ABSTRACT
Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution.
Subject(s)
Cattle , Genomics , Animals , Open Reading Frames , Phenotype , Sequence Analysis, DNAABSTRACT
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.
Subject(s)
Cattle/genetics , Genetic Variation , Genome , Africa , Alleles , Animals , Chromosome Mapping , Europe , Genomics , MaleABSTRACT
BACKGROUND: Gestational diabetes mellitus (GDM) is associated with increased risk of mortality and morbidity for pregnant women and newborns. Identifying pregnant women with risk factors for GDM based on the clinical suspicion is a popular approach. However, the effectiveness of the use of a structured checklist of risk factors is yet to be evaluated. This study assessed the effectiveness of a structured checklist of risk factors in identifying pregnant women at risk of GDM at the University College Hospital, Ibadan. MATERIALS AND METHODS: It was a comparative cross-sectional study implemented in two phases. The first phase (Group A) of the study was a prospective study that involved 530 pregnant women who presented at the booking clinic. A structured checklist containing risk factors was used to identify women at the risk of GDM. The second phase (Group B) was a retrospective study of 530 pregnant women managed 2 years previously who were selected by systematic random technique. RESULTS: The mean age, gestational age at booking, gestational age at delivery and birth weight were 30.2 ± 5.2 years, 21 ± 10.8 weeks, 38.7 ± 2.7 weeks and 3.1 ± 0.7 kg respectively. The prevalence of GDM in Group A and B were 4.9% and 1.6% respectively ( P < 0.05). There was about three fold increase in identification of women at risk of GDM by use of a checklist. CONCLUSION: Identification of women at risk of GDM was approximately 3-4 fold higher with the use of checklist of risk factors. Exhaustive clinical identification with a checklist of risk factors for GDM should be encouraged.
Subject(s)
Diabetes, Gestational/diagnosis , Prenatal Diagnosis/methods , Adolescent , Adult , Cross-Sectional Studies , Diabetes, Gestational/epidemiology , Diabetes, Gestational/physiopathology , Female , Gestational Age , Humans , Logistic Models , Multivariate Analysis , Nigeria/epidemiology , Pregnancy , Prevalence , Retrospective Studies , Risk Factors , Young AdultABSTRACT
A trial was conducted to compare the cellular responses in the respiratory tract in intranasal vaccination against caprine Peste des petits ruminant lineage 1 variant virus infection with intramuscular and subcutaneous vaccinations in order to elucidate the mechanism of the protection. Twenty four goats were divided into four equal groups. Group 1 was vaccinated intranasaly, group 2 was vaccinated subcutaneously, and group 3 intramuscularly, while Group 4 was the unvaccinated control group. In each group the vaccinations were carried out once. All goats were challenged intratrachealy with PPR virus at a concentration of 106.5 TCID50 two weeks after vaccination and were euthanised 21 days after the challenge. The bronchoalveolar lavage differential count, bronchial associated lymphoid tissue (BALT) responses were measured using standard techniques. Descriptive Statistics and ANOVA was employed and significance was at p < 0.05. The exposure also resulted into significant increase in the number and size of BALT as well as the number of lymphocytes in BALT. This study showed the mechanism of the protective effect of intranasal vaccination of PPR vaccine observed with the strong mucosal and defensive cellular responses in the respiratory tract observed than the subcutaneous and intramuscular routes.
Se realizó un ensayo para comparar las respuestas celulares en las vías respiratorias después de la vacunación intranasal contra la variante caprina de la infección del virus peste de pequeños rumiantes linaje 1 con vacunas intramusculares y subcutáneas con el fin de dilucidar el mecanismo de protección. Veinticuatro cabras fueron divididas en cuatro grupos iguales. El Grupo 1 fue vacunado por vía intranasal, el grupo 2 vía subcutánea, el grupo 3 vía intramuscular y el grupo 4 control no vacunado. En cada grupo se vacunó sólo una vez. Todas las cabras fueron expuestas al virus peste de pequeños rumiantes por vía intratraqueal a una concentración de 106.5 TCID50 2 semanas después de la vacunación, y fueron sometidos a eutanasia 21 días después. Se midieron el recuento diferencial del lavado broncoalveolar y las respuestas de los tejidos linfoides asociados bronquios (BALT) utilizando técnicas estándar. Los resultados se evaluaron por estadística descriptiva y ANOVA, con una significación p<0,05. La exposición también mostró un aumento significativo en el número y tamaño del BALT, así como el número de linfocitos en este. El estudio mostró que el mecanismo del efecto protector de la vacunación intranasal contra el virus peste de pequeños rumiantes posee una respuesta mucosa y celular defensiva en el tracto respiratorio mayor que la observada por vacunación vía subcutánea e intramuscular.