During November 2004, veinal chlorosis on mature cassava leaves, typical of cassava brown streak disease (CBSD), was observed at Mukono in central Uganda. Five out of 11 cultivars at the site showed CBSD symptoms (incidence range 4 to 64%). In a survey of farmers' fields, CBSD was observed in Wakiso and Mukono districts. Incidence of cassava mosaic disease was also recorded and averaged 60% for landraces (range 16.7 to 100%) and 20% for resistant varieties (range 0 to 65%). Leaf samples of plants with CBSD symptoms produced an amplicon of 222 bp using reverse transcription-polymerase chain reaction with primers that amplify a fragment of the coat protein (CP) gene of Cassava brown streak virus. Sequence comparisons based on the amplified CP gene fragment indicated that the isolates have 77 to 82.9% nucleotide and 43.9 to 56.8% amino acid identity with those from Mozambique and Tanzania. There was 95.9 to 99.5% nucleotide and 85.1 to 90.5% amino acid identity among the Ugandan isolates. These results confirm the re-emergence of CBSD in Uganda after it was first observed in the 1930s in cassava introduced from Tanzania and controlled by eradication. Prior to this report, CBSD was known to be restricted to the coastal lowlands of East Africa.

Cassava (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.For millions of people in the tropics, cassava is the third most consumed carbohydrate source, after rice and maize 1 . Even though cassava was domesticated in Latin America 2,3 , it has spread widely and has become a major staple crop in Africa. Although its wild progenitor, M. esculenta sp. falbellifolia, reproduces by seed 4 , cultivated cassava is notably almost exclusively clonally propagated via stem cutting 5 . The limited number of recombination events in such vegetatively propagated crops may result in an accumulation of deleterious alleles throughout the genome 6 . Thus, mutation burden in cassava is expected to be more severe than that in sexually propagated species. Deleterious mutations are considered to be at the heart of inbreeding depression 7 . Even in elite cassava accessions, inbreeding depression is extremely severe, and a single generation of inbreeding may result in a >60% decrease in fresh root yield 8,9 . In this study, we sought to identify deleterious mutations in cassava populations, with the goal of accelerating cassava breeding by allowing breeders to purge deleterious mutations more efficiently.We conducted a comprehensive characterization of genetic variation by whole-genome sequencing (WGS) of 241 cassava accessions ( Fig. 1, Supplementary Fig. 1 and Supplementary Table 1). On average, more than 30× coverage was generated for each accession. To ensure high-quality variant discovery, variants from low-copynumber regions of the cassava genome 10,11 were identified to develop the cassava haplotype map II (HapMapII) (Supplementary Fig. 2), containing 25.9 million SNPs and 1.9 million insertions/deletions (indels) (Supplementary Table 2), of which nearly 50% were rare (minor-allele frequency <0.05) (Supplementary Fig. 3). The error rate of variant calling, i.e., the proportion of segregating sites in the reference accession, was 0.01%. The correlation between read depth and the proportion of SNP heterozygosity was extremely low (r 2 = 6 × 10...

Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: cross-validation within populations, cross-population prediction and cross-generation prediction. We also evaluated the impact of increasing the training population (TP) size by phenotyping progenies selected either at random or with a genetic algorithm. Cross-validation results were mostly consistent across programs, with nonadditive models predicting of 10% better on average. Cross-population accuracy was generally low (mean = 0.18) but prediction of cassava mosaic disease increased up to 57% in one Nigerian population when data from another related population were combined. Accuracy across generations was poorer than within-generation accuracy, as expected, but accuracy for dry matter content and mosaic disease severity should be sufficient for rapid-cycling GS. Selection of a prediction model made some difference across generations, but increasing TP size was more important. With a genetic algorithm, selection of one-third of progeny could achieve an accuracy equivalent to phenotyping all progeny. We are in the early stages of GS for this crop but the results are promising for some traits. General guidelines that are emerging are that TPs need to continue to grow but phenotyping can be done on a cleverly selected subset of individuals, reducing the overall phenotyping burden.

