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.

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)

Effects of different spray formulations on the reproductive parameters of engorged Rhipicephalus (Boophilus) microplus females detached from experimentally infested cattle

This present study aimed to evaluate the deleterious effects of some commercially available spray formulations (15% Cypermethrin+25% Chlorpyriphos+1% Citronellal and 8% Cypermethrin+60% Ethion) on the reproductive parameters of engorged Rhipicephalus (Boophilus) microplus females that detached from experimentally infested cattle. The following reproductive parameters of engorged female ticks were analyzed: female weight, egg mass weight, percentage of hatchability, percentage of reduction in oviposition, percentage of reduction in hatchability, reproductive efficiency and percent control/efficacy of formulations for reproductive parameters. Our findings showed that although the strain R. (B.) microplus used in both experiments was thought to be sensitive to the test compounds because of the acaricidal efficacy observed throughout these trials, it was not possible to observe overall deleterious effects on the reproductive parameters of this tick species with both spray formulations. However, the 8% Cypermethrin+60% Ethion showed short-term significant effects on the weight of female ticks between the 14th and 16th days post-treatment and the weight of female and the egg mass weight between the 20th and 22nd days post-treatment. New studies should be conducted to show if these results regarding the reproductive parameters of fully engorged R. (B.) microplus females, combined with the acaricidal efficacy can be sufficient to reduce the number of chemical treatments administered to cattle.

First genetic identification of Cryptosporidium parvum subtype IIaA14G2R1in beef cattle in Brazil

The presence of Cryptosporidium spp. in a cattle herd registered with an outbreak of diarrhea was investigated and the the molecular subtyping of Cryptosporidium parvum was characterized. Fecal samples from 85 Nellore beef cattle (Bos indicus) were collected and examined with Ziehl-Neelsen modified staining method. Fifty-four cattle (63.52%) had Cryptosporidium spp. oocysts in their feces. Fragments of genes encoding the 18S ribosomal RNA subunit and a 60-kDa glycoprotein (gp60) were amplified by nested PCR accomplished in the 11 most heavily parasitized samples, and the amplicons were sequenced. Eight of the 11 analyzed samples were positive for 18S rRNA sequences and identified monospecific infections with C. parvum. Seven samples were positive for gp60 and identified subtypes IIaA15G2R1 (6/11) and IIaA14G2R1 (1/11). This report is the first for C. parvum subtype IIaA14G2R1 in beef cattle in Brazil.

The manipulation of progesterone profiles during progesterone + estradiol timed ai protocols in dairy cattle: effects on fertility

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

Períodos de adaptação de bovinos Nelore confinados a dietas de alto teor de concentrado

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

Altura do pasto e suplementação na recria de tourinhos e efeitos sobre a terminação

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

Desempenho e qualidade da carne de bovinos cruzados alimentados com diferentes dietas em confinamento

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Greenhouse gas emissions and N2o mitigation in beef cattle production on tropical pasture

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

Desempenho de bovinos cruzados terminados em confinamento e qualidade dos músculos longissimus e semitendinosus in natura e maturados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Protocolos para o uso combinado de monensina sódica e virginiamicina em dietas de bovinos Nelore confinados

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

Energy sources in the supplementation of beef cattle grazing Brachiaria brizantha cv. Xaraés

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

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)

Drivers of change in animal protein production systems: changes from 'traditional' to 'modern' beef cattle production systems in Brazil

Until 1990, beef cattle production in Brazil was recognized as an enterprise of low investment, low cost of production, as well as an extensive production system that used large land areas to be economically feasible. The situation changed for the Brazilian beef market when the economy stabilized in 1994 and all sectors involved in the beef supply chain were able to predict their associated costs and profits. During the same period, purchasing power of the Brazilian population grew, and as a consequence, consumers began to demand higher quality beef products. This new scenario in the late 1990s and early 2000s has led to more intensive beef production systems in Brazil as well as the need for a greater understanding of how technologies might be applied. As consequence of this evolution, in the last five years, a necessity to increase beef production has occurred. The quality of Brazilian beef has improved compared with beef produced 15 years ago, but continued improvements are needed to achieve excellence in terms of large-scale production of high quality beef, be sustainable over a long period of time, and increase our contribution to global food security.