Identification and molecular phylogenetics of lasiodiplodia parva associated with white, yam (dioscorea rotundata L.) in Ghana

Ten isolates of the fungus obtained from diseased yam tubers were identified using morphological characterisation, complemented with phylogenetic study, involving sequences of the rDNA-ITS region and part of the beta-tubulin gene of isolates. The pathogenicity of the isolates was tested on healthy yam tubers. The conidial morphology and size indicated that the isolates were Lasiodiplodia parva. In the phylogram, the isolates clustered with the type strain of L. parva and other L. parva strains of confirmed identities, in clade supported by a high bootstrap value. The fungus was able to cause the disease symptoms on artificially inoculated tubers, showing that it was responsible for the disease symptoms. The results showed that L. parva was responsible for the hard rot disease of yam in storage in Ghana, rather than the L. theobromae cited in the literature

Genotype-environment-interaction and stability of root mealiness and other organoleptic properties of boiled cassava roots

Open Access Journal; Published online: 03 Dec 2022Genetic enhancement of cassava aimed at improving cooking and eating quality traits is a major goal for cassava breeders to address the demand for varieties that are desirable for the fresh consumption market segment. Adoption of such cassava genotypes by consumers will largely rely not only on their agronomic performance, but also on end-user culinary qualities such as root mealiness. The study aimed to examine genotype × environment interaction (GEI) effects for root mealiness and other culinary qualities in 150 cassava genotypes and detect genotypes combining stable performance with desirable mealiness values across environments using GGE biplot analysis. Experiments were conducted using an alpha-lattice design with three replications for two years in three locations in Nigeria. The analysis of variance revealed a significant influence of genotype, environment, and GEI on the performance of genotypes. Mealiness scores showed no significant relationship with firmness values of boiled roots assessed by a penetration test, implying that large-scale rapid and accurate phenotyping of mealiness of boiled cassava roots remains a major limitation for the effective development of varieties with adequate mealiness, a good quality trait for direct consumption (boil-and-eat) as well as for pounding into ‘fufu’. The moderate broad-sense heritability estimate and relatively high genetic advance observed for root mealiness suggest that significant genetic gains can be achieved in a future hybridization program. The genotype main effects plus genotype × environment interaction (GGE) biplot analysis showed that the different test environments discriminated among the genotypes. Genotypes G80 (NR100265) and G120 (NR110512) emerged as the best performers for root mealiness in Umudike, whereas G13 (B1-50) and the check, G128 (TMEB693) performed best in Igbariam and Otobi. Based on the results of this study, five genotypes, G13 (B1-50), G34 (COB6-4), G46 (NR010161), the check, G128 (TMEB693), and G112 (NR110376), which were found to combine stability with desirable mealiness values, were the most suitable candidates to recommend for use as parents to improve existing cassava germplasm for root mealiness

Genome-wide association study of root mealiness and other texture-associated traits in cassava

Open Access Journal; Published online: 17 Dec 2021Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low

Genetic characterization of cassava (Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers

Open Access Article; Published online: 23 Dec 2019Dearth of information on extent of genetic variability in cassava limits the genetic improvement of cassava genotypes in Sierra Leone. The aim of this study was to assess the genetic diversity and relationships within 102 cassava genotypes using agro-morphological and single nucleotide polymorphism markers. Morphological classification based on qualitative traits categorized the germplasm into five different groups, whereas the quantitative trait set had four groups. The SNP markers classified the germplasm into three main cluster groups. A total of seven principal components (PCs) in the qualitative and four PCs in the quantitative trait sets accounted for 79.03% and 72.30% of the total genetic variation, respectively. Significant and positive correlations were observed between average yield per plant and harvest index (r = 0.76***), number of storage roots per plant and harvest index (r = 0.33*), height at first branching and harvest index (0.26*), number of storage roots per plant and average yield per plant (r = 0.58*), height at first branching and average yield per plant (r = 0.24*), length of leaf lobe and petiole length (r = 0.38*), number of leaf lobe and petiole length (r = 0.31*), width of leaf lobe and length of leaf lobe (r = 0.36*), number of leaf lobe and length of leaf lobe (r = 0.43*), starch content and dry matter content (r = 0.99***), number of leaf lobe and root dry matter (r = 0.30*), number of leaf lobe and starch content (r = 0.28*), and height at first branching and plant height (r = 0.45**). Findings are useful for conservation, management, short term recommendation for release and genetic improvement of the crop

