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.

Atrichia, abnormal EEG, epilepsy and mental retardation in two sisters

Two daughters of a nonconsanguineous couple are described. Both present mental retardation, epileptic seizures, congenital atrichia, histologically anomalous skin and abnormal EEG pattern. From a discussion of the literature on atrichia, the forms without involvement of teeth, nails and hidrosis, among which recessive inheritance prevails, are distinguished from each other. None of them coincide with the syndrome described here.

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

Armazenamento, tolerância à dessecação e o potencial fisiológico de sementes de híbridos de milho e seus recíprocos

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Conceitos de gene: construção histórico-epistemológica e percepções de professores do Ensino Superior

Considering the importance that the discussion of concepts related to genetics has on the society and the necessity to approach science as a dynamic and historical activity, it will be discussed an essential concept to the understanding of biological inheritance: the concept of gene. This way, the article aims to discuss the differents concepts of genes in the history of biology and the relevance of addressing in teaching context this concept in a systemic perception of phenomena. Also, the paper have an analyses of the ideas about the concept of the gene from teachers from two university. The results indicate the presence of different definitions of the gene in the discourse of university teachers, with the predominance of gene concept as a structural, functional and/or informational unit.

Características fenotípicas do nanismo em pôneis neonatos: relato de casos

Three newborn Mini-Horses and one Brazilian Pony horses were presented to the Veterinary Hospital with phenotypic appearance of dwarfism. They had relatively larger head conformation, occlusive dental defect and musculoskeletal changes such as abnormal short limbs and deformation on the third metatarsal bone. The radiographic examination showed abnormal growth plates on femoral condyle and proximal thirds metatarsal bones. Due to the high possibility of future complications and quality of life loss, the animals were euthanized. We emphasize the importance of recognition of phenotypic changes related to dwarfism in horses, enabling the phenotypic diagnosis can direct crossings for nontransmission of this abnormality as genetic inheritance.

O direito de pertencer a si mesmo: a despatologização do transexualismo e sua regulamentação jurídica como direito fundamental ao gênero

Pós-graduação em Direito - FCHS