ghanaopendata/ghanaian-research-english huggingface dataset:
Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers

Sorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

Source: UG
Genetic diversity in Echinochloa spp. collected from different geographic origins and within rice fields in Côte d'lvoire

Diversity studies of Echinochloa spp. are complicated by problems in taxonomy and species identification, caused by the existence of morphologically intergrading types. Six amplified fragment length polymorphism (AFLP) primer combinations and five microsatellites were used to assess variation in 24 samples morphologically identified as E. crus-galli, E. colona and E. crus-pavonis, from Bangladesh, India, Colombia, Costa Rica, Côte d'Ivoire and Philippines. Out of 909 AFLP bands generated, 775 were polymorphic. Genotype diversity for the microsatellites ranged from 0.28 to 0.72. Similarity matrices were calculated using Jaccard coefficient, and input into cluster and principal coordinates analyses. AFLP and microsatellite results were highly correlated. Echinochloa crus-pavonis and E. crus-galli were intermixed, consistent with the view that E. crus-galli occurs as numerous intergrading races in the four countries (Bangladesh, India, Côte d'Ivoire and Philippines). The E. colona samples clustered as a distinct group. In 15 samples of E. crus-pavonis collected from rice fields in a valley in Côte d'Ivoire (over a 2-km distance), four different genotypes were found in a 4 m x 4 m area. These results suggest that AFLPs and SSRs may be useful not only for discriminating genotypes and studying population structure but also for helping to resolve taxonomic relationships in Echinochloa spp.

Source: UG
Genetic diversity in mycobacterium ulcerans isolates from Ghana revealed by a newly identified locus containing a variable number of tandem repeats

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
Genetic diversity of bonytongue fish Heterotis niloticus (Cuvier, 1829) in Cameroon, Central Africa

The African bonytongue (Heterotis niloticus) fish is the only species of the Osteoglossidae family in Africa. The characterization of this fish was carried out from January to June 2020 in Cameroon where this fish is distributed in native zones. This study aimed at contributing to the genetic characterization of Heterotis niloticus population in Cameroon. A total of 96 Heterotis niloticus were sampled from five regions namely Centre, South, Littoral, North and Far North. Caudal fins where randomly collected for genomic DNA (gDNA) extraction. Following standard procedures for simple sequence repeat markers available for this species, seven microsatellites were used for genotyping through Polymerase Chain Reaction (PCR) and electrophoresis. Genetic parameters were scored using the GenAlex 6.503 software and the population structure of Heterotis niloticus was assessed under STRUCTURE Version 2.3.4 software. The results showed that the local pop ulation of Heterotis niloticus in North-Cameroon has a higher number of allele (Na=6.00) and effective number of allele (Ne=3.66) while the highest Observed Heterozygosity (Ho) was observed for the population of Heterotis niloticus in the Far-North. The highest genetic distance is observed between the population of Far North and Centre, Far-North and South, Far-North and North. In general, similarity within the sub-population of Heterotis niloticus is higher than 65%. Genetically, the population of Heterotis niloticus in Cameroon was grouped into three genetic sub populations based on microsatellites appraisal. Further investigations are suggested for analysis concerning productive traits for domestication and aquaculture purposes.

Source: UG
Genetic diversity of forest and savannah chicken ecotypes of Ghana as estimated by microsatellite markers

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco-zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations – a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright’s F-statistics revealed negligible genetic differentiation (FST) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south-north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.

Source: UG
Genetic diversity of helmeted guineafowl (Numida meleagris) based on microsatellite analysis

Characterization of the genetic diversity of indigenous animal populations is a prerequisite for providing needed information for the conservation of useful genotypes against future uncertainties. In this study, a total of 232 helmeted guineafowls (Numida meleagris) sampled from three populations in Ghana, one population in Benin and two populations in Japan were genotyped across six autosomal microsatellite loci. Three vulturine guineafowls (Acryllium vulturinum) were included as outgroup A total of 66 alleles were observed with an average of 11.0 alleles per locus. The indigenous West African populations (Ghana and Benin) were more genetically diverse (Na = 9.8; Ho = 0.457) but less differentiated (FST = 0.162) compared to the non-indigenous populations in Japan (Na = 4.2; Ho = 0.236; FST = 0.389) The information from this study would be useful for selection and improvement programs necessary for the sustainable exploitation of this agriculturally and commercially important species as a suitable alternative to chicken.

