Genetic diversity, population structure, and a genome-wide association study of sorghum lines assembled for breeding in Uganda.

Sorghum is an important source of food and feed worldwide. Developing sorghum core germplasm collections improves our understanding of the evolution and exploitation of genetic diversity in breeding programs. Despite its significance, the characterization of the genetic diversity of local germplasm pools and the identification of genomic loci underlying the variation of critical agronomic traits in sorghum remains limited in most African countries, including Uganda.

Assessment of Cassava Pollen Viability and Ovule Fertilizability under Red-Light, 6-Benzyl Adenine, and Silver Thiosulphate Treatments.

Understanding pollen and ovule fertility as factors influencing fruit and seed set is important in cassava breeding. Extended daylength with red light (RL) and plant growth regulators (PGRs) have been used to induce flowering and fruit set in cassava without any reference to effects on pollen viability or ovule fertilizability. This study investigated the effects of field-applied RL and PGR on pollen viability and ovule fertilizability.

Genetic Variation and Heritability for Hydrogen Cyanide in Fresh Cassava Roots: Implications for Low-Cyanide Cassava Breeding.

Breeding for low-hydrogen-cyanide (HCN) varieties is a major objective of programs targeting boiled cassava food products. To enhance the breeding of low-HCN varieties, knowledge of genetic variation and trait heritability is essential. In this study, 64 cassava clones were established across four locations and evaluated for HCN using three HCN assessment methods: one with a 1 to 9 scale, on with a 0 ppm to 800 ppm scale, and a quantitative assay based on spectrophotometer readings (HCN_Spec).

Identification of Genomic Regions for Traits Associated with Flowering in Cassava ( Crantz).

Flowering in cassava ( Crantz) is crucial for the generation of botanical seed for breeding. However, genotypes preferred by most farmers are erect and poor at flowering or never flower. To elucidate the genetic basis of flowering, 293 diverse cassava accessions were evaluated for flowering-associated traits at two locations and seasons in Uganda.

The tricot approach: an agile framework for decentralized on-farm testing supported by citizen science. A retrospective.

Matching crop varieties to their target use context and user preferences is a challenge faced by many plant breeding programs serving smallholder agriculture. Numerous participatory approaches proposed by CGIAR and other research teams over the last four decades have attempted to capture farmers' priorities/preferences and crop variety field performance in representative growing environments through experimental trials with higher external validity. Yet none have overcome the challenges of scalability, data validity and reliability, and difficulties in capturing socio-economic and environmental heterogeneity.

Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava.

This study focuses on meeting end-users' demand for cassava (Manihot esculenta Crantz) varieties with low cyanogenic potential (hydrogen cyanide potential [HCN]) by using near-infrared spectrometry (NIRS). This technology provides a fast, accurate, and reliable way to determine sample constituents with minimal sample preparation. The study aims to evaluate the effectiveness of machine learning (ML) algorithms such as logistic regression (LR), support vector machine (SVM), and partial least squares discriminant analysis (PLS-DA) in distinguishing between low and high HCN accessions.

Development and validation of near-infrared spectroscopy procedures for prediction of cassava root dry matter and amylose contents in Ugandan cassava germplasm.

Background: Cassava utilization for food and/or industrial products depends on inherent properties of root dry matter content (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.

Genetic diversity and population structure of Uganda's yam (Dioscorea spp.) genetic resource based on DArTseq.

Assessing the genetic diversity of yam germplasm from different geographical origins for cultivation and breeding purposes is an essential step for crop genetic resource conservation and genetic improvement, especially where the crop faces minimal attention. This study aimed to classify the population structure, and assess the extent of genetic diversity in 207 Dioscorea rotundata genotypes sourced from three different geographical origins. A total of 4,957 (16.

Utility of Ugandan genomic selection cassava breeding populations for prediction of cassava viral disease resistance and yield in West African clones.

Cassava ( 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.

Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm.

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.

Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses.

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.

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz).

Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions.

Outlook of Cassava Brown Streak Disease Assessment: Perspectives of the Screening Methods of Breeders and Pathologists.

Cassava production and productivity in Eastern, Central, and Southern Africa are ravaged by cassava brown streak disease (CBSD), causing yield losses of up to 100% when susceptible varieties are grown. Efforts to develop CBSD-resistant clones are underway. However, the methods for screening CBSD resistance currently vary between breeders and pathologists, with the limited empirical data to support their choices.

