Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm.
Williams Esuma, Oscar Eyoo, Francisca Gwandu, Settumba Mukasa, Titus Alicai, Alfred Ozimati, Ephraim Nuwamanya, Ismail Rabbi, Robert Kawuki
Author Information
Williams Esuma: National Crops Resources Research Institute, Kampala, Uganda.
Oscar Eyoo: National Crops Resources Research Institute, Kampala, Uganda.
Francisca Gwandu: College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda.
Settumba Mukasa: College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda.
Titus Alicai: National Crops Resources Research Institute, Kampala, Uganda.
Alfred Ozimati: National Crops Resources Research Institute, Kampala, Uganda.
Ephraim Nuwamanya: National Crops Resources Research Institute, Kampala, Uganda.
Ismail Rabbi: International Institute of Tropical Agriculture (IITA), Oyo, Nigeria.
Robert Kawuki: National Crops Resources Research Institute, Kampala, Uganda.
Introduction: The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. Methods: We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. Results: Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. Discussion: The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.
