 9,073,403 animals that were born between 1900 and 2019 from Denmark, Finland, Germany, Latvia, Lithuania, the Netherlands, Norway, Poland, and Sweden, and covered 32 breeds. The numerically largest breeds were Red Dairy Cattle and Meuse-Rhine-Yssel.ResultsThe deepest average complete generation equivalent (9.39) was found for Red Dairy Cattle in 2017. Mean pedigree completeness ranged from 0.6 for Finncattle to 7.51 for Red Dairy Cattle. An effective population size of 166 animals was estimated for the total pedigree and ranged from 35 (Rotes Höhenvieh) to 226 (Red Dairy Cattle). Average generation intervals were between 5 and 7 years. The mean inbreeding coefficient for animals born between 1960 and 2018 was 1.5%, with the highest inbreeding coefficients observed for Traditional Angler (4.2%) and Rotes Höhenvieh (4.1%). The most influential animal was a Dutch Meuse-Rhine-Yssel bull born in 1960. The mean inbreeding level for animals born between 2016 and 2018 was 2% and highest for the Meuse-Rhine-Yssel (4.64%) and Rotes Hohenvieh breeds (3.80%).ConclusionsWe provide the first detailed analysis of the genetic diversity and inbreeding levels of the European red dairy cattle breeds. Rotes Höhenvieh and Traditional Angler have high inbreeding levels and are either close to or below the minimal recommended effective population size, thus it is necessary to implement tools to monitor the selection process in order to control inbreeding in these breeds. Red Dairy Cattle, Vorderwälder, Swedish Polled and Hinterwälder hold more genetic diversity. Regarding the Meuse-Rhine-Yssel breed, given its decreased population size, increased inbreeding and low effective population size, we recommend implementation of a breeding program to prevent further loss in its genetic diversity.

Phylogenetic Study of Philippine Pigs (Sus scrofa L.) from Ifugao and Kalinga Based on Mitochondrial DNA D-loop Analysis

Conservation genetic studies for Philippine pigs are essential to sustain global biodiversity. To study the phylogenetic relationship of Philippine pigs, 79 samples were collected from Ifugao (n = 41) and Kalinga (n = 38) provinces located in the Cordillera Administrative Region, northern Philippines. Mitochondrial DNA control region analysis was undertaken to investigate the phylogenetic relationship between the pig populations from the two provinces and other Asian and European pig breeds. Fourteen (14) haplotypes (H1–H14) were detected in the Ifugao and Kalinga samples. Several haplotypes – specifically, H1, H4, H9, H12, and H14 – formed an independent clade with the Type I Lanyu haplotypes, which are known to be unique in Taiwan pigs. The remaining haplotypes (H2, H3, H5–H8, H10, H11, and H13) clustered with the haplotypes of other Asian pig breeds within the major Asian clade. These results suggest the close relationship between Kalinga and Ifugao pigs and Type I Lanyu pigs. The existence of duplicate motifs also revealed that the native pigs from Ifugao and Kalinga belong to a distinct genetic lineage that clustered with other Philippine pig samples and separate from other Asian pigs, whereas the other samples may represent a recent introgression of modern lineages.

P469 Feline aspergillosis caused by Aspergillus candidus: A case report

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PMAspergillosis is an emerging mycosis that can occur in apparently healthy animals under environmental stress or immune-compromised condition. In cats, the clinical forms described are sinonasal, synoorbital, and, less frequently, invasive and disseminated forms.Feline aspergillosis is caused mainly by cryptic species of Aspergillus closely related to Aspergillus fumigatus. It is rare to recover species such as A. candidus, an endophytic fungus, opportunistic pathogen, and contaminant of cereals, nuts, and flour. It is described to cause allergic alveolitis or asthma, mycotoxicosis, and other related diseases. Mycelial fragments, inhaled spores, and substances such as terpenoids, flavones, and indoles in the lungs could be involved in the underlying pathogenesis.This presentation aims to describe a clinical case of feline pneumonia caused by A. candidus.Clinical caseWe present the clinical case of a common European breed feline of ∼ 7 years of age. The cat was rescued from the streets of an urban area in Buenos Aires and examined in April 2021. The feline suffered from mild hyperthermia, 39.4°C, had pale to slightly purple mucous membranes, cachexia, dehydration, dyspnea (abdominal respiration), tachycardia, and a large number of parasites. There were no nasal discharge, cough, or skin lesions. A hemogram with a blood biochemistry profile showed no significant alterations. Chest X-rays showed a pattern compatible with severe miliary pneumonia. A bronchoalveolar lavage (BAL) was performed for cytology and microbiological culture; direct examination showed nucleated superficial epithelial cells without atypia, few macrophages, no leukocytes, and gram-positive cocci, while ZN and mycological direct examination were negative. Treatment with doxycycline 10 mg/k every 12 h and dexamethasone was indicated. Flea treatment and control were conducted every 72 h. During the following consultations, the cat continued tachypnoeic and showed increased vesicular murmur with rales and cough. Corticosteroids (Fluticasone propionate 125 mg) were given every 12 h intranasal. Oral parasitization was performed due to the presence of Dipylidium caninum in feces. After 7 days of incubation, white cottony colonies phenotypically identified as Aspergillus grew on Sabouraud dextrose agar. Even though serum galactomannan GM (Platelia Aspergillus EIA BIORAD®) is useful as a biomarker in humans with OD >0.5 positive for invasive aspergillosis, it was used in this case and the result was OD 0.75. Antifungal treatment was started with itraconazole orally at 5 mg/kg/d. A mycobacterial culture was negative.The isolate was identified by partial sequencing of the calmodulin gene CaM as A. candidus.The feline showed a remarkable recovery. After 35 days from the start of the treatment, the final consultation showed a decrease in the pattern of military pneumonia through radiological images and an absence of any evident respiratory symptoms.ConclusionWe describe a fungal infection in a cat caused by an unusual species of Aspergillus. Moreover, this clinical case was proved to be pneumonia. Given this, it is important to consider this species as an emerging pathogen in cats.

Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle

BackgroundIn cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array.ResultsWe found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS.ConclusionsOur results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.

New Insight into the Genome-Wide Diversity and Admixture of Six Colombian Sheep Populations

Creole sheep represent a strategic genetic resource for populations living in marginal areas under financial restrictions on the American continent. Six Colombian sheep breeds (two wool (BCL-Boyacá and NCL-Nariño, 12 and 14 samples) and four hair (OPCE-Ethiopian, 54 samples; OPCS-Sudan, 74 samples; OPCP-Pelibeuy, 59 samples; OPCW-Wayúu, 24 samples) were genotyped using the Illumina Ovine SNP50 BeadChip. Data was also included from international 44 breeds from International Sheep Genomics Consortium (ISGC) and from data published in previous a previous work on the Caribbean and African breeds. Although geographically separated, wool (NCL, BCL) and hair types (OPCE, OPCS, OPCW) presented little genetic differentiation (FST 0.05) at a global level but several groups of animals separated suggesting local clustering due to geographical isolation. The OPCP underwent a recent crossing with Mexican Pelibuey, explaining its differentiation. Findings in this work such as the proximity to West African Djallonké (WAD) and Barbados Black Belly (BBB), suggest different introductions of African type animals from the Caribbean region on a pre-existing genetic basis formed by animals deriving from the first importations coming from Europe in colonial times. As expected, Colombian wool breeds showed, in particular in Admixture software results, a greater genomic component in common with European breeds and in particular with Iberian ones (Churra). This study provides a basis for future research into the genetic diversity within and between the Colombian sheep breeds analysed, and scientific data for policy decisions on Farm Animal Genetic Resources (FAnGR).

Evolutionary insights into porcine genomic structural variations based on a novel‐constructed dataset from 24 worldwide diverse populations

AbstractStructural variations (SVs) are important DNA polymorphisms that contribute to genetic diversity and evolution in humans, animals, and plants. In this study, we present a novel swine SV dataset of 79,919 deletions, 23,638 duplications, and 9333 inversions with average sequence depths of 24.1× from 24 varieties of worldwide pig populations, encompassing 305 individuals. Genotypes of SVs, particularly deletions, can accurately group individuals based on their population identity. We showed that exon‐covering deletions were subject to negative selection. Fixation index and differential allele frequency analysis identified highly differentiated SVs between European and Asian indigenous pigs, including deletions in NR6A1 and PLAG1, which are significantly associated with vertebrate numbers and growth performances, respectively. The growth‐enhancing allele at the deletion in PLAG1 was shared by European commercial pigs and Northern Chinese indigenous pigs including Laiwu and Min pigs, suggesting potential introgression from European commercial breeds into Chinese indigenous breeds. Moreover, we uncovered highly differentiated SVs in 139 genes between domesticated pigs and wild boars in Asia, temperature and altitude adaptation‐associated SVs in 41 genes, and population‐specific SVs in 718 genes. This study provides novel insights into the role of porcine SVs in domestication, environmental adaptation, and breed formation.

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.

Domestication and genetic characteristics of pig – a review

Pigs are one of the main types of livestock kept by humans because of their high reproductive system and the ability to survive in all kinds of conditions. Modern pigs have gone through a long history of domestication processes, ranging from migration, selection, adaptation, and other natural events. Important records of pig origins have divided the domestic pig population into two main groups namely Asian and European breeds. These two groups clearly separated about 58,000 years ago. In particular it is recorded that the European wild boar was domesticated around the 4th century BC. European pigs then got new genes since the introduction of the Asian pig which is thought to have occurred at the end of the 18th century. Domestication of pigs affects the genetic diversity of these animals which in turn will disrupt the availability of pig germplasm. However, the need for superior breeds with high productivity values will be indispensable given the increasing food supply for the community both in terms of food quality and quantity. This fulfilment is actually not just for a moment but in a very long and sustainable period, and the latter can only be fulfilled if the genetic resources of pigs are maintained through good gene conservation programs.Keywords: Pig, genetic diversity, domestication, livestock genetic conservation