ghanaopendata/ghanaian-research-english huggingface dataset:
Genetic Diversity and Genome-wide Association Studies of Bush Yam(Dioscorea praehensilis Benth.)

ABSTRACT Bush yam (Dioscorea praehensilis Benth.) is a wild yam that provides food and contributes to the livelihoods of people in West Africa. Several socio-cultural, nutritional and agronomic factors impede its production and commercialization. A participatory rural survey conducted in 2019 in 23 communities across Ghana's three main growing regions revealed poor culinary quality (39.9%) and agronomic traits (20.7%) as the leading causes of decreasing productivity and abandonment. A preliminary investigation of genetic diversity among 43 bush accessions previously collected and maintained at School of Agriculture, University of cape Coast, Central Region, Ghana using 11 simple sequence repeats (SSRs) revealed low genetic diversity, suggesting a need for regional germplasm collection. Quantitative traits (15) grouped 162 accessions into best performing accessions for tuber yield and yield-related traits, best in resistance to yam mosaic virus resistance and best for post-harvest tuber quality traits. Using 24 qualitative traits, a high variation among the accessions. Potential sources of genes for yield and quality attributes in 162 accessions of D. praehensilis to improve the predominant yam species, D. rotundata was evaluated. For tuber yield (23.47 t ha-1), yam mosaic virus (YMV) resistance (AUDPC=147.45) and tuber size (2.37), D. praehensilis accessions outperformed the best D. rotundata landraces. Population structure analysis based on hierarchical clustering, admixture and principal component analyses using 4,525 single nucleotide polymorphism (SNP) markers grouped D. praehensilis accessions into five clusters. Genome-wide association study revealed twenty-one SNPs associated with the agronomic and tuber quality traits. The identified SNPs accounted for approximately 16% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes with functions related to growth and development of tubers, quality traits and defence mechanisms against yam mosaic virus. This study provides the first insight into the genetic diversity and marker- trait association of bush yam using farmers’ indigenous knowledge, morphological and molecular approaches and genome-wide association studies

Source: UCC
Genetic diversity and population structure of Peronosclerospora sorghi isolates of Sorghum in Uganda

Sorghum is the third most important staple cereal crop in Uganda after maize and millet. Downy mildew disease is one of the most devastating fungal diseases which limits the production and productivity of the crop. The disease is caused by an obligate fungus, Peronosclerospora sorghi (Weston & Uppal) with varying symptoms. Information on the genetic diversity and population structure of P.sorghi in sorghum is imperative for the screening and selection for resistant genotypes and further monitoring possible mutant(s) of the pathogen. Isolates of P. sorghi infecting sorghum are difficult to discriminate when morphological descriptors are used. The use of molecular markers is efficient, and reliably precise for characterizing P. sorghi isolates. This study was undertaken to assess the level of genetic diversity and population structure that exist in P. sorghi isolates in Uganda. A total of 195 P. sorghi isolates, sampled from 13 different geographic populations from 10 different regions (agro-ecological zones) was used. Eleven (11) molecular markers, comprising of four Random amplified microsatellite (RAM) and seven (7) Inter-Simple Sequence Repeat (ISSR) markers were used in this study. The analysis of molecular variation (AMOVA) based on 11 microsatellite markers showed significant (P < 0.001) intra-population (88.9 %, PhiPT = 0.111) and inter-population (8.4 %, PhiPR = 0.083) genetic variation, while the genetic variation among regions (2.7 %, PhiRT = 0.022) was not significant. The highest genetic similarity value (0.987 = 98.7 %) was recorded between Pader and Lira populations and the lowest genetic similarity (0.913 = 91.3 %) was observed between Namutumba and Arua populations. The mean Nei’s genetic diversity index (H) and Shannon Information Index (I) were 0.308 and 0.471 respectively. Seven distinct cluster groups were formed from the 195 P. sorghi isolates based on their genetic similarity. Mantel test revealed no association between genetic differentiation and geographical distance (R 2 = 0.0026, p = 0.02) within the 13 geographic populations

Source: UCC
Genetic Diversity Of Cassava Mosaic Gemniviruses (Cmgs) In The Volta Region Of Ghana And Resistance Screening Of Improved Cassava Vareties To Cassava Mosaic Disease (Cmd)

