Development of Dual Virus Resistant Cultivars and Rapid Propagation Methods for Cassava in Kenya

Abstract

Cassava (Manihot esculenta Crantz) is a subsistence crop for many people in the tropics. However, yields are low due to farmers growing cultivars susceptible to two major viral diseases whose genetic diversity remains unknown. Though cassava mosaic disease (CMD) tolerant cultivars have been found, all the cultivars grown in Kenya succumb to cassava brown streak disease (CBSD). Resistant cultivars of CBSD have been introduced to Kenya from South American landraces to improve present germplasm. The objectives of this study were to (1) determine the genetic diversity among cassava local cultivars (2) Develop cassava clones with dual resistance to cassava mosaic disease and cassava brown streak disease, and (3) determine the most effective technique that could be used for rapid propagation of cassava stakes. Before introducing a new cultivar as a valuable gene resource for cassava breeding, there was the need to collect traditional cultivars in Lamu County, and associated farmer knowledge was documented. Forty informant farmers were interviewed. Cuttings of 58 sampled traditional landraces were planted for leaf sampling and genotyping. Leaves from collected mature cultivars were characterized to determine incidences of CBSD and CMD causal viruses. The landraces were genotyped using a low-density panel of single nucleotide polymorphism (SNP) markers from DartRSeq. Data was analysed using R-script to identify duplicates and unique cultivars. Genetic fingerprints of unique cultivars were analysed with formerly genotyped landraces and breeding lines. The results show EACMV incidences were more prevalent at 39.2% and a p-value=.009, and UCBSV at a p-value = 0.026 but CBSV was not significant. Overall, 15 unique genotypes were identified while the rest were duplicates. According to SNP data, germplasm from Lamu County were closely related to one another and more distantly related to landraces from Tanzania and breeding lines. Low genetic diversity was noted in this County. This shows there is restricted movement and introductions of cassava germplasm into the County. For Objective two, 337 F1 progenies were developed from a hand pollinated crosses for CBSD and CMD resistance using both phenotypic data and molecular markers. Three SNP markers (S12_7926132, S12_7926163 and S14_4626854) previously converted into Kompetitive allele – specific PCR (KASP) assay, as well as CMD and CBSD incidences and severity scores were used for selection. Data were analysed by descriptive using Microsoft Excel Software. Progenies expressing dual resistance for both CBSD and CMD and a phenotypic score of 1 were as follows: 8.98% (22 out of 245), 4.92% (3 out of 61), and 3 2.44% (1 out of 41) in populations 1, 2 and 3 respectively. Population 1 (236) was the largest in this study. This population was used to predict the accuracy (true positive and true negatives) of the major CMD2 locus on chromosome 12, which was found to be 84.32%. Our study provides information on the potential use of marker-assisted selection in cassava breeding programmes for CMD resistance.