S. K. Offei

Linking science and farmers' innovative capacity: diagnostic studies from Ghana and Benin

The article is an introduction to a series of articles about diagnostic studies carried out by eight PhD students in Ghana and Benin. These studies form a prelude to their experimental action research with groups of farmers to develop technologies that work in local conditions and are acceptable to farmers. A last article reports on a comparison of these eight studies by the ninth PhD student in the Convergence of Sciences (CoS) project. In this introductory article, it is argued that the need to ground agricultural research in the needs and circumstances of farmers is as strong as the need to ground research in the international scientific discourse. It explores the reasons why the West African context requires careful diagnostic studies to be able to design agricultural research that is of any use. It introduces preanalytical choice as an overriding concept to explain why choices that reduce the degrees of freedom have to be made explicitly on the basis of criteria. Such criteria are suggested for the quality of preanalytical choices, and the paper ends by examining the way the CoS project made some of its choices

RAPD-based genetic diversity study of fifty cassava (Manihot esculenta Crantz) genotypes

Fifty cassava clones were studied using RAPD technique. They included landraces from the Wenchi, Nkoranza, Dormaa Ahenkoro and Asonafo districts of the Brong Ahafo region of Ghana and three improved varieties. Genetic diversity of these genotypes was studied using four primers, OPK-01, OPR-02, OPR-09 and OPJ-14. A total of 41 different bands were detected. Levels of polymorphic fragments detected by the four primers ranged from 90% to 100%. By pooling bands from individual accessions together, mean number of fragments per accession per primer ranged from 5.50±1.04 for the Improved cultivars to 7.00±0.71 for populations of landraces from Dormaa. Mean frequencies of fragments not detected by the primers for the accessions were 0.524±0.12, 0.460±0.12, 0.561±0.12 and 0.523±0.12 for landraces from Wenchi, Nkoranza, Dormaa Ahenkro, Asonafo and the Improved varieties, respectively. The grand mean frequency of individuals showing fragments not present in populations was 0.522±0.10. Genetic diversity estimates ranged from 0.290 to 0.425 (mean 0.352±0.05) for primer OPK-01, 0.001 to 0.381 (mean 0.309±0.06) for primer OPR-02, 0.335 to 0.344 (mean 0.283±0.04) for primer OPR-09 and 0.152 to 0.352 (mean 0.261±0.07) for primer OPJ-14. Within the accessions mean gene diversity estimates were 0.316±0.03, 0.293±0.09, 0.331±0.02, 0.322±0.07 and 0.247±0.03 for accessions from Wenchi, Nkoranza, Dormaa Ahenkro, Asonafo districts and the Improved varieties, respectively. Interpopulational genetic divergence ranged from 0.069 to 0.203 (mean 0.119±0.04). Rate of nucleotide substitution among the landraces was 9.8 per cent per site per year, while that for the Improved varieties was 15 per cent.

Assessing production constraints, management and use of sorghum diversity in north-east Ghana: a diagnostic study

This paper reports on the results of a diagnostic study conducted to assess the problems and needs of sorghum farmers in north-east Ghana with the aim of determining the type of research that would be useful for them in their own context. The importance of the crop and its position within the cropping system are identified. Sorghum is still an integral part of the livelihoods of farmers. The crop is very versatile and not only contributes to food security but also plays a part in the socio-cultural, socioeconomic, and religious aspects of the lives of farmers. Farmers have different uses for the varieties they grow, which depends on the morphological, agronomic and gastronomic traits of the crop. Sorghum varieties introduced from the research institutions have several problems including lodging, poor grain quality, bird damage and precocious germination. Farmers have developed management strategies for dealing with some of these problems. Nevertheless, further work is required by breeders to make the varieties more acceptable to users. Sorghum production constraints identified include poor soils, erratic rainfall and pest infestation of the grain during storage. The diagnostic study suggests that because farmers produce their own seed, enhancing their ability to improve the quality of their seed would be of benefit to them. The study further underscores the importance and value of diversity for farmers. It also highlights their understanding of diversity, and management and use of variation in their agronomic practices. Areas identified for further research together with farmers aim at enhancing farmers’ knowledge towards strengthening their practices in diversity management and improving seed storage practices.

Diversity in 113 cowpea (Vigna unguiculata (L) Walp) accessions assessed with 458 SNP markers

Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection.

GENETIC CONTROL OF SEED SIZE IN COWPEA (Vigna unguiculata (L.) Walp)

Seed size contributes to yield and it is also a consumer trait of cowpea in Ghana and other parts of the world. Ghanaian consumers tend to prefer large seeded cowpea to small sizes although, Ghanaian varieties have smaller seeds compared to the imported types. This might be a contributing factor to high importation of cowpea to Ghana. To breed cowpeas with large grains, it is paramount to understand the inheritance of the trait. Generation mean analysis was performed to estimate gene actions on seed size of cowpea using CB27 and Gh3710 as the large and small seeded parents respectively. It was observed that eight genes control seed size and that small seed is partially domi- nant over large seed. The estimated broad sense heritability was 84% while the narrow sense was 35%. Both additive and non-additive genes with their interactions in the exception of additive - additive had significant effect on seed size inheritance in cowpea. The inheritance of seed size was observed to be complex, it was suggested that combinations of methods such as single seed descent and backcross methods with selection from early generations through advanced level would help improve seed size of cowpea.

Identification of Pro-vitamin A Cassava (Manihot esculenta Crantz) Varieties for Adaptation and Adoption through Participatory Research

In spite of diligent efforts by National Root Crops Research Institute (NRCRI) Umudike and International Institute of Tropical Agriculture (IITA) to make Nigeria the largest producer of cassava in the world, the adoption rate of elite cultivars by farmers is about 40% and that is unacceptable. In addition, all cassava cultivars presently grown in Nigeria are low in essential minerals, vitamins, and protein content, and high in cyanogenic content. Cassava with yellow roots contains elevated levels of β-carotene (pro-vitamin A), an essential nutrient, but they are not commonly grown in Nigeria. Because farmers select cultivars based on multiple criteria, participatory rural appraisal and selection are essential for a successful adoption of new improved varieties. A participatory rural appraisal (PRA) and sensory evaluation were conducted in Abia, Imo, and Ebonyi states of Nigeria to assess farmers’ preferences for pro-vitamin A cassava. Some of the farmer-preferred traits included high yield, early maturity, tolerance to pests and diseases, sweetness, high amount of dry matter (DM) content, easy peeling, marketable roots, and roots that keep long in the ground without decaying. High pro-vitamin A cassava cultivars TMS 01-1368, TMS 05-1636, and TMS 05-0473 were better than farmers’ cultivar NR 8082, because of their color, high premium price, nutritional value, texture, among others, and were selected for adoption.

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.

Identification and molecular characterisation of Colletotrichum species from avocado, citrus and pawpaw in Ghana

Owing to previous identifications based solely on morphological characteristics, the identity of the causal agents of anthracnose disease of pawpaw and avocado in Ghana is in doubt. In addition, the pathogen has not been identified previously on citrus. In this study, isolates of the pathogen were obtained from anthracnose lesions on avocado and pawpaw, and atypical anthracnose lesions on citrus. The isolates were identified using PCR with species-specific primers, complemented by phylogenetic analysis of nucleotide sequences of the internal transcribed spacer region and partial glyceraldehyde-3-phosphate dehydrogenase gene. The pathogenicity of the isolated fungi was determined on detached matured fruits. All isolates, including those isolated from citrus, were identified as Colletotrichum gloeosporioides from the expected 480 bp PCR products amplified by PCR. The phylogenetic analysis showed that isolates from avocado and pawpaw were C. siamense, rather than C. gloeosporioides, whereas isolates from citrus were C. gloeosporioides sensu stricto. The pathogens were able to induce disease only on wounded mature fruits.

Agronomic performance and genotypic diversity for morphological traits among cassava genotypes in the guinea savannah ecology of Ghana

We evaluated the agronomic performance and diversity for morphological traits among a collection of local and exotic cassava genotypes in the Guinea Savannah agroecology of Ghana. One hundred and fifty cassava genotypes were assessed using 28 agro-morphological (18 qualitative and 10 quantitative) traits recorded from three months after planting until harvesting at 12 months after planting. There was significant genetic variability among the genotypes for most of the traits evaluated. High broad sense heritability was observed for most of the traits. Principal component analyses of the traits indicated that the first three principal component axes which accounted for more than 55% of the variation for 10 quantitative traits included storage root yield, number of leaves, harvest index, height at first branching, and plant height as the most important traits. A greater proportion of the phenotypic variances of plant height, height at branching, and harvest index were accounted for by genetic variances indicating that progress could made with selection. Pearson correlation analysis indicated that a number of traits were related to growth and yield of cassava in the Guinea Savanna ecology, making indirect selection for root yield possible. The study revealed ample genotypic variation in these morphological and agronomic traits to support selection for improved varieties.

Conversion of Microsatellite Markers to Single Nucleotide Polymorphism (SNP) Markers for Genetic Fingerprinting of Theobroma cacao L.

The majority of the worlds cacao for chocolate manufacture is produced in West Africa. Cocoa breeding programs in West Africa need genetic markers to reduce the time needed for improving cocoa by screening seedlings for the presence of the markers rather than mature plants for the phenotypic traits (i.e., marker-assisted selection [MAS]). For MAS to be successful, the breeder must have both access to markers linked to desired traits and a convenient marker-assay system that can be performed locally. In this study, microsatellite markers that flanked disease resistance quantitative trait loci (QTL) but could not be assayed conveniently in West Africa were converted using a genome walking method into single nucleotide polymorphism (SNP) markers that could be assayed locally. The SNP and microsatellite markers were equally effective in identifying off-types in two different mapping populations of cacao. Also, SNPs cast doubt on whether all microsatellite markers are identical by descent.