Genetic variability and Kasp marker validation for provitamin carotenoids and dry matter content in West African Cassava germplasm evaluated in Uganda

Abstract

The cassava breeding program in Uganda has released numerous white fleshed varieties, but no the evaluated yellow provitamin A varieties have been released to date. The latter are more prone to virus diseases and have low genetic gains due to the negative relationship between dry matter content (DMC) and total carotenoid (provitamin A) content (TCC). West Africa (WA), particularly Nigeria, has successfully released numerous provitamin A clones, prompting their introduction to Uganda. Therefore, the objectives of this study were to assess genetic diversity between and within the Ugandan genotypes and the WA provitamin A cassava genotypes for TCC and DMC and to evaluate the effectiveness of allele-specific KASP markers for the selection of TCC and DMC. This study involved 640 WA clones planted in an augmented design with 3 local checks in 2 locations of Uganda for 2 seasons and 13 Ugandan accessions planted in a randomized complete block design (RCBD). TCC was assessed using colour charts, iCheck, and NIRS, whereas DMC by NIRS and oven drying methods. Genotyping for molecular diversity by high-density SNPs was done using DArTSeq, and clones were also genotyped with 6 provitamin A and 5 DMC KASP markers for the validation study. Genetic diversity (GD) within the WA population was measured using indices like minor allele frequency (MAF), expected heterozygosity (He), observed heterozygosity (Ho), and the polymorphism information content (PIC). The WA clones evaluated in Namulonge for TCC through color charts and iCheck had an average of 3.91 color intensity and 8.13 μg/g, respectively, while those evaluated in Serere using iCheck had an average of 3.2 μg/g. However, the Ugandan clones had a TCC mean of 7.12 μg/g. With DMC, the WA clones evaluated in Namulonge using oven drying and NIRS had an average of 30.36% and 30.72%, respectively, while those evaluated in Serere using oven drying had a mean of 36%. Conversely, Ugandan clones had a DMC mean of 30.30%. Comparably, WA clones accumulated higher levels of TCC and DMC than Ugandan clones. Both the Ugandan and WA clones showed a negative correlation between TCC and DMC. The Ugandan clones had r = -0.43, whereas WA clones evaluated in Namulonge had r = 0.48 and those evaluated in Serere had r = -0.32. WA population revealed genetic diversity with MAF, He, Ho, and PIC means of 0.179, 0.262, 0.256, and 0.217, respectively. The analysis of molecular variance (AMOVA) reveals that each cluster has 59.6% genetic diversity. The TCC marker PSY2_572 had the highest coefficient of determination (R2) of 0.67 hence the marker of choice. In conclusion, moderate variation among the WA genotypes suggests that the useful alleles for desirable traits could be exploited for breeding purposes, whereas deploying TCC marker PSY2_572 in MAS will increase selection efficiency and accelerate TCC gain.