Association mapping and molecular marker development for cassava brown streak disease resistance

Cassava brown streak disease (CBSD) - caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) - severely threatens cassava production and food security in sub-Saharan Africa. Breeding for resistance is the most sustainable control strategy, but it requires reliable resistance sources and a clear understanding of the underlying genetic mechanisms.

In this study, we utilized resistance introduced from Latin American cassava germplasm and mapped the genetic basis of CBSD resistance relevant to African environments. Whole-genome sequencing (WGS) was applied to a segregating population consisting of 426 F1 progeny derived from crosses with CBSD-resistant lines and genome-wide association studies (GWAS) conducted to dissect the genetic basis of resistance.

A major QTL on chromosome 11 was consistently and significantly associated with CBSD resistance across multiple GWAS models tested and marker types (SNPs and indels), explaining up to 34.89% of the phenotypic variation. Three Kompetitive Allele Specific PCR (KASP) markers were developed and validated from the associated SNPs. All three markers successfully differentiated between known resistant and susceptible parental lines and the mapping population, and one remained significantly associated with resistance in a broader validation population. Interestingly, the same resistance region was previously reported in genetic mapping of East African germplasm, highlighting the central role of this locus across diverse genetic backgrounds. Developing these markers targeting the major chromosome 11 QTL provides a practical molecular tool to accelerate marker-assisted selection and facilitate the development of resistant cassava varieties, ultimately enhancing food security and supporting farmer livelihoods in regions affected by CBSD in Africa.