Cassava Mosaic Disease is one of the major virus diseases limiting cassava production in Ghana and Africa. The disease accounts for low yields of cassava with over forty (40) improved cassava varieties (ICVs) bred and released to improve cassava production in Ghana. Household surveys in six cassavagrowing districts in the Volta Region indicates that all 180 respondents had experienced CMD on their farms but did not know the cause and majority (74.4%) do not control the disease. A field survey in the six districts showed CMD was prevalent and severe with high incidence of coinfections with ACMV and EACMV after serological analysis. PCR detected ACMV (78.9%), EACMV (1.1 %) and co-infection (20%) in all the districts but not in all the farms surveyed. Next generation sequencing of field samples using lllumina MiSeq sequencing platform led to the assembly of twelve full length CMGs genomes (6 ACMV DNA-A components, 3 ACMV DNA-B components and 3 DNA-A EACMV components) which aligned closely to already published isolates identified in West Africa. TAS ELISA screening of21 ICVs evaluated in 2018/2019 detected ACMV in all varieties but not 'Hemaa' and' AGRA' from the coastal savannah. EACMV was detected in varieties' Ampong, TEK, Sika, Lamesese, Abasafita, Amansan, and Esam'from the Coastal savannah and varieties 'Ampong, Lamesese, Botan, Sika, AGRA, IFAD, and Capevars' from the Forest zone. Graft challenge of rcvs in the screen house using CMDinfected rootstocks showed that all the rcvs are resistant to EACMV except Amansan, Abrabopa and AGRA. Generally, all the rcvs are showed mild to moderate infection to CMD following screening using T AS-ELISA, PCR and graft challenge with infected rootstocks in two years.

Source: UCC
Genetic Diversity Studies on the West African Mangrove Oyster, Crassostrea Tulipa Along the Coast of Ghana

ABSTRACT The West African mangrove oyster, Crassostrea tulipa (Lamarck 1819) is abundant in many coastal ecosystems and they are a rich source of protein. Despite its abundance, ecological, and economic importance, little is known about their diversity and evolutionary history. There are challenges associated with the use of morphological characters only, therefore, there has been a shift to the use of genetic markers to determine the oyster species diversity and taxonomy. The study sought primarily to undertake genetic diversity studies on the West African mangrove oyster, C. tulipa occurring along the coast of Ghana by the utilization of microsatellite markers. This was an attempt to characterize and establish if the same species of C. tulipa was occurring along the coast of Ghana from the Volta estuary (Anyanui), Densu estuary, Narkwa lagoon, Amisano lagoon, Benya lagoon, Whin estuary and Dominli lagoon. The physico-chemical parameters recorded in all the seven brackish systems were within tolerable ranges. The oysters exhibited negative allometric growth in their morphometric relationships. Low genetic variability was observed within the populations (He = 0.391, FIS = 0.791) and this may be attributed to inbreeding and limited gene flow. Small to moderate genetic differentiation was discovered between the populations where the FST range was between 0.033 and 0.100. Anyanui and Narkwa populations were more genetically differentiated whiles Densu and Dominli populations were vice versa. There was no relationship between genetic distance and geographical distance therefore the genetic structure of C. tulipa occurring along the coast of Ghana did not follow any geographical pattern of distribution.

Source: UCC
Genetic estimates of water stress in tomato (Lycopersicum esculentum

Availability of moisture is a major environmental constraint militating against crop yield world-wide especially in Semi-Alid Tropics. SAMTOM 3 was used to obtain genetic information assess four drought criteria and their associations. Simulated drought condition was applied (3- and 14-day watering interval). The experiment was Randomized Complete Block Design, replicated 4 times. Differential trait responses were obtained, number of flowers ab01ti01L number of fruit/plants, number of flower buds/plant and fruit weight were severely affected by simulated water stress. The calculated quantitative drought tolerance indices; Mean Productivity (MP), Geometric Mean GMP) Tolerance Index (TI) and Percent Injury (%I) are effective in improving yield under drought condition. However, compellation analysis indicated that the most suitable drought tolerance QHte1ia are TI and %I. Valiance components and heritability estimates were calculated for all the traits studied

Source: UCC
Genetic markers associated with Striga Gesnerioides resistance and seed sizes in cowpea [Vigna Unguiculata (L.) Walp.] Inbred lines

