Browsing by Author "Ephraim Nuwamanya"

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A high throughput phenotyping technique for banana cultivar Sukali Ndizi based on internal fruit quality attributes
(International Journal of Science and Technology Research Archive, 2022-12-30) Henry Buregyeya; Steven Kashub. Tumwesigye; Ephraim Nuwamanya; Moses Matovu; Priver Namanya; Kephas Nowankunda; Wilberforce K Tushemereirwe; Patrick Rubaihayo
Background: Sukali Ndizi quality traits such as Total soluble solid (TSS) content, pulp texture and sugar/acid (S/A) ratio are critical in quality assessment. Screening very large numbers of fruit genotypes has prompted the development of a high throughput method using Near Infrared spectrometry (NIRS). Results: The calibration procedure for the attributes of TSS, pulp texture and S/A ratio was optimized with respect to a reference sampling technique, scan averaging, spectral window, data pre-treatment and regression procedure. Calibration equations for all analytical characteristics were computed by NIR Software ISI Present WINISI using Modified Partial Least Squares (MPLS) and Partial Least Squares. The quality of calibration models were evaluated by Standard Error of Calibration and coefficient of determination parameters between the measured and the predicted values. The results obtained with FOSS NIR systems 2500 spectrometer (model DS 2500) using the 350-2500 nm range, showed good prediction of the quality traits TSS content, pulp texture and S/A ratio. The MPLS method produced satisfactory Calibration model performance for TSS, texture and S/A ratio, with typical Rc2 of 0.73%Brix, 0.69kgf and 0.7; and root mean squared standard error of calibration of 0.73%Brix, 0.25kgf and 5.36 respectively. This is a good set of quality traits predicting Sukali Ndizi quality with NIRS with robustness, as it was obtained by using diverse Ndizi populations. Conclusions: This can be a useful tool to phenotype large numbers of Ndizi hybrids per day, making it possible to reduce on the resources spent when utilizing organoleptic evaluation selection technique.
Development and validation of near-infraredspectroscopy procedures for prediction ofcassava root dry matter and amylose contentsin Ugandan cassava germplasm
(Journal of The Science of Food and Agriculture, 2023-11-23) Ephraim Nuwamanya; Enoch Wembabazi; Michael Kanaabi; Fatumah Babirye Namakula; Arnold Katungisa; Ivan Lyatumi; Williams Esuma; Emmanuel Oladeji Alamu; Dominique Dufour; Robert Kawuki; Fabrice Davrieux
BACKGROUND: Cassava utilization for food and/or industrial products depends on inherent properties of root dry matter con- tent (DMC) and the starch fraction of amylose content (AC). Accordingly, in the present study, near-infrared reflectance spectroscopy (NIRS) models were developed to aid breeding and selection of DMC and AC as critical industrial traits taking care of root sample preparation and cassava germplasm diversity available in Uganda. RESULTS: Upon undertaking calibrations and cross-validations, best models were adopted for validation. DMC in calibration samples ranged from 20 to 45 g 100g−1, whereas, for amylose content, it ranged from 14 to 33 g 100g−1. In the validation set, average DMC was 29.5 g 100g−1, whereas, for amylose content, it was 24.64 g 100g−1. For DMC, a modified partial least square regression model had regression coefficients (R2) of 0.98 and 0.96, respectively, in the calibration and validation set. These were also associated with low bias (−0.018) and ratio of performance deviation that ranged from 4.7 to 5.0. In addition, standard error of prediction values ranged from 0.9 g 100g−1 to 1.06 g 100g−1. For AC, the regression coefficient was 0.91 for the calibration set and 0.94 for the validation set. A bias equivalent to −0.03 and a ratio of performance deviation of 4.23 were observed. CONCLUSION: These findings confirm the robustness of NIRS in the estimation of dry matter content and amylose content in cassava roots and thus justify its use in routine cassava breeding operations.
East African highland cooking banana: towards an efficient selection of hybrids with user-preferred food quality traits
(Journal of The Science of Food and Agriculture, 2023-10-24) Kephas Nowakunda; Elizabeth Khakasa; Hernan Ceballos; Akankwasa Kenneth; Robooni Tumuhimbise; Christophe Bugaud; Moreen Asasira; Brigitte Uwimana; Alexandre Bouniol; Ephraim Nuwamanya; Lora Forsythe; Pricilla Marimo; Dominique Dufour; Wilberforce Tushemereirwe
BACKGROUND: Determinants of culinary qualities of East African highland cooking bananas (EAHCB) are not well known. This constrains the inclusion of user-preferred traits in breeding. The present study aimed to quantify key indicators of user-preferred characteristics to enable selection of acceptable hybrids. RESULTS: Qualitative characteristics that drive preference were big bunches (15–34 kg), long straight/slightly curved fingers (12–23 cm), yellowness and soft texture. Descriptive sensory analysis of the intensity of colour and texture the 23 genotypes revealed that landraces Kibuzi, Mbwazirume, Nakitembe and Mpologoma had higher intensity of yellowness and lower intensity of hardness (softer) and a low score (≤ 1.0) of astringency taste. A preference test showed that they had higher acceptability scores. Biochemical, instrumental and sensory data revealed correlations between sensory firmness and instrumental hardness (r = 0.5), sensory firmness and amylopectin (r = −0.54), suggesting that qualitative descriptions can be predicted by instrumental and biochemical indicators. Significant (P < 0.05) variations in amylose and total starch content were observed in different varieties. Moderate correlations between instrumental hardness and firmness in mouth (r = 0.55), cohesiveness and firmness in the mouth (r = 0.57), and adhesiveness and firmness in the mouth (r = 0.64) were observed. Surprisingly, carotenoids content was not correlated with yellowness in cooked matooke. However, positive correlations were observed between chroma (b*) parameters of raw matooke and sensorial assessed color on cooked samples. CONCLUSION: Qualitative characteristis; the bunch, pulp colour and texture; that drive users-preference in the EAHCB were quantified, paving way for breeders to use them to select genotypes with these attributes early in the breeding process. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
East African highland cooking banana: towards an efficient selection of hybrids with user-preferred food quality traits
(Journal of The Science of Food and Agriculture, 2023-11-13) Kephas Nowakunda; Elizabeth Khakasa; Hernan Ceballos; Akankwasa Kenneth; Robooni Tumuhimbise; Christophe Bugaud; Moreen Asasira; Brigitte Uwimana; Alexandre Bouniol; Ephraim Nuwamanya; Lora Forsythe; Pricilla Marimo; Dominique Dufour; Wilberforce Tushemereirwe
BACKGROUND: Determinants of culinary qualities of East African highland cooking bananas (EAHCB) are not well known. This constrains the inclusion of user-preferred traits in breeding. The present study aimed to quantify key indicators of user-preferred characteristics to enable selection of acceptable hybrids. RESULTS: Qualitative characteristics that drive preference were big bunches (15–34 kg), long straight/slightly curved fingers (12–23 cm), yellowness and soft texture. Descriptive sensory analysis of the intensity of colour and texture the 23 genotypes revealed that landraces Kibuzi, Mbwazirume, Nakitembe and Mpologoma had higher intensity of yellowness and lower intensity of hardness (softer) and a low score (≤ 1.0) of astringency taste. A preference test showed that they had higher acceptability scores. Biochemical, instrumental and sensory data revealed correlations between sensory firmness and instrumental hardness (r = 0.5), sensory firmness and amylopectin (r = −0.54), suggesting that qualitative descriptions can be predicted by instrumental and biochemical indicators. Significant (P < 0.05) variations in amylose and total starch content were observed in different varieties. Moderate correlations between instrumental hardness and firmness in mouth (r = 0.55), cohesiveness and firmness in the mouth (r = 0.57), and adhesiveness and firmness in the mouth (r = 0.64) were observed. Surprisingly, carotenoids content was not correlated with yellowness in cooked matooke. However, positive correlations were observed between chroma (b*) parameters of raw matooke and sensorial assessed color on cooked samples. CONCLUSION: Qualitative characteristis; the bunch, pulp colour and texture; that drive users-preference in the EAHCB were quantified, paving way for breeders to use them to select genotypes with these attributes early in the breeding process. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Flowering and fruit-set in cassava under extended red-light photoperiod supplemented with plant-growth regulators and pruning