Source: UG
Genetic diversity of polymorphic vaccine candidate antigens (apical membrane antigen-1, merozoite surface protein-3, and erythrocyte binding antigen-175) in Plasmodium falciparum isolates from Western and Central Africa

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
Genetic diversity of provitamin-A cassava (Manihot esculenta Crantz) in Sierra Leone

Understanding the genetic diversity among accessions and germplasm is an important requirement for crop development as it allows for the selection of diverse parental combinations for enhancing genetic gain in varietal selection, advancement and release. The study aimed to characterize 183 provitamin A cassava (Manihot esculenta Crantz) accessions and five Sierra Leonean varieties using morphological traits, total carotenoid content and SNP markers to develop a collection for conservation and further use in the cassava breeding program. Both morphological parameters and 5634 SNP markers were used to assess the diversity among the provitamin-A cassava accessions and varieties. Significant differences were observed among the accessions for most of the traits measured. The first five PCs together accounted for 70.44% of the total phenotypic variation based on yield and yield components among the 183 provitamin- A cassava accessions and five Sierra Leonean varieties. The present study showed that provitamin-A cassava accessions in Sierra Leone have moderate to high diversity based on morphological and molecular assessment studies. The similarity index among the 187 and 185 cassava accessions grouped them into 6 and 9 distinct clusters based on morphological and molecular analyses, respectively. A significant positive, but low correlation (r = 0.104; p\0.034), was observed between the two dendrograms. The results obtained will serve as a guide and basis of germplasm management and improvement for total carotenoid content, yield and African cassava mosaic disease resistance in Sierra Leone.

Source: UG
Genetic Diversity of Staphylococcus aureus in Buruli Ulcer

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
Genetic evidence of the unique identity of the West African Mangrove Oyster (Crassostrea tulipa) from the Gulf of Guinea

This research enabled the genetic identification of the West African mangrove oysters, Crassostrea tulipa, as well as establishing the evolutionary relationship between it and other Crassostrea species. Essentially, the study assisted in clearing up a long-standing confusion over this species’ synonymy with C. gasar. Also, the population structure of 60 C. tulipa individuals, from three different ecotypes, was analyzed using the mitochondrial cyto chrome oxidase I (COI) genes as a marker. Results provided the first genetic sequences for C. tulipa and deposited in the GeneBank. Optimal and consensus bootstrap Neighbor-Joining trees distinctively differentiated C. tulipa from other Crassostrea species and consistently formed a different clade with C. gasar, with no bootstrap value from either NJ, MPT, or UPG trees supporting their similarity. C. tulipa sequences occurred as different haplo types from other Crassostrea sp, with a mutation value as high as 288 and a haplotype diversity of 0.893 between C. tulipa and C. gasar sequences. High estimates of genetic distance (1.40–1.55) and patristic divergence were recorded between C. tulipa and C. gasar, in the same range as with seven other species. The study thus reveals the unique identity of C. tulipa as genetically distinct from C. gasar and other Crassostrea species. Based on the population structure analyses from the neutrality test, a low to high haplotype diversity h (0.000–0.963) and low nucleotide diversity π (0.00–0.378) were obtained. A negative mean Tajima’s D (− 0.65247), and a positive Fu’s Fs (3.194), suggest rare variations or low-frequency polymorphisms. In addition to serving as the basis for phylogeny, the identification of C. tulipa and the recent data on its population structure also serve as the basis for conservation efforts and hatchery-based aquaculture.

