The process and lessons of exchanging and managing in-vitro elite germplasm to combat CBSD and CMD in Eastern and Southern Africa

Varieties with resistance to both cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) can reverse food and income security threats affecting the rural poor in Eastern and Southern Africa. The International Institute of Tropical Agriculture is leading a partnership of five national (Malawi, Mozambique, Kenya, Tanzania and Uganda) cassava breeding programs to exchange the most elite germplasm resistant to both CMD and CBSD. This poster documents the process and the key learning lessons. Twenty to 25 stem cuttings of 31 clones comprising of 25 elite clones (5 per country), two standard checks (Kibandameno from Kenya and Albert from Tanzania), and four national checks (Kiroba and Mkombozi from Tanzania, Mbundumali from Malawi, and Tomo from Mozambique) were cleaned and indexed for cassava viruses at both the Natural Resources Institute in the United Kingdom and Kenya Plant Health Inspectorate Services, in Kenya. About 75 in-vitro plantlets per clone were sent to Genetic Technologies International Limited, a private tissue culture lab in Kenya, and micro-propagated to ≥1500 plantlets. Formal procedures of material transfer between countries including agreements, import permission and phytosanitary certification were all ensured for germplasm exchange. At least 300 plantlets of each elite and standard check clones were sent to all partner countries, while the national checks were only sent to their respective countries of origin. In each country, the in-vitro plantlets were acclimatized under screen house conditions and transplanted for field multiplication as a basis for multi-site testing. Except for Tomo, a susceptible clone, all the clones were cleaned of the viruses. However, there was varied response to the cleaning process between clones, e.g. FN-19NL, NASE1 and Kibandameno responded slowly. Also, clones responded differently to micro-propagation protocols at GTIL, e.g. Pwani, Tajirika, NASE1, TME204 and Okhumelela responded slowly. Materials are currently being bulked at low disease pressure field sites in preparation for planting at 5-8 evaluation sites per country. The process of cleaning, tissue culture mass propagation, exchange and local hardening off/bulking has been successful for the majority of target varieties. Two key lessons derived from the process are that adequate preparations of infrastructure and trained personnel are required to manage the task, and that a small proportion of varieties are recalcitrant to tissue culture propagation

Distribution of single nucleotide polymorphism markers towards tagging sources of resistance to cassava brown streak disease in cassava

Cassava roots represent the future of food and income generation for over 800 million people in the world however, its production is threatened by virus disease; Cassava brown streak disease (CBSD). Biotechnology approaches are fast and powerful methodologies in cassava improvement and breeding. Construction of high-density and high quality genetic map in cassava would be of great benefit in combating CBSD. Conventional study was conducted in Naliendele, Kibaha and Dodoma for Tanzania and Molecular work performed at the International Livestock Research Institute, Kenya and University of Berkeley in United States of America. This study involved assessing the integrity of F1 population from a cross between AR40-6 x Albert cassava cultivars using simple sequence repeat (SSR) polymorphisms. An F1 population of 156 individuals were developed. Population evaluation resulted into 72% individuals as true F1 hybrids, 18.7% were non hybrids and 8.2% were selfed individual plants. Evaluation of F1 population validated SSR markers to be useful and efficient tools in identification of true F1 hybrids in controlled crosses. On the other hand, the true F1hybrids obtained were used to construct high dense SNP based linkage map using high throughput genotyping by sequencing (GBS) approach. The GBS is simple, low cost and de novo sequencing that makes an attractive option for large number of markers and individuals. Linkage analysis resulted into comprehensive genetic map with 19 linkage groups with a total of 4784 SNP markers: 2159 of these were mapped to the female genetic map, 2169 to the male map, and 3449 SNP markers to the integrated genetic map. Comprehensive genetic map encompassed 4250cM with mean distance of 1.26cM between the markers. This high density SNP based genetic linkage map of cassava can be used as base in locating genes controlling resistance to cassava brown streak disease and other genomic studies such as QTL detection, sequence assembly and genome comparison of the crop.National Root and Tuber Research Program

Distribution of single nucleotide polymorphism markers towards tagging sources of resistance to cassava brown streak disease in cassava

Cassava roots represent the future of food and income generation for over 800 million people in the world however, its production is threatened by virus disease; Cassava brown streak disease (CBSD). Biotechnology approaches are fast and powerful methodologies in cassava improvement and breeding. Construction of high-density and high quality genetic map in cassava would be of great benefit in combating CBSD. Conventional study was conducted in Naliendele, Kibaha and Dodoma for Tanzania and Molecular work performed at the International Livestock Research Institute, Kenya and University of Berkeley in United States of America. This study involved assessing the integrity of F1 population from a cross between AR40-6 x Albert cassava cultivars using simple sequence repeat (SSR) polymorphisms. An F1 population of 156 individuals were developed. Population evaluation resulted into 72% individuals as true F1 hybrids, 18.7% were non hybrids and 8.2% were selfed individual plants. Evaluation of F1 population validated SSR markers to be useful and efficient tools in identification of true F1 hybrids in controlled crosses. On the other hand, the true F1hybrids obtained were used to construct high dense SNP based linkage map using high throughput genotyping by sequencing (GBS) approach. The GBS is simple, low cost and de novo sequencing that makes an attractive option for large number of markers and individuals. Linkage analysis resulted into comprehensive genetic map with 19 linkage groups with a total of 4784 SNP markers: 2159 of these were mapped to the female genetic map, 2169 to the male map, and 3449 SNP markers to the integrated genetic map. Comprehensive genetic map encompassed 4250cM with mean distance of 1.26cM between the markers. This high density SNP based genetic linkage map of cassava can be used as base in locating genes controlling resistance to cassava brown streak disease and other genomic studies such as QTL detection, sequence assembly and genome comparison of the crop.National Root and Tuber Research Program

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

Abstract 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