(BMC Plant Biology, 2023-06-23) Julius K. Baguma; Settumba B Mukasa; Ephraim Nuwamanya; Titus Alicai; Christopher Omongo; Peter T. Hyde; Tim L. Setter; Mildred Ochwo‐Ssemakula; William Esuma; Michael Kanaabi; Paula Iragaba; Yona Baguma; Robert S. Kawuki
Background Cassava (Manihot esculenta Crantz) is staple food and major source of calories for over 500 million people in sub‐Saharan Africa. The crop is also a source of income for smallholder farmers, and has increasing potential for industrial utilization. However, breeding efforts to match the increasing demand of cassava are impeded by its inability to flower, delayed or unsynchronized flowering, low proportion of female flowers and high fruit abortions. To overcome these sexual reproductive bottlenecks, this study investigated the effectiveness of using red lights to extend the photoperiod (RLE), as a gateway to enhancing flowering and fruit set under field conditions. Materials and methods Panels of cassava genotypes, with non‐ or late and early flowering response, 10 in each case, were subjected to RLE from dusk to dawn. RLE was further evaluated at low (LL), medium (ML) and high (HL) red light intensities, at ~ ≤ 0.5; 1.0 and 1.5PFD (Photon Flux Density) in μmol m−2 s−1 respectively. Additionally, the effect of a cytokinin and anti‐ethylene as plant growth regulators (PGR) and pruning under RLE treatment were examined. Results RLE stimulated earlier flower initiation in all genotypes, by up to 2 months in the late‐flowering genotypes. Height and number of nodes at first branching, particularly in the late‐flowering genotypes were also reduced, by over 50%. Number and proportion of pistillate flowers more than doubled, while number of fruits and seeds also increased. Number of branching levels during the crop season also increased by about three. Earlier flowering in many genotypes was most elicited at LL to ML intensities. Additive effects on flower numbers were detected between RLE, PGR and pruning applications. PGR and pruning treatments further increased number and proportion of pistillate flowers and fruits. Plants subjected to PGR and pruning, developed bisexual flowers and exhibited feminization of staminate flowers. Pruning at first branching resulted in higher pistillate flower induction than at second branching. Conclusions These results indicate that RLE improves flowering in cassava, and its effectiveness is enhanced when PGR and pruning are applied. Thus, deployment of these technologies in breeding programs could significantly enhance cassava hybridizations and thus cassava breeding efficiency and impact.
Genetic clustering, and diversity of African panel of released common bean genotypes and breeding lines
(Springer Nature, 2023-03-08) Winnyfred Amongi; Stanley Tamusange Nkalubo; Mildred Ochwo‐Ssemakula; Arfang Badji; Isaac Onziga Dramadri; Thomas Lapaka Odongo; Ephraim Nuwamanya; Phineas Tukamuhabwe; Paulo Izquierdo; Karen Cichy; James Kelly; Clare Mukankusi
Common bean is a grain legume of global importance especially for proteins and micronutrients. The crop is a staple food in sub-Saharan Africa, where it has gained importance in iron bioforti cation for people prone to anemia. However, biotic and abiotic constraints, long cooking time, and high phytic acid and polyphenols both of which affect bioavailable iron, hinder the production and health benefits. To inform breeding decisions, the study determined genetic diversity and population structure within 725 breeding lines, varieties, or landraces mostly from Uganda and South America. Genotyping by sequencing and diversity array technology (DarTseq) were used to generate single nucleotide polymorphic markers on Set1 (427) and Set2 (298) germplasm, respectively. The germplasm were grouped into Andean and Mesoamerican gene pools, with the latter as the larger subpopulation. Analysis of molecular variance revealed 46% (Set1) and 50% (Set2) of genetic variation among the subpopulations, with fixation indices (FST) of 0.54 (Set1) and 0.71 (Set2) among Andean and Mesoamerican beans, respectively. The overall germplasm’s gene diversities were 0.206 (Set1) and 0.332 (Set2). Admixtures were the most diverse (0.193) in both sets of germplasm. The germplasm exhibited high genetic diversity and as a result they have a high potential for use in plant breeding. Inter- gene pool crosses within and across market classes are possible and considering both approaches is expected to increase diversity to realize genetic gain. The structure and polymorphic information generated provided useful perspectives for genomic breed- ing and genome-wide association study using the population.
