Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop. 13 International Institute of Tropical Agriculture (IITA), Nairobi, Kenya. 14 Dow AgroSciences, Indianapolis, Indiana, USA. 15 Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan. 16 In this report we use "cassava" to refer to cultivated and/or domesticated varieties of M. esculenta, and the shorthand M. esc. flabellifolia for wild accessions 3 . We also shotgun-sequenced five Manihot accessions related to cassava, including three from the wild species M. glaziovii Muell. Arg., one named M. pseudoglaziovii Pax & K. Hoffman, and "tree" cassava, a suspected hybrid sometimes called M. catingea Ule 12,18 . The Ceará or India rubber tree species M. glaziovii, also domesticated in South America, was imported to East Africa in the early twentieth century. It is interfertile with cassava and has been used in African breeding programs to exploit the natural resistance of M. glaziovii to cassava pathogens 18 . To analyze genetic variation present in African varieties, we also characterized 268 cultivars of cassava using reduced representation genotypingby-sequencing (GBS) 19 (Table 2). RESULTS Chromosome structureTo produce a high-quality chromosome-scale reference genome for cassava, we augmented our earlier draft sequence 20 of the reference genotype AM560-2 with additional whole genome shotgun sequencing and mate pair data, fosmid-end sequences, and a paired-end library developed using proximity ligation of in vitro reconstituted chromatin 21 (Methods and Supplementary Note 1). AM560-2 is an S3 line bred at Centro Internacional de Agricultura Tropical (CIAT) from MCOL1505 (also known as Manihoica P-12 (ref. 22). Compared with the previous draft 23 , the contiguity of our new shotgun assembly has more than doubled (N50 length 27.7 kb vs. 11.5 kb), and an additional 135 Mb is anchored to chromosomes 23 (Supplementary Note 1). To organize the sequence into chromosomes we integrated the shotgun ...

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...

BackgroundRoot and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop.ResultsTo accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage.ConclusionsGuinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.

Cassava mosaic disease (CMD), caused by different species of cassava mosaic geminiviruses (CMGs), is the most important disease of cassava in Africa and the Indian sub-continent. The cultivated cassava species is protected from CMD by polygenic resistance introgressed from the wild species Manihot glaziovii and a dominant monogenic type of resistance, named CMD2, discovered in African landraces. The ability of the monogenic resistance to confer high levels of resistance in different genetic backgrounds has led recently to its extensive usage in breeding across Africa as well as pre-emptive breeding in Latin America. However, most of the landraces carrying the monogenic resistance are morphologically very similar and come from a geographically restricted area of West Africa, raising the possibility that the diversity of the single-gene resistance could be very limited, or even located at a single locus. Several mapping studies, employing bulk segregant analysis, in different genetic backgrounds have reported additional molecular markers linked to supposedly new resistance genes. However, it is not possible to tell if these are indeed new genes in the absence adequate genetic map framework or allelism tests. To address this important question, a high-density single nucleotide polymorphism (SNP) map of cassava was developed through genotyping-by-sequencing a bi-parental mapping population (N=180) that segregates for the dominant monogenic resistance to CMD. Virus screening using PCR showed that CMD symptoms and presence of virus were strongly correlated (r=0.98). Genome-wide scan and high-resolution composite interval mapping using 6756 SNPs uncovered a single locus with large effect (R(2)=0.74). Projection of the previously published resistance-linked microsatellite markers showed that they co-occurred in the same chromosomal location surrounding the presently mapped resistance locus. Moreover, their relative distance to the mapped resistance locus correlated with the reported degree of linkage with the resistance phenotype. Cluster analysis of the landraces first shown to have this type of resistance revealed that they are very closely related, if not identical. These findings suggest that there is a single source of monogenic resistance in the crop's genepool tracing back to a common ancestral clone. In the absence of further resistance diversification, the long-term effectiveness of the single gene resistance is known to be precarious, given the potential to be overcome by CMGs due to their fast-paced evolutionary rate. However, combining the quantitative with the qualitative type of resistance may ensure that this resistance gene continues to offer protection to cassava, a crop that is depended upon by millions of people in Africa against the devastating onslaught of CMGs.

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.