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

• Published in: Nature Biotechnology Vol. 34; no. 5; pp. 562 - 570
• Main Authors: Bredeson, Jessen V, Lyons, Jessica B, Prochnik, Simon E, Wu, G Albert, Ha, Cindy M, Edsinger-Gonzales, Eric, Grimwood, Jane, Schmutz, Jeremy, Rabbi, Ismail Y, Egesi, Chiedozie, Nauluvula, Poasa, Lebot, Vincent, Ndunguru, Joseph, Mkamilo, Geoffrey, Bart, Rebecca S, Setter, Tim L, Gleadow, Roslyn M, Kulakow, Peter, Ferguson, Morag E, Rounsley, Steve, Rokhsar, Daniel S
• Format: Journal Article
• Language: English
• Published: New York Springer Science and Business Media LLC 01.05.2016; Nature Publishing Group US; Nature Publishing Group; Springer Nature
• Subjects: 45; 45/23; 631/208/457/649; 631/449/2491; 631/449/2492; 631/449/711; Agriculture; amélioration des plantes; BASIC BIOLOGICAL SCIENCES; Bioinformatics; Biological diversity; Biological Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Cassava; Chromosome Mapping; Chromosome Mapping - methods; Chromosomes; Comparative studies; Conserved Sequence; Conserved Sequence - genetics; Crops; Cultivation; DNA; DNA sequencing; DNA, Plant; DNA, Plant - genetics; Ecology; F30 - Génétique et amélioration des plantes; F70 - Taxonomie végétale et phytogéographie; Genetic; Genetic aspects; Genetic diversity; Genetic research; Genetic Variation; Genetics; Genome; Genome, Plant; Genome, Plant - genetics; Genomics; génome; Hevea; http://aims.fao.org/aos/agrovoc/c_1070; http://aims.fao.org/aos/agrovoc/c_1556; http://aims.fao.org/aos/agrovoc/c_15975; http://aims.fao.org/aos/agrovoc/c_1767; http://aims.fao.org/aos/agrovoc/c_1972; http://aims.fao.org/aos/agrovoc/c_24126; http://aims.fao.org/aos/agrovoc/c_26794; http://aims.fao.org/aos/agrovoc/c_27812; http://aims.fao.org/aos/agrovoc/c_2895; http://aims.fao.org/aos/agrovoc/c_3224; http://aims.fao.org/aos/agrovoc/c_32886; http://aims.fao.org/aos/agrovoc/c_4086; http://aims.fao.org/aos/agrovoc/c_4579; http://aims.fao.org/aos/agrovoc/c_4580; http://aims.fao.org/aos/agrovoc/c_5159; http://aims.fao.org/aos/agrovoc/c_5182; http://aims.fao.org/aos/agrovoc/c_5956; http://aims.fao.org/aos/agrovoc/c_714; http://aims.fao.org/aos/agrovoc/c_7608; http://aims.fao.org/aos/agrovoc/c_7690; http://aims.fao.org/aos/agrovoc/c_7701; http://aims.fao.org/aos/agrovoc/c_8038; http://aims.fao.org/aos/agrovoc/c_8157; http://aims.fao.org/aos/agrovoc/c_8355; Human Genome; hybridation interspécifique; Hybridization; Hybridization, Genetic; Hybridization, Genetic - genetics; Life Sciences; Manihot; Manihot - classification; Manihot - genetics; Manihot esculenta; Manihot glaziovii; Methods; Nucleotide sequencing; Nutrition; Pathogens; Plant; Plant breeding; Plant Breeding - methods; plant domestication; Plant genetics; plante de culture; plante sauvage; resource; Rubber; Rubber trees; Sequence Analysis; Sequence Analysis, DNA; Sequence Analysis, DNA - methods; Species Specificity; séquence d'adn; Tropical environments; tétraploïdie; variation génétique; variété; variété indigène
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/nbt.3535

The global genetic diversity of cassava and related Manihot species is revealed by sequencing of 53 cultivated and wild accessions and genotyping of 268 African cassavas, providing a vital resource for breeding. 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.