Genetic Structure and Diversity Study of Cassava (Manihot esculenta) Germplasm for African Cassava Mosaic Disease and Fresh Storage Root Yield
(Open Journal of Genetics, 2023-03-14) Janatu Veronica Sesay; Aiah Lebbie; Richard Wadsworth; Ephraim Nuwamanya; Souleymane Bado; Prince Emmanuel Norman
A better understanding of population structure and genetic diversity among cassava germplasm for African cassava mosaic disease and fresh root yield traits is useful for cassava improvement programme. Phenotype-based selection for these traits is cumbersome due to phenotypic plasticity and difficulty in screening of phenotypic-induced variations. This study assessed quantitative trait loci (QTL) regions associated with African cassava mosaic disease (ACMD) and fresh storage root yield (FSRY) in 131 cassava (Manihot esculenta) genotypes using a genome-wide association study (GWAS). The single nucleotide polymorphism (SNP) loci and associated candidate genes, when validated, would be a valuable resource for marker-assisted selection in the breeding process for development of new cassava genotypes with improved resistance to ACMD and desirable high root yield. Population structure analysis using 12,500 SNPs differentiated the 131 genotypes into five distinct sub-groups (K = 5). Marker-trait association (MTA) analysis using the generalized linear model identified two QTL regions significant for ACMD and three for FSRY. This study demonstrated that DArTseq markers are useful genomic resources for genome-wide association studies of ACMD and FSRY traits in cassava for the acceleration of varietal development and release.
NIRS Predictions, Phenotypic Variability and Optimization of Cooking Time for Evaluation of the Root Softness of Boiled Cassava
(National Agricultural Research Organisation, 2023-09-01) Babirye Fatumah Namakula; Ephraim Nuwamanya; Michael Kanaabi; Paul Gibson; Enoch Wembabazi; Iragaba Paula; Robert Sezi Kawuki
This study aimed at quantifying the extent of genetic variability of softness in cassava germplasm across varied cooking times and root sections. It also examined the possibility of using Near Infrared Spectroscopy (NIRS) for measurement of cassava root softness. Softness was evaluated using a penetrometer. This was done at 15, 30 and 45minutes cooking time, all across proximal, middle and distal root sections. These measurements were done on 57 accessions. For each sample, spectra were acquired using NIRS Benchtop (FOSS DS2500) on a composite of each root section of mashed fresh cassava sample. Modified Partial Least Squares regression (MPLS) was used for NIRS calibration development using WINISI software. Significant (P < 0.001) variability in softness was established. Cooking time significantly influenced softness and there were significant accession and root part interaction (P < 0.001). Wide variability and high heritability (H = 0.8) were found for softness at 30 minutes cooking time. Highest association was found with 30- and 45-minutes cooking time (r = 0.58). Strong association was observed between middle root section with distal (r = 0.74) and proximal (r = 0.73). NIRS softness calibration (R2c) were 0.445, 0.413 and 0.521 for 15-, 30-, and 45-minutes cooking time respectively. NIRS prediction (R2p) were 0.322, 0.192, and 0.390 for 15-, 30-, and 45-minutes cooking time respectively. These results suggest that 30 minutes cooking time and middle root section are optimum for softness phenotyping.
Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm
(Frontiers, 2022-11-23) Williams Esuma; Oscar Eyoo; Francisca Gwandu; Settumba Mukasa; Titus Alicai; Alfred Ozimati; Ephraim Nuwamanya; Ismail Rabbi; Robert Kawuki
Introduction: The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high- density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. Methods: We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. Results: Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. Discussion: The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.