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

Journal Article · · Nature Biotechnology
DOI:https://doi.org/10.1038/nbt.3535· OSTI ID:1616047
 [1];  [1];  [2];  [2];  [3];  [3];  [4];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [11];  [12];  [13];  [5];  [14];  [15] more »;  [16] « less
  1. Univ. of California, Berkeley, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Univ. of California, Berkeley, CA (United States); Univ. of Colorado, Denver, CO (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  5. International Institute of Tropical Agriculture (IITA), Ibadan (Nigeria)
  6. National Root Crops Research Institute (NRCRI), Umudike (Nigeria)
  7. Ministry of Primary Industries, Koronivia Research Station (Fiji)
  8. Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Port-Vila (Vanuatu)
  9. Mikocheni Agricultural Research Institute (MARI), Dar es Salaam (Tanzania)
  10. Naliendele Agricultural Research Institute (NARI), Mtwara (Tanzania)
  11. Donald Danforth Plant Science Center, St. Louis, MO (United States)
  12. Cornell Univ., Ithaca, NY (United States)
  13. Monash Univ., Melbourne, VIC (Australia)
  14. International Institute of Tropical Agriculture (IITA), Nairobi (Kenya)
  15. Dow AgroSciences, Indianapolis, IN (United States)
  16. Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Okinawa Institute of Science and Technology Graduate University, Onna (Japan)
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.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
Bill and Melinda Gates Foundation (BMGF); National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1616047
Journal Information:
Nature Biotechnology, Journal Name: Nature Biotechnology Journal Issue: 5 Vol. 34; ISSN 1087-0156
Publisher:
Springer NatureCopyright Statement
Country of Publication:
United States
Language:
English

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Additional file 10 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 11 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 12 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 13 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 14 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 15 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 16 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 17 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 18 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 19 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 1 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 20 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 21 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 2 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 3 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 4 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 5 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 6 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 7 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 8 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 9 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity dataset January 2021
Additional file 3 of Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae dataset January 2022
Additional file 4 of Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae dataset January 2022
Additional file 5 of Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae dataset January 2022
Additional file 7 of Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae dataset January 2022
Additional file 8 of Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae dataset January 2022
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Provitamin A biofortification of cassava enhances shelf life but reduces dry matter content of storage roots due to altered carbon partitioning into starch journal December 2017
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Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 reduces cassava brown streak disease symptom severity and incidence journal October 2018
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