Genetic diversity and population structure of Uganda cassava germplasm.

Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.

Use of low cost near-infrared spectroscopy, to predict pasting properties of high quality cassava flour.

Determination of pasting properties of high quality cassava flour using rapid visco analyzer is expensive and time consuming. The use of mobile near infrared spectroscopy (SCiO™) is an alternative high throughput phenotyping technology for predicting pasting properties of high quality cassava flour traits. However, model development and validation are necessary to verify that reasonable expectations are established for the accuracy of a prediction model. In the context of an ongoing breeding effort, we investigated the use of an inexpensive, portable spectrometer that only records a portion (740-1070 nm) of the whole NIR spectrum to predict cassava pasting properties. Three machine-learning models, namely glmnet, lm, and gbm, implemented in the Caret package in R statistical program, were solely evaluated. Based on calibration statistics (R2, RMSE and MAE), we found that model calibrations using glmnet provided the best model for breakdown viscosity, peak viscosity and pasting temperature. The glmnet model using the first derivative, peak viscosity had calibration and validation accuracy of R2 = 0.56 and R2 = 0.51 respectively while breakdown had calibration and validation accuracy of R2 = 0.66 and R2 = 0.66 respectively. We also found out that stacking of pre-treatments with Moving Average, Savitzky Golay, First Derivative, Second derivative and Standard Normal variate using glmnet model resulted in calibration and validation accuracy of R2 = 0.65 and R2 = 0.64 respectively for pasting temperature. The developed calibration model predicted the pasting properties of HQCF with sufficient accuracy for screening purposes. Therefore, SCiO™ can be reliably deployed in screening early-generation breeding materials for pasting properties.

Genotype by environment cultivar evaluation for cassava brown streak disease resistance in Tanzania.

Cassava brown steak disease (CBSD), caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), is the most important biotic constraint to cassava production in East and Central Africa. Concerted efforts are required to prevent further spread into West Africa as well as to reduce losses in areas already affected. The study reported here was part of a five-country (Kenya, Malawi, Mozambique, Tanzania and Uganda) programme that aimed to identify superior cassava cultivars resistant to CBSD and to disseminate them widely in the region. Seventeen tissue-cultured and virus-tested cultivars were evaluated in Tanzania across nine sites with diverse CBSD inoculum conditions. Experiments were planted using an alpha-lattice design and assessments were made of surrounding inoculum pressure, CBSD foliar and root incidence and root yield at harvest. There were large differences in CBSD infection between sites, with greatest spread recorded from the north-western Lake (Victoria) zone. Differences were driven by Bemisia tabaci whitefly vector abundance and CBSD inoculum pressure. Both CBSV and UCBSV were almost equally represented in cassava fields surrounding experimental plots, although CBSV predominated in the north-west whilst UCBSV was more frequent in coastal and southern sites. However, the incidence of CBSV was much greater than that of UCBSV in initially virus-free experimental plots, suggesting that CBSV is more virulent. Cultivars could be categorised into three groups based on the degree of CBSD symptom expression in shoots and roots. The seven cultivars (F10_30R2, Eyope, Mkumba, Mkuranga1, Narocass1, Nase3 and Orera) in the most resistant category each had shoot and root incidences of less than 20%. Fresh root yield differed between sites and cultivars, but there was no genotype by environment interaction for this trait, probably attributable to the large fertility and soil moisture differences between sites. Susceptible cultivars and the local check performed well in the absence of CBSD pressure, highlighting the importance of exploiting quality and yield traits of local landraces in breeding programmes. Overall, our results emphasized the importance of applying a balanced strategy for CBSD management. This should use both improved and local germplasm resources to generate high yielding cultivars for specific end-user traits, and combine the deployment of improved cultivars with phytosanitary control measures including the use of healthy planting material and planting during periods of reduced CBSD infection.

Exchanging and managing in-vitro elite germplasm to combat Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD) in Eastern and Southern Africa.

Cassava varieties resistant to cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are needed for the food and income security of the rural poor in eastern and southern Africa (ESA). The International Institute of Tropical Agriculture led five national cassava breeding programs (Malawi, Mozambique, Kenya, Tanzania and Uganda) in virus-cleaning and exchanging elite cassava germplasm resistant to both diseases. This paper documents the experiences and lessons learned from the process. Thirty-one clones (25 elite, two standard and four national) were submitted by the five breeding programs to the Natural Resources Institute and Kenya Plant Health Inspectorate Services for virus cleaning and indexing. Subsequently, ca 75 invitro virus-indexed plantlets per clone were sent to Genetic Technologies International Limited (GTIL), a private tissue culture (TC) lab in Kenya, and micro-propagated to produce ≥1500 plantlets. After fulfilling all the formal procedures of germplasm exchange between countries ≥300 plantlets per clone were sent to each partner country. National check clones susceptible to CMD/CBSD were sent only to their countries of origin. In each country, the in-vitro plantlets were acclimatized under screen house conditions and transferred to clean isolated sites for field multiplication. All the clones were cleaned of the viruses, except Tomo. The cleaning process was slow for F19-NL, NASE1, and Kibandameno and TC micro-propagation at GTIL was less efficient for Pwani, Tajirika, NASE1, and Okhumelela than for the other clones. Difficulties in cleaning recalcitrant clones affected the timeline for establishing the multi-site evaluation trials in target countries. The initiative is the one of the kind to successfully clean and exchange elite germplasm as a joint action to combat CBSD in ESA. Adequate preparation in terms of infrastructure and personnel are critical to successfully receiving and adapting the indexed in-vitro plants as new germplasm.