Production of cowpea is severely hampered by different races of the parasitic weed, Striga gesnerioides. Cultivation of Striga-resistant cowpea is the most reliable protocol to effectively combat the parasite. The current study reported the identification of genetic markers associated with multi-race-Striga resistance and seed size across the genome of cowpea RIL populations. The landrace GH3684 from Ghana was tested for resistance against all known races of Striga gesnerioides in West Africa. Pot experiments were used to test for resistance in each line against Striga populations collected from Northern Ghana (GH) and Nigeria (SG3). Seed size was measured in field trials. SSR and SNP markers were identified and used for phylogenetic analysis and genetic mapping. A genetic linkage map was constructed with QTL IciMapping. Segregation of SSR-1 marker with known association with the Striga resistance gene rsg3 was 100 % consistent with the cowpea phenotypes in SG3. This study indicated that the SG3 resistance gene is located at 12.60 cM away from that of the GH race. On the whole, 70 % of the inbred lines of cowpea were resistant to Striga in Ghana and the lines designated UCC-11, UCC-24, UCC-32, UCC-122, UCC-221, UCC-241, UCC-328 (best RIL candidates for release) and GH3684 were immune to all 7 known races of Striga in West Africa. SARC-LO2 had resistance to four races of Striga (SG2, SG4z, SG5 and SG6). The low genetic diversity and polymorphism information content suggest close genetic relatedness within the RIL population. One and five SNP marker(s) were found to be associated with cowpea seed size and Striga resistance respectively.

Source: UCC
Genetic studies on the inheritance of storage-induced cooking time in cowpeas [Vigna unguiculata (L.) Walp]

Cowpeas provide food and income for many small-holder farmers in Africa. Cowpea grains contain substantial quantities of protein, carbohydrates, vitamins, and fiber. In areas where subsistence farming is practiced, cowpea’s protein is cheaper than that obtained from other sources such as fish, meat, poultry or dairy products and combines well with cereal grains in diets. However, long-cooking times, typical of many grain legumes, is a major limitation to the utilization of cowpeas especially among the lowincome and growing middle-income population of Africa. Long periods of cooking cowpeas lead to loss of nutrients, loss of useful time and increased greenhouse gas emission through increased burning of firewood. Fast-cooking cowpeas has the potential to deliver highly nutritious food to the hungry within shorter periods, encourage less use of firewood, improve gender equity, increase the consumption of cowpeas respectively while narrow sense heritabilities were 0.84 and 0.88 respectively. Genetic advances were 27.09 and 40.40 respectively. High narrow-sense heritabilities and moderate genetic advance for the fast-cooking trait indicated the presence of additive genes in the trait and the possibility of introgressing the trait into farmer-preferred varieties using conventional selection methods. However, due to significant epistatic gene effects observed, effective selection for fast-cooking trait would be appropriate at advanced generations

Source: UCC
Genetic Susceptibility for Cervical Cancer in African Populations: What Are the Host Genetic Drivers?

Human papillomavirus (HPV) is an essential but not a sufficient cervical cancer etiological factor. Cancer promoters, such as host genetic mutations, significantly modulate therapeutic responses and susceptibility. In cervical cancer, of interest have been viral clearing genes and HPV oncoprotein targets, for which conflicting data have been reported among different populations. This expert analysis evaluates cervical cancer genetic susceptibility biomarkers studied in African populations. Notably, the past decade has seen Africa as a hotbed of biomarker and precision medicine innovations, thus potentially informing worldwide biomarker development strategies. We conducted a critical literature search in PubMed/MEDLINE, Google Scholar, and Scopus da- tabases for case–control studies reporting on cervical cancer genetic polymorphisms among Africans. We found that seven African countries conducted cervical cancer molecular epidemiology studies in one of Casp8, p53, CCR2, FASL, HLA, IL10, TGF-beta, and TNF-alpha genes. This analysis reveals a remarkable gap in cervical cancer molecular epidemiology among Africans, whereas cervical cancer continues to disproportionately have an impact on African populations. Genome-wide association, whole exome- and whole-genome sequencing studies confirmed the contribution of candidate genes in cervical cancer. With such advances and omics technologies, the role of genetic susceptibility biomarkers can be exploited to develop novel interventions to improve current screening, diagnostic and prognostic methods worldwide. Exploring these genetic variations is crucial because African populations are genetically diverse and some variants or their combined effects are yet to be discovered and translated into tangible clinical applications. Thus, translational medicine and flourishing system sciences in Africa warrant further emphasis in the coming decade.

