Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Abstract

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 haplotype map highlights fixation of deleterious mutations during clonal propagation

“…Whole-genome sequences were generated from 241 cassava accessions including 203 elite breeding accessions, 16 progenitors (M. falbellifolia and M. peruviana) 2,3 , 11 hybrid/tree cassava accessions and 11 wild relative cassava accessions (M. glaziovii and others) (Supplementary Table 1). Wild M. glaziovii has been extensively used in cassava breeding programs to transfer disease-resistance alleles to cultivated cassava (for example, in the Amani Breeding Program) 10 . Among 241 cassava accessions, 172 accessions were sequenced at the Genomic Diversity Facility at Cornell University.…”

“…The 518.5-Mb cassava genome (v6.1) has ~51% repetitive elements with several common recent retrotransposons 10 . To exclude misalignment and to ensure high-quality variant discovery, these repeats were prefiltered by aligning the reads to a bait 10 containing repeat sequences and organelle sequences (Supplementary Fig.…”

“…Both lines of evidence supported the hypothesis that cultivated cassava was domesticated from M. esculenta sp. flabelifolia 2,3,10 . To evaluate population differentiation of cassava, a principal component analysis (PCA) was performed and showed substantial differentiation among all cassava species and hybrids (Fig.…”

“…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.…”

“…To estimate the individual mutation burden, we used rubber (Hevea brasiliensis), which diverged from the cassava lineage 27 million years (Myr) ago 10 , as an outgroup to identify derived deleterious alleles in cassava. The derived allele frequency (DAF) spectrum showed that cassava (4.6%, Fig.…”