Cassava (Manihot esculenta Crantz) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Biparental mapping studies suggest primarily a single major gene mediates resistance. To investigate this genetic architecture, we conducted the first genome-wide association mapping study in cassava with up to 6128 genotyping-by-sequenced African breeding lines and 42,113 reference genome-mapped single-nucleotide polymorphism (SNP) markers. We found a single region on chromosome 8 that accounts for 30 to 66% of genetic resistance in the African cassava germplasm. Thirteen additional regions with small effects were also identified. Further dissection of the major quantitative trait locus (QTL) on chromosome 8 revealed the presence of two possibly epistatic loci and/or multiple resistance alleles, which may account for the difference between moderate and strong disease resistances in the germplasm. Search of potential candidate genes in the major QTL region identified two peroxidases and one thioredoxin. Finally, we found genomic prediction accuracy of 0.53 to 0.58 suggesting that genomic selection (GS) will be effective both for improving resistance in breeding populations and identifying highly resistant clones as varieties.

Key messageConsolidates relevant molecular and phenotypic information on cassava to demonstrate relevance of heterosis, and alternatives to exploit it by integrating different tools. Ideas are useful to other asexually reproduced crops.AbstractAsexually propagated crops offer the advantage that all genetic effects can be exploited in farmers’ production fields. However, non-additive effects complicate selection because, while influencing the performance of the materials under evaluation, they cannot be transmitted efficiently to the following cycle of selection. Cassava can be used as a model crop for asexually propagated crops because of its diploid nature and the absence of (known) incompatibility effects. New technologies such as genomic selection (GS), use of inbred progenitors based on doubled haploids and induction of flowering can be employed for accelerating genetic gains in cassava. Available information suggests that heterosis, non-additive genetic effects and within-family variation are relatively large for complex traits such as fresh root yield, moderate for dry matter or starch content in the roots, and low for defensive traits (pest and disease resistance) and plant architecture. The present article considers the potential impact of different technologies for maximizing gains for key traits in cassava, and highlights the advantages of integrating them. Exploiting heterosis would be optimized through the implementation of reciprocal recurrent selection. The advantages of using inbred progenitors would allow shifting the current cassava phenotypic recurrent selection method into line improvement, which in turn would allow designing outstanding hybrids rather than finding them by trial and error.

Cassava (Manihot esculenta Crantz) production is currently under threat from cassava brown streak disease (CBSD), a disease that is among the seven most serious obstacles to world’s food security. Three issues are of significance for CBSD. Firstly, the virus associated with CBSD, has co-evolved with cassava outside its center of origin for at least 90 years. Secondly, that for the last 74 years, CBSD was only limited to the low lands. Thirdly, that most research has largely focused on CBSD epidemiology and virus diversity. Accordingly, this paper focuses on CBSD genetics and/or breeding and hence, presents empirical data generated in the past 11 years of cassava breeding in Uganda. Specifically, this paper provides: 1) empirical data on CBSD resistance screening efforts to identify sources of resistance and/or tolerance; 2) an update on CBSD resistance population development comprising of full-sibs, half-sibs and S1 families and their respective field performances; and 3) insights into chromosomal regions and genes involved in CBSD resistance based on genome wide association analysis. It is expected that this information will provide a foundation for harmonizing on-going CBSD breeding efforts and consequently, inform the future breeding interventions aimed at combating CBSD.

Cassava (Manihot esculenta) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Bi-parental mapping studies suggest primarily a single major gene mediates resistance. To be certain and to potentially identify new loci we conducted the first genome-wide association mapping study in cassava with 6128 African breeding lines. We also assessed the accuracy of genomic selection to improve CMD resistance. We found a single region on chromosome 8 accounts for most resistance but also identified 13 small effect regions. We found evidence that two epistatic loci and/or alternatively multiple resistance alleles exist at major QTL. We identified two peroxidases and one thioredoxin as candidate genes. Genomic prediction of additive and total genetic merit was accurate for CMD and will be effective both for selecting parents and identifying highly resistant clones as varieties.

Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda. Our GWAS study found two regions associated to CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. Predictive accuracy values varied between CBSD foliar severity traits at 3 months after planting (MAP) (0.27–0.32), 6 MAP (0.40–0.42) and root severity (0.31–0.42). For all traits, Random Forest and reproducing kernel Hilbert spaces regression showed the highest predictive accuracies. Our results provide an insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding.