ghanaopendata/ghanaian-research-english huggingface dataset:
The genetics of docility of the grasscutter (Thryonomys swinderianus)

The objectives of this study were to estimate non-genetic effects on docility, and calculate phenotypic and genetic parameters for docility in the grasscutter. The study was carried out at the grasscutter section of the Department of Animal Science Education, University of Education, Winneba, Mampong-Ashanti campus, Ghana from 2006 to 2009. Docility was defined as ability of an animal to accept human presence. A docility test was carried out on 321 animals (162 females and 159 males) which were selected at random at weaning (2 months). Docility was scored on a scale of 1 to 4; docile (1), flighty (2), restless (3) and aggressive (4). Each animal was tested 8 times. Average docility score of the population was 2.6. Litter size, sex, parity, year of birth, season of mating and season of birth, and their interactions did not influence (p>0.05) docility. Moderate direct and maternal genetic variations were observed for docility. The permanent environmental influence due to the dam on offspring accounted for a significant proportion (48.0%) of the phenotypic variation in docility. Direct heritability for docility was high (0.58) while the maternal heritability was medium (0.41).There were low genetic and phenotypic correlations between docility and all traits (body weight, growth rate, days of joining to conception, survival, feed intake and feed conversion ratio), except litter size. Litter size had a moderate negative genetic correlation with docility, but a low negative phenotypic correlation. Repeatability of docility was high (0.84). It was concluded that selection for grasscutters with more favourable docility scores would be effective in producing animals with more acceptable temperaments. Selection for grasscutters belonging to large litters is likely to produce docile animals, which are easier to handle. Addition of maternal effects to the genetic evaluation of docility in the grasscutteris recommended. One or two records on the animal's docility are enough to make selection decisions.

Source: UG
The genetics of morphological traits in the grasscutter

The objectives of this study were to estimate phenotypic and genetic parameters of morphological traits of the grasscutter, and to find the best morphological trait predictor of body weight. The study was carried out at the grasscutter section of the Department of Animal Science Education, University of Education, Winneba, Mampong-Ashanti campus, Ghana from 2009 to 2010. Data were recorded on morphological characteristics and body weights of 116 animals (66 females and 50 males) selected at random. Body weights and linear body measurements were recorded for the animals at birth, at weaning (2 months) and at 6 months. Mean body, tail and head lengths, heart girth and height-at-withers were 35.6, 10.2, 8.2, 18.0 and 11.6 cm, respectively. At birth, males and females had similar (P &gt; 0.05) body measurements for all the morphological traits. However, at 2 and 6 months, males had significantly (P &lt; 0.05) longer body, head and tail lengths, larger heart girth and taller height-at-withers than females. The best predictor of body weight was heart girth. Direct genetic diversity (variability) of body length, head length and heart girth were low whilst those of tail length and height-at-withers were moderate. Proportion of phenotypic variance due to permanent environmental effects of dam (c 2) was low to moderate (3-23%). Covariances between direct and maternal effects were negative (-2.3 to -29.2). Direct heritability for all traits was high (0.52-0.60) and maternal heritability was medium to high (0.39-0.75). Correlations between direct and maternal genetic effects were high negative (-0.61 to -0.78). Genetic correlations among morphological traits were medium (0.45) to high (0.85), whilst their phenotypic correlations were high (0.71 to 0.90). Genetic correlations between body weight and all morphological traits were low (0.04 to 0.23), whilst their phenotypic correlations were high (0.75 to 0.90). It was concluded that genetic selection will be effective in improving all the morphological traits. However, little to no correlated response in body weight would be expected. It was also concluded that heart girth can be used by farmers to predict body weight of grasscutters. It was recommended that farmers should not use head shape for sex determination at birth.

Source: UG
Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania

The Bacteriology Department aims to improve the quality of life first for Ghanaians and the world at large by conducting research into bacterial diseases of public health importance to Ghana and globally. In addition to working on enteric pathogens and sexually transmitted diseases, the department’s current main focus is on the two most important mycobacterial diseases of public health importance to Ghana, namely Buruli ulcer (BU) and tuberculosis (TB).

