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.

Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference

An important goal of Zebu breeding programs is to improve reproductive performance. A major problem faced with the genetic improvement of reproductive traits is that recording the time for an animal to reach sexual maturity is costly. Another issue is that accurate estimates of breeding values are obtained only a long time after the young bulls have gone through selection. An alternative to overcome these problems is to use traits that are indicators of the reproductive efficiency of the herd and are easier to measure, such as age at first calving. Another problem is that heifers that have conceived once may fail to conceive in the next breeding season, which increases production costs. Thus, increasing heifer's rebreeding rates should improve the economic efficiency of the herd. Response to selection for these traits tends to be slow, since they have a low heritability and phenotypic information is provided only later in the life of the animal. Genome-wide association studies (GWAS) are useful to investigate the genetic mechanisms that underlie these traits by identifying the genes and metabolic pathways involved. Data from 1853 females belonging to the Agricultural Jacarezinho LTDA were used. Genotyping was performed using the BovineHD BeadChip (777 962 single nucleotide polymorphisms (SNPs)) according to the protocol of Illumina - Infinium Assay II ® Multi-Sample HiScan with the unit SQ ™ System. After quality control, 305 348 SNPs were used for GWAS. Forty-two and 19 SNPs had a Bayes factor greater than 150 for heifer rebreeding and age at first calving, respectively. All significant SNPs for age at first calving were significant for heifer rebreeding. These 42 SNPs were next or within 35 genes that were distributed over 18 chromosomes and comprised 27 protein-encoding genes, six pseudogenes and two miscellaneous noncoding RNAs. The use of Bayes factor to determine the significance of SNPs allowed us to identify two sets of 42 and 19 significant SNPs for heifer rebreeding and age at first calving, respectively, which explain 11.35 % and 6.42 % of their phenotypic variance, respectively. These SNPs provide relevant information to help elucidate which genes affect these traits.

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.

Detecção de Histophilus somni (Haemophilus somnus) no sêmen bovino mediante reação em cadeia pela polimerase (PCR)

The present study evaluated the use of PCR for Histophilus somni detection in bovine semen. Semen samples were experimentally infected with H. somni at dilutions ranging from 107 to 101 bacteria/mL and subjected to DNA extraction by the phenol/chloroform method, followed by PCR amplification. The amplification products were analyzed by electrophoresis in 8% acrylamide gel. The oligonucleotide primers used yielded an amplification fragment of 400 base pairs from the bacterial DNA. Positive amplification was obtained even for the 101 bacteria/mL dilution. PCR proved to be an efficient method for the detection of H. somni. The results obtained in this study have brought relevant information for the diagnosis of H. somni, justifying the need for the diagnosis of this bacterium in bulls, especially in semen samples that should be free of contamination. The PCR method has shown to be a useful tool for the quality control of semen produced in artificial insemination centers.

Influence of lineage of oocyte donor on the yield and morphology of oocytes recovered by ultrasound-guided follicular aspiration in nellore cows

The objective of this study was to investigate the influence of lineage of oocytes donors on the number and quality of oocytes obtained through ultrasound-guided follicular aspiration in Nellore breed cows derived from two lineages of bulls (Karvadi; K and Taj-Mahal; T). Both maternal (Km and Tm) and paternal (Kp and Tp) lineages, as well as their combinations were investigated. Oocyte aspirations were repeatedly performed with an aspiration interval of 15 days in 56 donor females. Recovered cumulus oocyte-complexes (COCs) were counted, morphologically examined and classified into seven categories (grades from I to VII) according to the number of layers of the cumulus oocyte and cytoplasm appearance. The mean number of oocytes retrieved from donors of lineage Tp-Tm was significantly higher (28.23±1.92, P<0.05) than those obtained from lineages Kp-Tm, Kp-Km, and Tp-Km (21.34±1.32, 21.28±1.73, and 16.72±1.31, respectively). There was no significant difference in the mean number of recovered oocytes between donors of lineages Kp-Km and Kp-Tm, whereas animals of lineage Tp-Km yielded the lowest number of oocytes. Higher mean number of grade III oocytes was recovered from donors of lineage Kp than lineage Tp (10.11±0.66 versus 8.79±0.58, respectively), with more grade III oocytes being obtained in both lineages as compared to the others. Paternal lineage did not influence the quality of recovered oocytes in any other category, but both Kp and Tp yielded a great mean number of oocytes graded as I, II, and III (3.14±0.21; 4.93±0.33, and 10.11±0.66 versus 3.19±0.21, 5.59±0.44, and 8.79±0.58, respectively) than those classified as IV, V, VI, and VII. However, when considering the data from the maternal lineage significantly more oocytes (P<0.05) of grade I, II and III were obtained from Taj-Mahal (11.67 ± 0.67, 5.9±0.42 and 3.64±0.25, respectively) than for lineage Karvadi, with similar results for oocytes of grades IV, V, VI, and VII. Similarly to the paternal lineage, the number of oocytes of grade III was superior (P<0.05) when compared to other categories for both lineages. In conclusion, we demonstrate here a direct influence of lineage of oocyte donor on the production and quality of oocytes obtained through ultrasound-guided follicular aspiration in Nellore cows.

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)

Protocolos experimentais de confinamento para bovinos Nelore alimentados com dietas contendo glicerina bruta

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

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)

Grão de soja moído e níveis de amido na terminação de tourinhos Nelore confinados

Pós-graduação em Zootecnia - FCAV

Association among residual feed intake, residual body weight gain, residual intake and body weight gain and temperament of Nellore cattle

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