Genetic Gains for Yield and Virus Disease Resistance of Cassava Varieties Developed Over the Last Eight Decades in Uganda.

Achieving food security for an ever-increasing human population requires faster development of improved varieties. To this end, assessment of genetic gain for key traits is important to inform breeding processes. Despite the improvements made to increase production and productivity of cassava in Uganda at research level, there has been limited effort to quantify associated genetic gains.

Effectiveness of genomic selection for improving provitamin A carotenoid content and associated traits in cassava.

Global efforts are underway to develop cassava with enhanced levels of provitamin A carotenoids to sustainably meet increasing demands for food and nutrition where the crop is a major staple. Herein, we tested the effectiveness of genomic selection (GS) for rapid improvement of cassava for total carotenoids content and associated traits. We evaluated 632 clones from Uganda's provitamin A cassava breeding pipeline and 648 West African introductions.

Assessment of end user traits and physicochemical qualities of cassava flour: a case of Zombo district, Uganda.

Cassava breeding programmes in Uganda do not currently select materials based on flour making quality, explaining in part the low adoption rates of many released varieties. In this study, we describe end user trait preferences, processing qualities and physicochemical properties of cassava flour. We found that higher proportion of women than men showed preference for most attributes of cassava flour quality evaluated in this study.

Expansion of the cassava brown streak pandemic in Uganda revealed by annual field survey data for 2004 to 2017.

Cassava brown streak disease (CBSD) is currently the most devastating cassava disease in eastern, central and southern Africa affecting a staple crop for over 700 million people on the continent. A major outbreak of CBSD in 2004 near Kampala rapidly spread across Uganda. In the following years, similar CBSD outbreaks were noted in countries across eastern and central Africa, and now the disease poses a threat to West Africa including Nigeria - the biggest cassava producer in the world.

Alternative Approaches for Assessing Cassava Brown Streak Root Necrosis to Guide Resistance Breeding and Selection.

Cassava brown streak disease (CBSD) caused by the rapidly evolving cassava brown streak viruses (CBSVs), causes immense yield losses to the cassava value chain in eastern and southern Africa. Western Africa, another region that heavily depends on cassava is under eminent threat from CBSD. Resistance breeding is the best practical solution.

Genetic Variation and Trait Correlations in an East African Cassava Breeding Population for Genomic Selection.

Cassava ( Crantz) is a major source of dietary carbohydrates for >700 million people globally. However, its long breeding cycle has slowed the rate of genetic gain for target traits. This study aimed to asses genetic variation, the level of inbreeding, and trait correlations in genomic selection breeding cycles.

Starch quality traits of improved provitamin A cassava ( Crantz).

Provitamin A cassava clones were analysed for starch yield and critical starch quality attributes, to understand possible applications in the food industry. Total carotenoids content in the test clones ranged from 0.03-11.

Training Population Optimization for Prediction of Cassava Brown Streak Disease Resistance in West African Clones.

Cassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector () may facilitate spread of CBSV to West Africa.

Prospects for Genomic Selection in Cassava Breeding.

Cassava ( Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities.

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation.

Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these deleterious mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions and identified >28 million segregating variants. We found that (i) although domestication has modified starch and ketone metabolism pathways to allow for human consumption, the concomitant bottleneck and clonal propagation have resulted in a large proportion of fixed deleterious amino acid changes, increased the number of deleterious alleles by 26%, and shifted the mutational burden toward common variants; (ii) deleterious mutations have been ineffectively purged, owing to limited recombination in the cassava genome; (iii) recent breeding efforts have maintained yield by masking the most damaging recessive mutations in the heterozygous state but have been unable to purge the mutation burden; such purging should be a key target in future cassava breeding.

Diallel analysis of provitamin A carotenoid and dry matter content in cassava ( Crantz).

Global efforts are underway to biofortify cassava ( Crantz) with provitamin A carotenoids to help combat dietary vitamin A deficiency afflicting the health of more than 500 million resource-poor people in Sub-Saharan Africa. To further the biofortification initiative in Uganda, a 6×6 diallel analysis was conducted to estimate combining ability of six provitamin A clones and gene actions controlling total carotenoid content (TCC), dry matter content (DMC) in cassava roots and other relevant traits. Fifteen F families generated from the diallel crosses were evaluated in two environments using a randomized complete block design.