Source: UCC
Genetic variation in rhizosheath, root hair, root system architecture and phosphorus use efficiency among cowpea genotypes (Vigna unguiculata (L) Walp)

Cowpea (Vigna unguiculata (L) Walp) is an economically important legume crop of vital importance to the livelihood of several millions of people. Even so, cowpea yields on African farmers’ fields are still below the potential yield of the crop. This is, largely, as a result of the use of unimproved genotypes and farming on phosphorus (P)-poor soils, which are pervasive in the tropics. Plants have evolved several strategies to obtain adequate P for their growth under P limiting conditions. These strategies include modification of root system architecture (RSA) and longer root hairs. Root hairs can be measured using rhizosheath, sheet of soil retained on roots after excavation and shaking. Breeding for cowpea genotypes with superior RSA, rhizosheath and root hair traits will help in achieving food security. The variation in rhizosheath, RSA and root hair were quantified among sixty (60) cowpea genotypes grown up to 21 d under greenhouse conditions. Twenty (20) genotypes were selected for further screening on three (3) external P concentrations [P]ext (i.e.: 0, 250 and 500 mg P/kg soil). Analyses were conducted on rhizosheath, root hair, RSA and biomass traits. The cowpea genotypes were also analysed for variation in P use efficiency (PUE) parameters including agronomic P use efficiency (APE), P uptake efficiency (PUpE), and P efficiency ratio (PER). There were genetic variations among cowpea genotypes in almost all the traits examined. Genotypes with longer root hairs produced larger rhizosheath mass compared to genotypes with larger root hair density. Increasing [P]ext resulted in a significant increase in rhizosheath mass, root hair density, biomass, shoot P concentration and content except for root hair length, which was reduced with increasing [P]ext. Substantial variation was observed for shoot-P, root-P and various measures of PUE among the cowpea genotypes. Some genotypes, including MU9, IT91, Sunshine and WC10*WC36 developed longer root hairs under low P conditions and these were categorised as P-efficient genotypes. Root system and root hair traits including root hair density, root hair length and total root length correlated with PUE in cowpea. The results could be used to select for cowpea -genotypes with improved PUE for use on P-poor soils and provide potential materials and targets for breeding new cowpea cultivars better adapted to P-poor soils in Ghana

Source: UCC
Genetically driven brain serotonin deficiency facilitates panic-like escape behavior in mice

Multiple lines of evidence implicate brain serotonin (5-hydroxytryptamine; 5-HT) system dysfunction in the pathophysiology of stressor-related and anxiety disorders. Here we investigate the influence of constitutively deficient 5-HT synthesis on stressor-related anxiety-like behaviors using Tryptophan hydroxylase 2 (Tph2) mutant mice. Functional assessment of c-Fos after associated foot shock, electrophysiological recordings of GABAergic synaptic transmission, differential expression of the Slc6a4 gene in serotonergic neurons were combined with locomotor and anxiety-like measurements in different contextual settings. Our findings indicate that constitutive Tph2 inactivation and consequential lack of 5-HT synthesis inTph2 null mutant mice (Tph results in increased freezing to associated foot shock and a differential c-Fos activity pattern in the basolateral complex of the amygdala. his is accompanied by altered GABA ergic transmission as observed by recordings of inhibitory postsynaptic currents on principal neurons in the basolateral nucleus, which may explain increased fear associated with hyperlocomotion and escape-like responses in aversive inescapable contexts. In contrast, lifelong 5-HT defciency as observed inTph2 heterozygous mice (Tph+/− ) is able to be compensated through reduced GABAergic transmission in the basolateral nucleus of the amygdala based onSlc6a4 mRNA upregulation in subdivisions of dorsal raphe neurons. This results in increased activity of the basolateral nucleus of the amygdala due to associated foot shock. In conclusion, our results reflect characteristic syndromal dimensions of panic disorder and agoraphobia. Thus, constitutive lack of 5-HT synthesis influence the risk for anxiety- and stressor-related disorders including panic disorder and comorbid agoraphobia through the absence of GABAergic-dependent compensatory mechanisms in the basolateral nucleus of the amygdala