Source: UG
A genome wide quantitative trait linkage analysis for serum lipids in type 2 diabetes in an African population

Lipid abnormalities are strongly linked with coronary heart disease and are common in type 2 diabetes. However, little is known about the genetic determinants of serum lipids in African populations. An autosomal genome scan was performed for linkage to five plasma lipid phenotypes (total cholesterol, triglycerides (TG), HDL-cholesterol (HDL-C), LDL-cholesterol (LDL-C) and VLDL-cholesterol (VLDL-C)) in the Africa-America Diabetes Mellitus (AADM) study. Two hundred and ninety-five affected sibling pairs with type 2 diabetes mellitus enrolled from Ghana and Nigeria were genotyped for 390 microsatellite markers with an average inter-marker distance of 9 cM. Multipoint variance components linkage analysis showed that HDL-C had a LOD score of 4.34 near marker D7S3061 and 3.00 near marker D7S513. Some clustering of linkage evidence to several lipid phenotypes was observed on chromosomes 5 (LDL-C, total cholesterol, VLDL-C), chromosome 7 (HDL-C, TG) and chromosome 19 (total cholesterol, LDL-C, TG). Principal component analysis of the five phenotypes yielded two factors, one (TG, HDL-C and VLDL) of which was linked to QTLs on chromosomes 2, 5 and 7, while the other (total cholesterol and LDL-C) was linked to a different set of QTLs on chromosomes 2, 5 and 18. Several of these regions have been reported to be linked to lipids in other studies. Follow up investigations are warranted in view of the central role serum lipids play in the aetiopathogenesis of cardiovascular disease. © 2005 Elsevier Ireland Ltd. All rights reserved.

Source: UG
Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

The Epidemiology Department contributes to the mission of the institute through basic and applied epidemiological research on, but not limited to, malaria and other diseases of public health importance. It is also home to the Social Science Unit of the Institute, including the Health Support Centre for HIV/AIDS and other communicable and noncommunicable health problems.

Source: UG
Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

The Bacteriology Department aims to improve the quality of life first for Ghanaians and the world at large by conducting research into bacterial diseases of public health importance to Ghana and globally. In addition to working on enteric pathogens and sexually transmitted diseases, the department’s current main focus is on the two most important mycobacterial diseases of public health importance to Ghana, namely Buruli ulcer (BU) and tuberculosis (TB).

Source: UG
Genome-wide associated loci influencing interleukin (IL)-10, IL-1Ra, and IL-6 levels in African Americans

Interleukins (ILs) are key mediators of the immune response and inflammatory process. Plasma levels of IL-10, IL-1Ra, and IL-6 are associated with metabolic conditions, show large inter-individual variations, and are under strong genetic control. Therefore, elucidation of the genetic variants that influence levels of these ILs provides useful insights into mechanisms of immune response and pathogenesis of diseases. We conducted a genome-wide association study (GWAS) of IL-10, IL-1Ra, and IL-6 levels in 707 nondiabetic African Americans using 5,396,780 imputed and directly genotyped single nucleotide polymorphisms (SNPs) with adjustment for gender, age, and body mass index. IL-10 levels showed genome-wide significant associations (p<5× 10 -8) with eight SNPs, the most significant of which was rs5743185 in the PMS1 gene (p=2.30×10 -10). We tested replication of SNPs that showed genome-wide significance in 425 non-diabetic individuals from West Africa, and successfully replicated rs17365948 in the YWHAZ gene (p= 0.02). IL-1Ra levels showed suggestive associations with two SNPs in the ASB3 gene (p=2.55×10 -7), ten SNPs in the IL-1 gene family (IL1F5, IL1F8, IL1F10, and IL1Ra, p= 1.04×10 -6 to 1.75×10 -6), and 23 SNPs near the IL1A gene (p=1.22×10 -6 to 1.63×10 -6).We also successfully replicated rs4251961 (p=0.009); this SNP was reported to be associated with IL-1Ra levels in a candidate gene study of Europeans. IL-6 levels showed genome-wide significant association with one SNP (RP11-314E23.1; chr6:133397598; p= 8.63×10 -9). To our knowledge, this is the first GWAS on IL-10, IL-1Ra, and IL-6 levels. Follow-up of these findings may provide valuable insight into the pathobiology of IL actions and dysregulations in inflammation and human diseases.

Source: UG
Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.

We combined two tuberculosis genome-wide association studies from Ghana and The Gambia with subsequent replication in a combined 11,425 individuals. rs4331426, located in a gene-poor region on chromosome 18q11.2, was associated with disease (combined P = 6.8 x 10(-9), odds ratio = 1.19, 95% CI = 1.13-1.27). Our study demonstrates that genome-wide association studies can identify new susceptibility loci for infectious diseases, even in African populations, in which levels of linkage disequilibrium are particularly low.