Groundnut production constraints and farmers’ trait preferences: a pre-breeding study in Togo

Background Groundnut is an important legume crop in Togo. However, groundnut yield has been steadily decreasing for decades as a result of lack of organized breeding program to address production constraints. Though, low yielding varieties and late leaf spot have been often reported as the most important constraints, there is no documented evidence. Identifying and documenting the major production constraints is a prerequisite for establishing a good breeding program with clearly defined priority objectives and breeding strategies. Thus, the objectives of this study were to identify groundnut production constraints and assess farmers’ preferred traits. Methods A participatory rural appraisal approach was used to collect data on agronomic practices, farmers’ preferences, and possible threats to production through individual and group interviews. Three regions and three villages per region were selected based on the representativeness of groundnut production systems. In each village, 20 farmers were randomly selected and interviewed; thus, a total of 180 farmers were interviewed. Content analysis was carried out for qualitative data and for quantitative data generated within and across regions, comparative descriptive statistics were carried out. Differences in perception and preferences were assessed using chi-square tests. Results The study has revealed that, though there were some variation across the regions, traits pertaining to yield such as pod yield (66.66%) and pod size (12.12%) were the most important. Leaf spot diseases, rosette and peanut bud necrosis (37.77%) and insects such as pod sucking bug and bruchid (27.77%) were considered to be the most important constraints limiting groundnut production. Among diseases, farmers in all the three regions indicated that late leaf spot is of economic importance which they associated to various causes such as maturity, drought, or insects. No gender differences were observed for the perception of constraints and groundnut traits preferences. Land size is significantly influenced by age and gender. Besides, farmers have pointed the lack of improved varieties and the unavailability of groundnut seeds highlighting the necessity of a sustainable groundnut seed system linked with a strong breeding program. Conclusion This study has enabled understanding of the farming practices, constraints, and farmers preferred characteristics, thus providing the basis for a participatory breeding program in Togo which should consider that farmers perceive low yielding varieties and diseases as major constraints to production

Genetic Diversification and Selection Strategies for Improving Sorghum Grain Yield Under Phosphorous-Deficient Conditions in West Africa

Sorghum, a major crop for income generation and food security in West and Central Africa, is predominantly grown in low-input farming systems with serious soil phosphorus (P) deficiencies. This study (a) estimates genetic parameters needed to design selection protocols that optimize genetic gains for yield under low-phosphorus conditions and (b) examines the utility of introgressed backcross nested association mapping (BCNAM) populations for diversifying Malian breeding materials. A total of 1083 BC1F5 progenies derived from an elite hybrid restorer “Lata-3” and 13 diverse donor accessions were evaluated for yield and agronomic traits under contrasting soil P conditions in Mali in 2013. A subset of 298 progenies were further tested under low-P (LP) and high-P (HP) conditions in 2014 and 2015. Significant genetic variation for grain yield was observed under LP and HP conditions. Selection for grain yield under LP conditions was feasible and more efficient than the indirect selection under HP in all three years of testing. Several of the BCNAM populations exhibited yields under LP conditions that were superior to the elite restorer line used as a recurrent parent. The BCNAM approach appears promising for diversifying the male parent pool with introgression of diverse materials using both adapted Malian breed and unadapted landrace material from distant geographic origins as donors

Combining ability studies of grain Fe and Zn contents of pearl millet (Pennisetum glaucum L.) in West Africa

Micronutrient malnutrition is a major challenge in Africa, where half a million children die each year because of lack of micronutrients in their food. Pearl millet is an important food and fodder crop for the people living in the Semi-Arid regions of West Africa. The present study was conducted to determine the stability, combining ability, and gene action conditions of the high level of Fe and Zn content in grain and selected agronomic traits. Hence, eight genotypes were selected based on the availability of grain Fe and Zn contents and crossed in a full diallel mating design. Progenies from an 8 × 8 diallel mating along with the parents were evaluated in an alpha lattice design with three replications in three locations for two years. The parental lines Jirani, LCIC 9702 and MORO, had positive significant general combining ability (GCA) effects for grain Fe concentration, while Jirani and MORO had positive significant GCA effects for grain Zn concentration. For the specific combining ability (SCA), among the 56 hybrids evaluated, only the hybrids LCIC 9702 × Jirani and MORO × ZANGO had positive significant SCA effects for grain Fe concentration across locations, and for grain Zn concentration, the hybrids Gamoji × MORO, LCIC 9702 × Jirani, and ICMV 167006 × Jirani had positive significant SCA effects. The reciprocal effects were significant for grain Zn concentration, grain yield, flowering time, plant height, test weight, and downy mildew incidence, suggesting that the choice of a female or male parent is critical in hybrid production. Grain Fe and Zn concentration, flowering time, plant height, panicle length, panicle girth, panicle compactness, and downy mildew incidence were found to be predominantly under additive gene action, while grain yield and test weight were predominantly under non-additive gene action. A highly positive correlation was found between grain Fe and Zn concentrations, which implies that improving grain Fe trait automatically improves the grain Zn content. The stability analysis revealed that the hybrid ICMV 167006 × Jirani was the most stable and high-yielding with a high level of grain Fe and Zn micronutrients

