Low frequency of Y anomaly detected in Australian Brahman cow-herds

Indicine cattle have lower reproductive performance in comparison to taurine. A chromosomal anomaly characterized by the presence Y markers in females was reported and associated with infertility in cattle. The aim of this study was to investigate the occurrence of the anomaly in Brahman cows. Brahman cows (n = 929) were genotyped for a Y chromosome specific region using real time-PCR. Only six out of 929 cows had the anomaly (0.6%). The anomaly frequency was much lower in Brahman cows than in the crossbred population, in which it was first detected. It also seems that the anomaly doesn't affect pregnancy in the population. Due to the low frequency, association analyses couldn't be executed. Further, SNP signal of the pseudoautosomal boundary region of the Y chromosome was investigated using HD SNP chip. Pooled DNA of non-pregnant and pregnant cows were compared and no difference in SNP allele frequency was observed. Results suggest that the anomaly had a very low frequency in this Australian Brahman population and had no effect on reproduction. Further studies comparing pregnant cows and cows that failed to conceive should be executed after better assembly and annotation of the Y chromosome in cattle.

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.

Male-specific contributions to the Brazilian population of Espirito Santo

Y chromosome markers have been widely studied due to their various applications in the fields of forensic and evolutionary genetics. In this study, 35 Y-SNPs and 17 Y-STRs were genotyped in 253 males from the State of Espirito Santo, Brazil. A total of 18 haplogroups and 243 haplotypes were detected; the haplogroup and haplotype diversities were 0.7794 and 0.9997, respectively. Genetic distance analysis using the Y-STR data showed no statistically significant differences between Espirito Santo and other admixed populations from Brazil. The classification of paternal lineages based on haplogroups showed a predominant European contribution (85.88 %), followed by African (11.37 %) and Amerindian (2.75 %) contributions.

A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

The aim of this study was to identify candidate genes and genomic regions associated with ultrasound-derived measurements of the rib-eye area (REA), backfat thickness (BFT) and rumpfat thickness (RFT) in Nellore cattle. Data from 640 Nellore steers and young bulls with genotypes for 290 863 single nucleotide polymorphisms (SNPs) were used for genomewide association mapping. Significant SNP associations were explored to find possible candidate genes related to physiological processes. Several of the significant markers detected were mapped onto functional candidate genes including ARFGAP3, CLSTN2 and DPYD for REA; OSBPL3 and SUDS3 for BFT; and RARRES1 and VEPH1 for RFT. The physiological pathway related to lipid metabolism (CLSTN2, OSBPL3, RARRES1 and VEPH1) was identified. The significant markers within previously reported QTLs reinforce the importance of the genomic regions, and the other loci offer candidate genes that have not been related to carcass traits in previous investigations.

Strategies for genotype imputation in composite beef cattle

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

Association between ACTA1 candidate gene and performance, organs and carcass traits in broilers

This study investigates the genetic association of the SNP present in the ACTA1 gene with performance traits, organs and carcass of broilers to help marker-assisted selection of a paternal broiler line (TT) from EMBRAPA Swine and Poultry, Brazil. Genetic and phenotypic data of 1,400 broilers for 68 traits related to body performance, organ weights, weight of carcass parts, and yields as a percentage of organs and carcass parts were used. The maximum likelihood method, considering 4 analytical models, was used to analyze the genetic association between the SNP and these important economic traits. The association analysis was performed using a mixed animal model including the random effect of the animal (polygenic), and the fixed effects of sex (2 levels), hatch (5 levels) and SNP (3 levels), besides the random error. The traits significantly associated (P < 0.05) with the SNP were analyzed, along with body weight at 42 days of age (BW42), by the restricted maximum likelihood method using the multi-trait animal model to estimate genetic parameters. The analysis included the residual and additive genetic random effects and the sex-hatch fixed effect. The additive effects of the SNP were associated with breast meat (BMY), liver yield (LIVY), body weight at 35 days of age (BW35); drumstick skin (DSW), drumstick (DW) and breast (BW) weights. The heritability estimates for these traits, in addition to BW42, ranged from 0.24 ± 0.06 to 0.45 ± 0.08 for LIVY and BW35, respectively. The genetic correlation ranged from 0.02 ± 0.18 for LIVY and BMY to 0.97 ± 0.01 for BW35 and BW42. Based on the results of this study, it can be concluded that ACTA1 gene is associated with performance traits BW35, LIV and BMY, DW, BW and DW adjusted for body weight at 42 days of age. Therefore, the ACTA1 gene is an important molecular marker that could be used together with others already described to increase the economically important traits in broilers.

Chemoreflex and baroreflex alterations in Parkinsonism induced by 6-OHDA in unanesthetized rats

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross

Rapid growth in broilers is associated with susceptibility to metabolic disorders such as pulmonary hypertension syndrome (ascites) and sudden death. This study describes a genome search for QTL associated with relative weight of cardio respiratory and metabolically important organs (heart, lungs, liver and gizzard), and hematocrit value in a Brazilian broiler-layer cross. QTL with similar or different effects across sexes were investigated. At 42 days of age after fasted for 6 h, the F2 chickens were weighed and slaughtered. Weights and percentages of the weight relative to BW42 of gizzard, heart, lungs, liver and hematocrit were used in the QTL search. Parental, F1 and F2 individuals were genotyped with 128 genetic markers (127 microsatellites and 1 SNP) covering 22 linkage groups. QTL mapping analyses were carried out using mixed models. A total of 11 genome-wide significant QTL and five suggestive linkages were mapped. Thus, genome-wide significant QTL with similar effects across sexes were mapped to GGA2, 4 and 14 for heart weight, and to GGA2, 8 and 12 for gizzard %. Additionally, five genome-wide significant QTL with different effects across sexes were mapped to GGA 8, 19 and 26 for heart weight; GGA26 for heart % and GGA3 for hematocrit value. Five QTL were detected in chromosomal regions where QTL for similar traits were previously mapped in other F2 chicken populations. Seven novel genome-wide significant QTL are reported here, and 21 positional candidate genes in QTL regions were identified.

Prospecting major genes in dairy buffaloes

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

Efeito da utilização de diferentes critérios de controle de qualidade dos genótipos em estudos de associação e seleção genômica ampla

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

Estudo da diversidade genética do MycobacteriUm leprae em pacientes com hanseníase no município de Rondonópolis (MT): uma contribuição para o melhor entendimento da sua transmissão

Pós-graduação em Doenças Tropicais - FMB

Estudo de associação entre polimorfismos de base única com características de eficiência de conversão, consumo e desempenho em bovinos da raça Nelore

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Papel do tecido adiposo perivascular em aorta de ratos treinados e alimentados com dieta hiperlipídica

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

Seleção e associação genômica para precocidade sexual em bovinos da raça Nelore

Pós-graduação em Genética e Melhoramento Animal - FCAV

Estudo genômico da produção de leite e seus constituintes em bovinos da raça Guzerá

Pós-graduação em Genética e Melhoramento Animal - FCAV