Source: UG
Genome-Wide Association Mapping And Genomic Prediction Analyses Reveal The Genetic Architecture Of Grain Yield And Agronomic Traits Under Drought And Optimum Conditions In Maize.

Background Drought is a major abiotic stress in sub-Saharan Africa, impacting maize growth and development leading to severe yield loss. Drought tolerance is a complex trait regulated by multiple genes, making direct grain yield selection inefective. To dissect the genetic architecture of grain yield and fowering traits under drought stress, a genome-wide association study (GWAS) was conducted on a panel of 236 maize lines testcrossed and evaluated under managed drought and optimal growing conditions in multiple environments using seven multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO, and FARMCPU) from mrMLM and GAPIT R packages. Genomic prediction with RR-BLUP model was applied on BLUEs across locations under optimum and drought conditions. Results A total of 172 stable and reliable quantitative trait nucleotides (QTNs) were identifed, of which 77 are associated with GY, AD, SD, ASI, PH, EH, EPO and EPP under drought and 95 are linked to GY, AD, SD, ASI, PH, EH, EPO and EPP under optimal conditions. Among these QTNs, 17 QTNs explained over 10% of the phenotypic variation (R2≥10%). Furthermore, 43 candidate genes were discovered and annotated. Two major candidate genes, Zm00001eb041070 closely associated with grain yield near peak QTN, qGY_DS1.1 (S1_216149215) and Zm00001eb364110 closely related to anthesis-silking interval near peak QTN, qASI_DS8.2 (S8_167256316) were identifed, encoding AP2-EREBP transcrip tion factor 60 and TCP-transcription factor 20, respectively under drought stress. Haplo-pheno analysis identifed supe rior haplotypes for qGY_DS1.1 (S1_216149215) associated with the higher grain yield under drought stress. Genomic prediction revealed moderate to high prediction accuracies under optimum and drought conditions.

Source: UG
Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda. Our GWAS study found two regions associated to CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. Predictive accuracy values varied between CBSD foliar severity traits at 3 months after planting (MAP) (0.27-0.32), 6 MAP (0.40-0.42) and root severity (0.31-0.42). For all traits, Random Forest and reproducing kernel Hilbert spaces regression showed the highest predictive accuracies. Our results provide an insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding. © 2018 The Author(s).

Source: UG
Genome-Wide Association Mapping of Oil Content and Seed-Related Traits in Shea Tree (Vitellaria paradoxa subsp. nilotica) Populations

Shea tree (Vitellaria paradoxa) is an important fruit tree crop because of its oil used for cooking and the industrial manufacture of cosmetics. Despite its essential benefits, quantitative trait loci linked to the economic traits have not yet been studied. In this study, we performed association mapping on a panel of 374 shea tree accessions using 7530 Single-Nucleotide Polymor phisms (SNPs) markers for oil yield and seed-related traits. Twenty-three SNP markers significantly (−log10 (p) = 4.87) associated with kernel oil content, kernel length, width, and weight were iden tified. The kernel oil content and kernel width had the most significant marker–trait associations (MTAs) on chromosomes 1 and 8, respectively. Sixteen candidate genes identified were linked to early induction of flower buds and somatic embryos, seed growth and development, substrate binding, transport, lipid biosynthesis, metabolic processes during seed germination, and disease resistance and abiotic stress adaptation. The presence of these genes suggests their role in promoting bioactive functions that condition high oil synthesis in shea seeds. This study provides insights into the important marker-linked seed traits and the genes controlling them, useful for molecular breeding for improving oil yield in the species

Source: UG
Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii

The Department of Parasitology conducts research into parasitic diseases of public health importance with the overall goal of reducing their transmission and the heavy disease burden that they impose on affected populations. The Department maintains focus on parasitic diseases in general. These include major diseases such as malaria, and others listed under the Neglected Tropical Diseases (NTD) control initiative such as, lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminthiasis, trypanosomiasis and leishmaniasis.

Source: UG
Genome-wide association study identifies seven novel susceptibility loci for primary open-angle glaucoma

The Epidemiology Department contributes to the mission of the institute through basic and applied epidemiological research on, but not limited to, malaria and other diseases of public health importance. It is also home to the Social Science Unit of the Institute, including the Health Support Centre for HIV/AIDS and other communicable and noncommunicable health problems.

Source: UG
Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21.