Cross-species gene expression analysis of species specific differences in the preclinical assessment of pharmaceutical compounds

Animals are frequently used as model systems for determination of safety and efficacy in pharmaceutical research and development. However, significant quantitative and qualitative differences exist between humans and the animal models used in research. This is as a result of genetic variation between human and the laboratory animal. Therefore the development of a system that would allow the assessment of all molecular differences between species after drug exposure would have a significant impact on drug evaluation for toxicity and efficacy. Here we describe a cross-species microarray methodology that identifies and selects orthologous probes after cross-species sequence comparison to develop an orthologous cross-species gene expression analysis tool. The assumptions made by the use of this orthologous gene expression strategy for cross-species extrapolation is that; conserved changes in gene expression equate to conserved pharmacodynamic endpoints. This assumption is supported by the fact that evolution and selection have maintained the structure and function of many biochemical pathways over time, resulting in the conservation of many important processes. We demonstrate this cross-species methodology by investigating species specific differences of the peroxisome proliferatoractivator receptor (PPAR) a response in rat and human

Genetic diversity and inter-trait relationships among maize inbreds containing genes from Zea diploperennis and hybrid performance under contrasting environments

Open Access Journal; Published online: 27 Sep 2020Accurate estimation of genetic variability present in tropical maize inbreds with varying reactions to Strigahermonthica infestation is essential for efficient and sustainable utilization to ensure increased genetic gain in a breeding program. Thirty-six early maturing maize inbred lines and 156 single cross hybrids were evaluated under Striga-infested and non-infested conditions in Nigeria during the 2014 and 2015 cropping seasons. Under Striga infestation, grain yield ranged from 1134 kg ha−1 for TZEI 26 × TZEI 5 to 5362 kg ha−1 for TZdEI 173 × TZdEI 280. The average yield reduction of the hybrids under Striga infestation was 44% relative to the performance under non-infested environments. Using 4440 high-quality DArT markers, clustering and population structure analyses separated the inbred lines into three distinct groups based on the genetic distance indicating high level of genetic variability among the lines. The base index of the International Institute of Tropical Agriculture (IITA) identified 50% of the inbred lines as Striga resistant. The genetic diversity study provided an opportunity for selecting divergent parents for tagging candidate genes and quantitative trait loci for marker-assisted introgression of Striga resistance genes into early maturing tropical maize breeding populations. The most reliable secondary trait for indirect selection for grain yield under Striga infestation was the ear aspect

Learning from farmers to improve sorghum breeding objectives and adoption in Mali

Many efforts have been made to improve sorghum [Sorghum bicolor (L.) Moench] varieties, but adoption of improved varieties remains low. Sorghum has diverse panicle architecture and grain qualities that vary within and between races, and utilization and adoption may depend on these traits. Recent efforts in West Africa to improve local guinea race germplasm as a base material have diversified potential options: there are breeding materials with a range of panicle types with increased grain number per panicle and a range of droopiness, as well as laxness and threshability. This study was designed to expand our understanding about sorghum grain and panicle traits that are important for farmers in the Sudan savanna zone of Mali. We combined a sorghum panicle sorting activity with qualitative interviews in Mande and Dioïla to understand farmers’ knowledge and preferences about sorghum characteristics. A total of 20 panicle sorting activities and 20 interviews were conducted with men and women sorghum producers. Based on their roles and responsibilities in sorghum production and processing, farmers associated specific panicle types, plant types, and grain traits with aspects of pest control, threshability, storage duration, and yield. Farmers preferred open panicles and droopy architecture for disease and pest control; hard grains for storage and appropriate ratios of flour and grits; high density of grain on the panicle for yield; and specific glume qualities for threshability. Breeding programs need to consider these regional preferences and gender roles to develop appropriate material and increase adoption of productive varieties