Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Article purchased; Published online: 17 April 2017Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these deleterious mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions and identified >28 million segregating variants. We found that (i) although domestication has modified starch and ketone metabolism pathways to allow for human consumption, the concomitant bottleneck and clonal propagation have resulted in a large proportion of fixed deleterious amino acid changes, increased the number of deleterious alleles by 26%, and shifted the mutational burden toward common variants; (ii) deleterious mutations have been ineffectively purged, owing to limited recombination in the cassava genome; (iii) recent breeding efforts have maintained yield by masking the most damaging recessive mutations in the heterozygous state but have been unable to purge the mutation burden; such purging should be a key target in future cassava breeding

Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm

Open Access Journal; Published online: 23 Nov 2022Introduction 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

Training population optimization for prediction of cassava brown streak disease resistance in west African clones

Published online: 29 Oct 2018; Open Access JournalCassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector (Bemisia tabaci) may facilitate spread of CBSV to West Africa. Thus, effort to pre-emptively breed for CBSD resistance in W. Africa is critical. Genomic selection (GS) has become the main approach for cassava breeding, as costs of genotyping per sample have declined. Using phenotypic and genotypic data (genotyping-by-sequencing), followed by imputation to whole genome sequence (WGS) for 922 clones from National Crops Resources Research Institute, Namulonge, Uganda as a training population (TP), we predicted CBSD symptoms for 35 genotyped W. African clones, evaluated in Uganda. The highest prediction accuracy (r = 0.44) was observed for cassava brown streak disease severity scored at three months (CBSD3s) in the W. African clones using WGS-imputed markers. Optimized TPs gave higher prediction accuracies for CBSD3s and CBSD6s than random TPs of the same size. Inclusion of CBSD QTL chromosome markers as kernels, increased prediction accuracies for CBSD3s and CBSD6s. Similarly, WGS imputation of markers increased prediction accuracies for CBSD3s and for cassava brown streak disease root severity (CBSDRs), but not for CBSD6s. Based on these results we recommend TP optimization, inclusion of CBSD QTL markers in genomic prediction models, and the use of high-density (WGS-imputed) markers for CBSD predictions across population

Limits of phytosanitation and host plant resistance towards the control of cassava viruses in Uganda

Published online: 30 Sept 2017Cassava (Manihot esculenta Crantz) and the viruses that infect it, notably cassava mosaic virus and cassava brown streak viruses, have a unique history of co-evolution and co-existence. While cassava originated in South America, both viruses and the diseases they cause have largely been limited to the East African region, where they have, and continue to be key yield-robbing stresses. For sustainable control, we assume that deployment of resistant varieties when carefully combined with phytosanitation will combat these viruses. We have thus generated empirical data and tested the limits, i.e., how long this strategy can last. This entailed the comparison of elite cassava varieties, one set of virus-indexed tissue culture plantlets, and the other set, re-cycled planting materials under farmer’s cyclic propagation for 6-23 years. Trials were established at diverse sites in Uganda. We observed that both officially-released and unofficially-released cassava varieties are common in farmer’s fields; these varieties have varying susceptibility levels to viruses. Worrisome was that some officially-released varieties like NASE 3 registered cassava mosaic disease (CMD) incidences of up to 71% (virus-indexed), which was not any different from its re-cycled counterparts. Other varieties like NASE 14 have maintained high levels of CMD resistance six years after official release. Predominant re-cycled cassava varieties notably TME 204, I92/0057, TME 14, and to a limited extent NASE 14, are key reservoirs for cassava brown streak disease (CBSD) associated viruses. These findings highlight the limits of phytosanitation, i.e., in areas like Kaberamaido associated with high CMD pressure, varieties NASE 1 and NASE 3 can not be recommended; on the contrary, these varieties can be deployed in Kalangala, where they can survive with phytosanitation. And for CBSD, the findings justify the urgent need for phytosanitation (community-led) and development of varieties with higher levels of resistance and/or tolerance, as no immune variety has so far been identified

Effectiveness of genomic selection for improving provitamin A carotenoid content and associated traits in cassava

Open Access Journal; Published online: 08 May 2021Global efforts are underway to develop cassava with enhanced levels of provitamin A carotenoids to sustainably meet increasing demands for food and nutrition where the crop is a major staple. Herein, we tested the effectiveness of genomic selection (GS) for rapid improvement of cassava for total carotenoids content and associated traits. We evaluated 632 clones from Uganda’s provitamin A cassava breeding pipeline and 648 West African introductions. At harvest, each clone was assessed for level of total carotenoids, dry matter content, and resistance to cassava brown streak disease (CBSD). All clones were genotyped with diversity array technology and imputed to a set of 23,431 single nucleotide polymorphic markers. We assessed predictive ability of four genomic prediction methods in scenarios of cross-validation, across population prediction, and inclusion of quantitative trait loci markers. Cross-validations produced the highest mean prediction ability for total carotenoids content (0.52) and the lowest for CBSD resistance (0.20), with G-BLUP outperforming other models tested. Across population, predictions showed low ability of Ugandan population to predict the performance of West African clones, with the highest predictive ability recorded for total carotenoids content (0.34) and the lowest for CBSD resistance (0.12) using G-BLUP. By incorporating chromosome 1 markers associated with carotenoids content as independent kernel in the G-BLUP model of a cross-validation scenario, prediction ability slightly improved from 0.52 to 0.58. These results reinforce ongoing efforts aimed at integrating GS into cassava breeding and demonstrate the utility of this tool for rapid genetic improvement

Genetic diversity of provitamin a cassava in Uganda

Global efforts are being made towards developing provitamin A cassava (Manihot esculenta Cranz) varieties for sustainably addressing vitamin A malnutrition commonly noted in communities where cassava is a major staple. To elucidate the diversity in Uganda’s core collection of yellow root cassava germplasm, genetic variability was assessed for 64 yellow and white root cassava accessions including Ugandan landraces, and accessions introduced from the International Center for Tropical Agriculture (CIAT) and the International Institute of Tropical Agriculture (IITA). Phenotypic characterization was based on 12 morphological descriptors, total carotenoid content (TCC) and dry matter content (DMC). Variation of twenty six simple sequence repeat (SSR) markers was assessed and compared with morphological data. Total carotenoid content varied from 1.2 to 14.2 ?g/100 g and correlated negatively (R2 = -0.46) with dry matter content which ranged from 27.2 to 39.8 %. Genetic diversity was high in all accession groups with an average heterozygosity of 0.5583 ± 0.0182. Phenetic analyses using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principle Coordinate Analysis (PCoA) clustered the CIAT accessions into a distinct group, discriminating them from the landraces and IITA accessions. Based on the clustering pattern, it suffices to suggest limited gene flow between CIAT accessions and the landraces/IITA accessions which is an opportunity for broadening the genetic base through hybridization by exploiting the heterotic pool in the germplasm