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.

We thank IR (IITA, Ibadan) for providing detailed technical information on the 13 KASP markers.

https://dx.doi.org/10.3389/fpls.2022.1017275

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Ismail Rabbihttps://orcid.org/0000-0001-9966-2941

https://dx.doi.org/10.3389/fpls.2022.1017275

Biotech and Plant Breeding

Agronomy; Cassava; Food Security; Plant Breeding; Plant Production

Genetic Gain; Cassava; Manihot Esculenta; Genetic Markers; Genotypes; Uganda

Africa; East Africa

Uganda

Headquarters and Western Africa Hub

Frontiers in Plant Science