Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Fungal Planet description sheets: 320-370

Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana malaysiana from Acacia mangium. Furthermore, Stachybotrys sansevieriicola is described from Sansevieria ehrenbergii (Tanzania), Phacidium grevilleae from Grevillea robusta (Uganda), Graphium jumulu from Adansonia gregorii and Ophiostoma eucalyptigena from Eucalyptus marginata (Australia), Pleurophoma ossicola from bone and Plectosphaerella populi from Populus nigra (Germany), Colletotrichum neosansevieriae from Sansevieria trifasciata, Elsinoë othonnae from Othonna quinquedentata and Zeloasperisporium cliviae (Zeloasperisporiaceae fam. nov.) from Clivia sp. (South Africa), Neodevriesia pakbiae, Phaeophleospora hymenocallidis and Phaeophleospora hymenocallidicola on leaves of a fern (Thailand), Melanconium elaeidicola from Elaeis guineensis (Indonesia), Hormonema viticola from Vitis vinifera (Canary Islands), Chlorophyllum pseudoglobossum from a grassland (India), Triadelphia disseminata from an immunocompromised patient (Saudi Arabia), Colletotrichum abscissum from Citrus (Brazil), Polyschema sclerotigenum and Phialemonium limoniforme from human patients (USA), Cadophora vitícola from Vitis vinifera (Spain), Entoloma flavovelutinum and Bolbitius aurantiorugosus from soil (Vietnam), Rhizopogon granuloflavus from soil (Cape Verde Islands), Tulasnella eremophila from Euphorbia officinarum subsp. echinus (Morocco), Verrucostoma martinicensis from Danaea elliptica (French West Indies), Metschnikowia colchici from Colchicum autumnale (Bulgaria), Thelebolus microcarpus from soil (Argentina) and Ceratocystis adelpha from Theobroma cacao (Ecuador). Myrmecridium iridis (Myrmecridiales ord. nov., Myrmecridiaceae fam. nov.) is also described from Iris sp. (The Netherlands). Novel genera include (Ascomycetes): Budhanggurabania from Cynodon dactylon (Australia), Soloacrosporiella, Xenocamarosporium, Neostrelitziana and Castanediella from Acacia mangium and Sabahriopsis from Eucalyptus brassiana (Malaysia), Readerielliopsis from basidiomata of Fuscoporia wahlbergii (French Guyana), Neoplatysporoides from Aloe ferox (Tanzania), Wojnowiciella, Chrysofolia and Neoeriomycopsis from Eucalyptus (Colombia), Neophaeomoniella from Eucalyptus globulus (USA), Pseudophaeomoniella from Olea europaea (Italy), Paraphaeomoniella from Encephalartos altensteinii, Aequabiliella, Celerioriella and Minutiella from Prunus (South Africa). Tephrocybella (Basidiomycetes) represents a novel genus from wood (Italy). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Perfil lipídico da membrana plasmática e alterações morfofuncionais de esperamatozóides de garanhões resistentes e sensíveis à criopreservação

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Carcinoma de células escamosas em assoalho vaginal de um bovino nelore associado a metástase em pulmão: relato de caso

The squamous cell carcinoma (SCC) is a neoplasm that affect pets and production animals and it’s very common in tropical countries like Brazil; develops in sparsely pigmented, stratified squamous epithelium and in mucosal surfaces exposed Ultraviolet action. The SCC is quite infiltrative but rarely causes metastases. Its occurrence in the female reproductive tract is recognized in the literature on cattle breeds from Europe. This case was a female bovine, Nelore, adult, who was referred to the "Hospital Veterinário Luiz Quintiliano de Oliveira" with dark brown fluid leakage and putrid odor, associated with ulcerative growth of the vagina. Because the extent of injury, the animal was euthanized and taken to the necropsy, which was observed on board structure, ulcerated and pus in the vaginal floor, infiltrated into the pelvic cavity to the serosa of the uterine body. The microscopic findings were detected neoplastic proliferation of epithelial cells in the floor and vaginal metastases in the lung parenchyma, and classified the primary tumor and metastasis as squamous cell carcinoma moderately differentiated.

Contagem de células somáticas para o diagnóstico da mastite subclínica ovina em diferentes raças em dois períodos de lactação

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Reatividade e tolerância ao calor de fêmeas ovinas de diferentes grupos genéticos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estrutura genômica de uma população de suínos base Landrace

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

O temperamento de bovinos confinados em diferentes disponibilidades de espaço e suas relações com o desempenho e a qualidade da carcaça e da carne

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Leveduras patogênicas em fezes de aves de cativeiro: relação fenotípica e genotípica entre os isolados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Lissencefalia em cães e gatos: revisão

Lissencephaly is a condition characterized by a lack of cerebral convolutions and sulci, which results from defective migration of nervous cells precursors in the telencephalus. The cause is presumably genetic. Lhasa-Apso dogs are most frequently affected, even though it may also occur in association with cerebellar hypoplasia in the Irish Setter, Wire-Haired Terrier and Samoieda breeds. This association was also reported in a cat. Clinical signs consist of dementia, aggressiveness, seizures, visual and olfactive dysfunctions, slow postural reactions and reduced menace response. Definitive diagnosis requires exams such as magnetic resonance imaging, cerebral biopsy or necropsy. There is no specific therapy for this disease, and seizures must be treated with anticonvulsants. The aim of this study is to review the literature regarding lissencephaly.

Quimiodectoma de corpo aórtico em cão

Chemodectomas are neoplasms originated from chemoreceptors mainly present on the aortic and carotid bodies. The etiology of this kind of tumor is related to genetic factors and chronic hypoxia. Brachycephalic breeds such as Boxer and Boston Terrier are predisposed to develop this neoplasia. This article reports the case of a 10-year-old female Boxer presented to the Veterinary Hospital of the Veterinary Medicine and Animal Science School in Botucatu with a two-day history of fatigue, exercise intolerance and dyspnea. Clinical signs, in association with radiographic and ultrasonographic findings, suggested a heart-base tumor. The worsening of the case led the owner to choose for euthanasia. Necropsy revealed a mass at the heart base adhered to the aortic body, and microscopic evaluation confirmed the diagnosis of chemodectoma.

Hiperadrenocorticismo em cães: revisão

Hyperadrenocorticism is a relatively common endocrinopathy in dogs, which is associated to an excessive production or administration of cortisol. The most affected breeds are Poodles, Teckels, Boxers, Boston Terriers and Beagles. The clinical signs most commonly observed are polyuria, polydipsia, polyfagia, panting, distended abdomen, endocrine alopecia, muscular weakness and lethargy. Laboratorial abnormalities include stress leukogram, increase in alkaline phosphatase and alanine aminotransferase activities, hypercholesterolemia, lipemia, hyperglycemia and hyposthenuria. The preferred essay to evaluate adrenal gland function is the low-dose dexamethasone suppression test, whereas the most used treatments include mitotane and trilostane. The objective of this paper is to review hyperadrenocorticism in dogs, because this disease is relatively common in small animal clinics and has many long-term complications.

Estudo do nível de infecção por Babesia bovis e Babesia bigemina em bovinos da raça Canchim naturalmente infestados com o carrapato Rhipicephalus (Boophilus) microplus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo de associação genômica e perfil de expressão gênica de folículos antrais em novilhas das raças nelore e angus, associadas ao fenótipo de alta e baixa população folicular

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Análise da ocorrência de metástase intraocular e pulmonar em cadelas portadoras de carcinoma mamário e correlação com mutação e expressão de E-caderina

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)