Source: UCC
The genetics of the butterfly hypolimnas misippus (L.): The classification of phenotypes and the inheritance of forms misippus and inaria

Hypolimnas misippus is a polymorphic and mimetic butterfly with a pantropicaP distribution. The polymorphism is autosomal and female-limited, the several female forms being generally regarded as Batesian mimics of the distasteful, toxic and polymorphic danaine butterfly Danaus chrysippus. The female phenotypes of H. misippus are described and classified. New data, from the rearing of 140 broods of H. misippus in Ghana and Sierra Leone, are analysed together with older material (21 broods) from other parts of Africa. Form misippus (genotype M-) is found to be genetically dominant to form maria (genotype mm). However, a large proportion of mm butterflies has an intermediate phenotype, especially in association with white on the hiudwing. Evidence is adduced to show that the genes giving hindwing white are variably epistatic over the 'maria' pattern in the mm genotype, producing a phenotype transitional to or even identical to misippus. The various intermediate phenotypes are poor mimics of D. chrysippus: their abundance, geographical range and, hence, significance have been much underestimated.

Source: UCC
The genetics of the butterfly Hypolimnasmisippus (L.):

Hypolimnas misippus is a polymorphic and mimetic butterfly with a pantropical distribution. The polymorphism is autosomal and female-limited, the several female forms being generally regarded as Batesian mimics of the distasteful, toxic and polymorphic danaine butterfly Danaus chrysippus. The female phenotypes of H. misippus are described and classified. New data, from the rearing of 140 broods of H. misippus in Ghana and Sierra Leone, are analysed together with older material (21 broods) from other parts of Africa. Form misippus (genotype M-) is found to be genetically dominant to form inaria (genotype mm). However, a large proportion of mm butterflies has an intermediate phenotype, especially in association with white on the hindwing. Evidence is adduced to show that the genes giving hindwing white are variably epistatic over the ‘inaria’ pattern in the mm genotype, producing a phenotype transitional to or even identical to misippus. The various intermediate phenotypes are poor mimics of D. chrysippus: their abundance, geographical range and, hence, significance have been much underestimated. © The Genetical Society of Great Britain.

Source: UCC
Genèse du conflit de genre : réflexions critiques dans C’est le soleil qui m’a brûlée et Tu t’appelleras Tanga de Calixthe Beyala

This paper examines the genesis of gender conflict in C’est le soleil qui m’a brulée and Tu t’appelleras Tanga of Calixthe Beyala. Driven by the impulsion of feminism, Beyala writes to bring to the fore the age ld conflict between man and woman. This antithetical situation resulting from biological differences between the two sexes is a potential source of perpetual conflict which serves as raw material for Beyala’s literary texts. The study seeks to critically examine the sources and the nature of this conflict, as brought to the fore in the two narrative texts. In so doing, it points to the fact that, gender conflict emanating from patriarchal oppression is inimical to the rights of women. As it remains a potential threat to sustainable human development. The paper is posited within Carolyn Allen’s (1978) feminist conceptual framework. It is informed by an analysis of textual data collected from the aforementioned narrative texts of Beyala

Source: UCC
Genèse du conflit de genre: Réflexions critiques dans C'est le soleil qui m'a brûlée et Tu t'appelleras Tanga de Calixthe Beyala

This paper examines the genesis of gender conflict in C'est le soleil qui m'a brulée and Tu t'appelleras Tanga of Calixthe Beyala. Driven by the impulsion of feminism, Beyala writes to bring to the fore the age-old conflict between man and woman. This antithetical situation resulting from biological differences between the two sexes is a potential source of perpetual conflict which serves as raw material for Beyala's literary texts. The study seeks to critically examine the sources and the nature of this conflict, as brought to the fore in the two narrative texts. In so doing, it points to the fact that, gender conflict emanating from patriarchal oppression is inimical to the rights of women. As it remains a potential threat to sustainable human development. The paper is posited within Carolyn Allen's (1978) feminist conceptual framework. It is informed by an analysis of textual data collected from the aforementioned narrative texts of Beyala.

Source: UCC