QTL Mapping for Virus Resistance in Cassava

Yields of cassava (Manihot esculenta Crantz.), Africa’s primary food security crop, are seriously compromised by two virus diseases; Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD). Two sources of CMD resistance have been recognized; CMD-1 (a polygenic source) and CMD-2 (a dominant gene), whereas CBSD resistance is thought to be controlled by two or more additive genes. The objective of this study was to identify QTL associated with CBSD resistance in five varieties, namely Namikonga, Nachinyaya, NDL06/132, AR40-6 and Kiroba, and two sources of CMD resistance, Albert and AR37-80, through the development of five F₁ mapping populations.

Populations ranged in size from 106 to 259 individuals, which were phenotyped in two environments in Tanzania, in 2013/14 and 2014/15. High density genotyping was performed using genotyping-by-sequencing (GBS). Results for CBSD root necrosis reveal one or several QTL within an approximately 6.5Mbp region on Chromosome 11. This QTL is supported by nine site/year combinations, across three varieties (Namikonga, NDL06/132 and Nachinyaya) but is rather depauperate in SNPs in certain areas, necessitating fine mapping. Kiroba, AR40-6 and Namikonga revealed QTL for root necrosis on a second chromosome, in addition to a number of other smaller, less consistent QTL.

Interestingly the so-called CMD2 locus on chromosome 12 was evident in the variety ‘Albert’, but could not be detected in AR37-80, which itself is a product of marker-assisted selection (MAS) to introgress the CMD2 locus at CIAT. With further fine-mapping, these QTL are likely to form the basis for MAS for virus resistance in Africa.