Conversion and Validation of Uniplex SNP Markers for Selection of Resistance to Cassava Mosaic Disease in Cassava Breeding Programs

Abstract

Cassava mosaic disease (CMD) is a major viral disease adversely affecting cassava production in Africa and Asia. Genomic regions conferring resistance to the disease have been mapped in African cassava germplasm through biparental quantitative trait loci (QTL) mapping and genome-wide association studies. To facilitate the utilization of these markers in breeding pipelines to support selections, proof-of-concept technical and biological validation research was carried out using independent pre-breeding and breeding populations. Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) assays were designed from three single nucleotide polymorphism (SNP) markers linked to a major resistance locus on chromosome 12 (S12_7926132, S12_7926163) and a minor locus on chromosome 14 (S14_4626854). The designed assays were robust and easy to score with >99% genotype call rate. The overall predictive accuracy (proportion of true positives and true negatives) of the markers (S12_7926132 and S14_4626854) was 0.80 and 0.78 in the pre-breeding and breeding population, respectively. On average, genotypes that carried at least one copy of the resistant allele at the major CMD2 locus had a significantly higher yield advantage. Nevertheless, variation was observed in prediction accuracies for the major locus (S12_7926132) among sub-families from the two populations, suggesting the need for context-specific utilization, for example, by screening for co-segregation of favorable SNP alleles with resistance in the parents being used for crosses. Availability of these validated SNP markers on the uniplex KASP genotyping platform represents an important step in translational genetics toward marker-assisted selection to accelerate introgression of favorable resistant alleles in breeding populations.

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)

“…(2) In addition, this could also be attributed to the fact that the CMD2 gene is not expressed on any of the five cassava tissues in this study (as seen in Supplementary Fig. S9 b—right side), as previously speculated by Adenike et al 59 . Previous studies on CMD resistance highlighted a single source of monogenic resistance in the cassava genepool 60 , especially in Africa.…”

Identifying New Resistance to Cassava Mosaic Disease and Validating Markers for the CMD2 Locus

“…Considering no intended introduction of CMD resistance to Vietnam before 2011, we proposed that the T allele in VNM142 might be in the haplotypes different from that in TME3 in Africa. Similarly, non-significant marker effects were also reported in some families of the breeding populations in Africa [22].…”

“…Three CMD markers, S12_7926132, S12_7926163, and S14_4626854, designed by Dr. Ismail Rabbi [18,22] on chromosomes 12 and 14, were used for the validation. Leaf tissues of the two populations were sent to Intertek following the protocol developed by CGIAR Excellence in Breeding (EiB; https://excellenceinbreeding.org/toolbox/services/ low-density-genotyping-service, accessed on 26 August 2021).…”

“…The Intertek platform is affordable for breeding programs and recommended by CGIAR Excellence in Breeding (EiB; https://excellenceinbreeding.org/toolbox, accessed on 26 August 2021.). Two tightly linked markers are on chromosome 12, S12_7926132 and S12_7926163, and one marker, S14_4626854, on chromosome 14 [18,22]. These markers were routinely used in the African breeding programs.…”

Validation of SNP markers for marker-assisted selection of genotypes with increased carotenoid and dry matter contents in cassava

“…The framework includes both technical and biological validation of the assays in a range of diverse germplasm to ascertain the relevance of the markers for predicting the trait values in independent populations. The KASP SNP platform was chosen due to its amenability for genotyping of any combination of individual samples and maker assays, and ease of automation to achieve high-throughput population screening (Semagn et al, 2014; Ige et al, 2021). The designed SNP assays were found to work under a wide range of DNA concentrations.…”