Source: UG
Genetic Improvement for Development of a Climate Resilient Food Legume Crops: Relevance of Cowpea Breeding Approach in Improvement of Food Legume Crops for Future

Review books or articles provide a critical and constructive analysis of existing published literature in a field, through summary, analysis, and comparison, often identifying specific gaps or problems and providing recommendations for future research. These are considered as secondary literature since they generally do not present new data from the author's experimental work. Review articles can be of three types, broadly speaking: literature reviews, systematic reviews, and meta-analyses. It also the researcher to stay abreast of new literature in the field.

Source: UG
Genetic incompatibilities in sweetpotato and implications for breeding end-user preferred traits

Sweetpotatoes utilization is low in Ghana due to lack of farmer and consumer preferred cultivars. Poor flowering and incompatibilities among genotypes limit breeding progress in its improvement. The objective was to assess compatibilities among sweetpotato genotypes to select good parents for breeding end-user preferred varieties for increased utilization. Twenty-one genotypes selected from 115 accessions evaluated across three contrasting environments were crossed using full diallel mating scheme. In all, 6388 crosses were carried out and 3214 seeds produced. This study sought to understand the genetic incompatibilities based on the number of seeds set per capsule after self- or cross-fertilization. Lack of flowering or poor flowering, and self- and cross-incompatibilities were major constraints to sweetpotato improvement found. Four genotypes (Histarch, Apomuden, Beauregard, and Ogyefo) were the best parents based on cross compatibilities and they can be used to determine the genetic control of beta-carotene, dry matter and sugar contents in sweetpotato. Histarch and Ogyefo are recommended as parents for the development of non-sweet, high dry matter sweetpotato varieties that are the preferred cultivars in Ghana because of their low sugar content. Use of many genotypes in hybridization and establishment of crossing blocks Hybridization in the minor cropping season is highly recommended.

Source: UG
Genetic interrelationships among phosphorus, nitrogen, calcium, and energy bioavailability in a growing chicken population

A random-mating population was used to study the genetic interrelationship between phytate P (PPB), Ca (CaB), N (NB), and energy bioavailability (EB), BW at 4 wk of age, relative growth (RG), and feed conversion ratio (FCR). Heritability estimates for PPB, CaB, NB, and EB were 0.09, 0.13, 0.16, and 0.10, respectively, and those of BW, RG, and FCR were 0.66, 0.15, and 0.10, respectively. Genetic correlations between PPB and BW, and FCR were moderate and negative, suggesting that improvement in PPB will impair growth. The genetic correlations between PPB and CaB, and EB and RG were positive and moderate, indicating that improvement in PPB would also lead to improved CaB, EB, and RG. Energy bioavailability was positively correlated with CaB, NB, PPB, and BW. Even though the genetic correlation between EB and the other traits measured, except RG and FCR, ranged from low to moderate, improving the ability of birds to utilize caloric energy in the feed would consequently improve PPB as well as growth. Improving PPB would reduce the amount of P in excreta and provide an additional savings if exogenous phytase were not added to poultry feed. The genetic correlation between PPB and NB was low but positive, whereas NB had a positive genetic correlation with BW. Therefore, selecting on NB will result in positive correlated responses in BW and PPB. Improving PPB and NB will not only improve productivity, but also reduce the polluting effects of P and N on the environment.

Source: UG
Genetic Markers of Benzimidazole Resistance among Human Hookworms (Necator americanus) in Kintampo North Municipality, Ghana

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
Genetic parameter estimates of growth traits of indigenous pigs in Northern Ghana

MTDFREML procedures were used to estimate heritabilities and genetic correlations for some growth traits using records of 1044 indigenous Ghanaian pigs. Growth traits analysed were birth weight (BW), pre-weaning average daily gain (ADG 1), weaning weight (WW), post-weaning average daily gain (ADG 2) and 180 day weight. Animal models employed had year of birth, season of birth, sex of piglet, parity of sow and litter size at birth as fixed effects and additive genetic value of animal, maternal genetic value of dam and permanent environmental effect of dam as random effects. Direct heritability for BW, ADG 1, WW, ADG 2 and 180 day weight was 0.06 ± 0.01, 0.21 ± 0.08, 0.14 ± 0.04, 0.22 ± 0.80 and 0.08 ± 0.69 respectively while corresponding maternal heritabilities were 0.75 ± 0.01, 0.24 ± 0.08, 0.57 ± 0.07, 0.63 ± 1.28 and 0.32 ± 1.03 respectively. Maternal heritabilities were therefore higher than direct heritabilities for growth traits. Genetic correlations found in this study among growth traits indicate that selection to improve one trait would be associated with favourable changes in the other traits. © 2009 Elsevier B.V. All rights reserved.