In search of common risk alleles for prostate cancer that could contribute to high rates of the disease in men of African ancestry, we conducted a genome-wide association study, with 1,047,986 SNP markers examined in 3,425 African-Americans with prostate cancer (cases) and 3,290 African-American male controls. We followed up the most significant 17 new associations from stage 1 in 1,844 cases and 3,269 controls of African ancestry. We identified a new risk variant on chromosome 17q21 (rs7210100, odds ratio per allele = 1.51, P = 3.4 × 10(-13)). The frequency of the risk allele is ∼5% in men of African descent, whereas it is rare in other populations (<1%). Further studies are needed to investigate the biological contribution of this allele to prostate cancer risk. These findings emphasize the importance of conducting genome-wide association studies in diverse populations.

Source: UG
Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm

Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers.

Source: UG
Genome-Wide Linkage Scan for Primary Open Angle Glaucoma: Influences of Ancestry and Age at Diagnosis

Primary open-angle glaucoma (POAG) is the most common form of glaucoma and one of the leading causes of vision loss worldwide. The genetic etiology of POAG is complex and poorly understood. The purpose of this work is to identify genomic regions of interest linked to POAG. This study is the largest genetic linkage study of POAG performed to date: genomic DNA samples from 786 subjects (538 Caucasian ancestry, 248 African ancestry) were genotyped using either the Illumina GoldenGate Linkage 4 Panel or the Illumina Infinium Human Linkage-12 Panel. A total of 5233 SNPs was analyzed in 134 multiplex POAG families (89 Caucasian ancestry, 45 African ancestry). Parametric and non-parametric linkage analyses were performed on the overall dataset and within race-specific datasets (Caucasian ancestry and African ancestry). Ordered subset analysis was used to stratify the data on the basis of age of glaucoma diagnosis. Novel linkage regions were identified on chromosomes 1 and 20, and two previously described loci—GLC1D on chromosome 8 and GLC1I on chromosome 15—were replicated. These data will prove valuable in the context of interpreting results from genome-wide association studies for POAG.

Source: UG
Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Primary open-angle glaucoma (POAG), is a heritable common cause of blindness world-wide. To identify risk loci, we conduct a large multi-ethnic meta-analysis of genome-wide association studies on a total of 34,179 cases and 349,321 controls, identifying 44 previously unreported risk loci and confirming 83 loci that were previously known. The majority of loci have broadly consistent effects across European, Asian and African ancestries. Cross ancestry data improve fine-mapping of causal variants for several loci. Integration of multiple lines of genetic evidence support the functional relevance of the identified POAG risk loci and highlight potential contributions of several genes to POAG pathogenesis, including SVEP1, RERE, VCAM1, ZNF638, CLIC5, SLC2A12, YAP1, MXRA5, and SMAD6. Several drug compounds targeting POAG risk genes may be potential glaucoma therapeutic candidates.

Source: UG
A genome-wide scan for quantitative trait loci linked to obesity phenotypes among West Africans

OBJECTIVE: To identify quantitative trait loci (QTL) for three obesity phenotypes: body mass index (BMI), fat mass (FM) and percent body fat (PBF) in West Africans with type 2 diabetes (T2DM). DESIGN: An affected sibling pair (ASP) design, in which both siblings had T2DM. Obesity was analyzed as a quantitative trait using a variance components approach. SUBJECTS: Sib-pairs affected with T2DM from the Africa America Diabetes Mellitus (AADM) study, comprising 321 sibling pairs and 36 half-sibling pairs. MEASUREMENTS: Weight was measured on an electronic scale to the nearest 0.1 kg, and height was measured with a stadiometer to the nearest 0.1 cm. Body composition was estimated using bioelectric impedance analysis (BIA). Genotyping was carried out at the Center for Inherited Disease Research (CIDR) with a panel of 390 trinucleotide and tetranucleotide repeats. RESULTS: The obesity-related phenotype showing the strongest linkage evidence was PBF on chromosome 2 (LOD 3.30 at 72.6 cM, marker D2S739). Suggestive linkage to FM was found on chromosomes 2 (LOD 2.56 at 80.4 cM) and 5 (LOD 2.25 at 98 cM, marker D5S1725). The highest LOD score for BMI was 1.68 (chromosome 4, 113.8 cM). The areas of linkage for the three phenotypes showed some clustering as all three phenotypes were linked to the same regions of 2p13 and 5q14, and our study replicated linkage evidence for several regions previously reported in other studies. CONCLUSION: We obtained evidence for several QTLs on chromosome 2, 4 and 5 to three obesity phenotypes. This study provides data on the genetics of obesity in populations that are currently under represented in the global effort directed at understanding the pathophysiology of excess adiposity in free living individuals.

Source: UG