Browsing by Author "Williams Esuma"

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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.
Mutations in DNA polymerase δ subunit 1 co- segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses
(Nature Communications, 2022-07-07) Yi-Wen Lim; Ben N. Mansfeld; Pascal Schläpfer; Kerrigan B. Gilbert; Narayanan N. Narayanan; Weihong Qi; Qi Wang; Zhenhui Zhong; Adam Boyher; Jackson Gehan; Getu Beyene; Zuh-Jyh Daniel Lin; Williams Esuma; Suhua Feng; Christelle Chanez; Nadine Eggenberger; Gerald Adiga; Titus Alicai; Steven E. Jacobsen; Nigel J. Taylor; Wilhelm Gruissem; Rebecca S. Bart
Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for this loss of resistance, whole genome sequencing and genetic variant analysis was performed and the CMD2 locus was fine-mapped to a 190 kilobase interval. Collectively, these data indicate that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase δ subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a CMD-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional candidate resistance alleles within MePOLD1. Genetic variation of MePOLD1, therefore, could represent an important genetic resource for resistance breeding and/or genome editing, and elucidating mechanisms of resistance to geminiviruses.
Utility of Ugandan genomic selection cassava breeding populations for prediction of cassava viral disease resistance and yield in West African clones
(Frontiers in Plant Science, 2022-11-23) Alfred A. Ozimati; Williams Esuma; Francis Manze; Paula Iragaba; Michael Kanaabi; Chukwuka Ugochukwu Ano; Chiedozie Egesi; Robert S. Kawuki
Cassava (Manihot esculenta Crantz) is a staple crop for ~800 million people in sub-Saharan Africa. Its production and productivity are being heavily affected by the two viral diseases: cassava brown streak disease (CBSD) and cassava mosaic disease (CMD), impacting greatly on edible root yield. CBSD is currently endemic to central, eastern and southern Africa, if not contained could spread to West Africa the largest cassava producer and consumer in the continent. Genomic selection (GS) has been implemented in Ugandan cassava breeding for accelerated development of virus resistant and high yielding clones. This study leveraged available GS training data in Uganda for pre-emptive CBSD breeding in W. Africa alongside CMD and fresh root yield (FRW). First, we tracked genetic gain through the current three cycles of GS in Uganda. The mean genomic estimated breeding values (GEBVs), indicated general progress from initial cycle zero (C0) to cycle one (C1) and cycle two (C2) for CBSD traits and yield except for CMD. Secondly, we used foliar data of both CBSD and CMD, as well as harvest root necrosis and yield data to perform cross-validation predictions. Cross-validation prediction accuracies of five GS models were tested for each of the three GS cycles and West African (WA) germplasm as a test set. In all cases, cross- validation prediction accuracies were low to moderate, ranging from -0.16 to 0.68 for CBSD traits, -0.27 to 0.57 for CMD and -0.22 to 0.41 for fresh root weight (FRW). Overall, the highest prediction accuracies were recorded in C0 for all traits tested across models and the best performing model in cross-validation was G-BLUP. Lastly, we tested the predictive ability of the Ugandan training sets to predict CBSD in W. African clones. In general, the Ugandan training sets had low prediction accuracies for all traits across models in West African germplasm, varying from -0.18 to 0.1. Based on the findings of this study, the cassava breeding program in Uganda has made progress through application of GS for most target traits, but the utility of the training population for pre-emptive breeding in WA is limiting. In this case, efforts should be devoted to sharing Ugandan germplasm that possess resistance with the W. African breeding programs for hybridization to fully enable deployment of genomic selection as a pre-emptive CBSD breeding strategy in W. Africa.
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.