Source: UG
Genetic parameter estimation and selection in advanced breeding population of white Guinea yam

White Guinea yam (Dioscorea rotundata Poir.) is an important tuber crop grown extensively in tropical regions of West African yam belt. Tuber yield, dry matter content, and tolerance to yam mosaic virus are key traits used for identification and selection of superior varieties for commercial deployment. In this study, we estimated genetic parameters for fresh tuber yield, tuber dry matter content, and quantitative field tolerance to yam mosaic virus in 49 clones grown in multi-environment trials (METs). We conducted genomic prediction involving 6337 single nucleotide polymorphisms (SNPs) and phenotypic field evaluation of data collected on the three traits from four sites. Additive genetic and non-genetic factors contributed significantly to phenotypic variation of studied yam traits in METs but to varying degrees. The non-genetic effects were relatively high for most of the measured traits. Narrow-sense heritability values were low (<0.30) for all studied traits. Further analysis of the performance of the clones at test sites with additive main effects and multiplicative interaction (AMMI) analysis exhibited significant genotype by environment interactions (GEI) for the three traits. The AMMI identified TDr10/00412, TDr11/00055, and TDr09/00135 clones with lowest mean trait stability index and outstanding performance for fresh tuber yield (t ha−1), tuber dry matter, and mosaic virus resistance across sites. The elite clones identified could serve as useful source of alleles for the genetic improvement of the crop and possibly considered for release to farmers.

Source: UG
Genetic polymorphisms in MDR1, CYP3A4 and CYP3A5 genes in a Ghanaian population: a plausible explanation for altered metabolism of ivermectin in humans?

Abstract Background Ivermectin, a substrate of multidrug resistance (MDR1) gene and cytochrome P450 (CYP) 3A4, has been used successfully in the treatment of onchocerciasis in Ghana. However, there have been reports of suboptimal response in some patients after repeated treatment. Polymorphisms in host MDR1 and CYP3A genes may explain the observed suboptimal response to ivermectin. We genotyped relevant functional polymorphisms of MDR1 and CYP3A in a random sample of healthy Ghanaians and compared the data with that of ivermectin-treated patients with a view to exploring the relationship between suboptimal response to ivermectin and MDR1 and CYP3A allelic frequencies. Methods Using PCR-RFLP, relevant polymorphic alleles of MDR1 and CYP3A4 genes were analysed in 204 randomly selected individuals and in 42 ivermectin treated patients. Results We recorded significantly higher MDR1 (3435T) variant allele frequency in suboptimal responders (21%) than in patients who responded to treatment (12%) or the random population sample (11%). CYP3A4*1B, CYP3A5*3 and CYP3A5*6 alleles were detected at varied frequencies for the sampled Ghanaian population, responders and suboptimal responders to ivermectin. CYP3A5*1/CYP3A5*1 and CYP3A5*1/CYP3A5*3 genotypes were also found to be significantly different for responders and suboptimal responders. Haplotype (*1/*1/*3/*1) was determined to be significantly different between responders and suboptimal responders indicating a possible role of these haplotypes in treatment response with ivermectin. Conclusion A profile of pharmacogenetically relevant variants for MDR1, CYP3A4 and CYP3A5 genes has been generated for a random population of 204 Ghanaians to address the scarcity of data within indigenous African populations. In 42 patients treated with ivermectin, difference in MDR1 variant allele frequency was observed between suboptimal responders and responders.

Source: UG