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.
- Authors:
-
[1];
[13];
[15]
more »
- Univ. of California, Berkeley, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of California, Berkeley, CA (United States); Univ. of Colorado, Denver, CO (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
- International Institute of Tropical Agriculture (IITA), Ibadan (Nigeria)
- National Root Crops Research Institute (NRCRI), Umudike (Nigeria)
- Ministry of Primary Industries, Koronivia Research Station (Fiji)
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Port-Vila (Vanuatu)
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam (Tanzania)
- Naliendele Agricultural Research Institute (NARI), Mtwara (Tanzania)
- Donald Danforth Plant Science Center, St. Louis, MO (United States)
- Cornell Univ., Ithaca, NY (United States)
- Monash Univ., Melbourne, VIC (Australia)
- International Institute of Tropical Agriculture (IITA), Nairobi (Kenya)
- Dow AgroSciences, Indianapolis, IN (United States)
- 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)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); Bill and Melinda Gates Foundation (BMGF)
- OSTI Identifier:
- 1616047
- Grant/Contract Number:
- AC02-05CH11231; OPPGD1493; OPP1048542; OPPGD1016; S10RR029668; S10RR027303
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Biotechnology
- Additional Journal Information:
- Journal Volume: 34; Journal Issue: 5; Journal ID: ISSN 1087-0156
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
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, and Rokhsar, Daniel S. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. United States: N. p., 2016.
Web. doi:10.1038/nbt.3535.
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. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. United States. https://doi.org/10.1038/nbt.3535
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, and Rokhsar, Daniel S. Mon .
"Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity". United States. https://doi.org/10.1038/nbt.3535. https://www.osti.gov/servlets/purl/1616047.
@article{osti_1616047,
title = {Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity},
author = {Bredeson, Jessen V. and Lyons, Jessica B. and Prochnik, Simon E. and Wu, G. Albert and Ha, Cindy M. and Edsinger-Gonzales, Eric and Grimwood, Jane and Schmutz, Jeremy and Rabbi, Ismail Y. and Egesi, Chiedozie and Nauluvula, Poasa and Lebot, Vincent and Ndunguru, Joseph and Mkamilo, Geoffrey and Bart, Rebecca S. and Setter, Tim L. and Gleadow, Roslyn M. and Kulakow, Peter and Ferguson, Morag E. and Rounsley, Steve and Rokhsar, Daniel S.},
abstractNote = {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.},
doi = {10.1038/nbt.3535},
journal = {Nature Biotechnology},
number = 5,
volume = 34,
place = {United States},
year = {Mon Apr 18 00:00:00 EDT 2016},
month = {Mon Apr 18 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 235 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Table 1: Whole genome shotgun sequenced Manihot accessions
All figures and tables
(6 total)
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Estimation of individual admixture: Analytical and study design considerations
journal, January 2005
- Tang, Hua; Peng, Jie; Wang, Pei
- Genetic Epidemiology, Vol. 28, Issue 4
Development and application of transgenic technologies in cassava
journal, November 2004
- Taylor, Nigel; Chavarriaga, Paul; Raemakers, Krit
- Plant Molecular Biology, Vol. 56, Issue 4
Transgenic RNA interference (RNAi)-derived field resistance to cassava brown streak disease: Resistance to cassava brown streak disease
journal, July 2012
- Ogwok, Emmanuel; Odipio, John; Halsey, Mark
- Molecular Plant Pathology, Vol. 13, Issue 9
Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009
- Li, H.; Durbin, R.
- Bioinformatics, Vol. 25, Issue 14
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
journal, September 2007
- Purcell, Shaun; Neale, Benjamin; Todd-Brown, Kathe
- The American Journal of Human Genetics, Vol. 81, Issue 3
Wild Manihot species: botanical aspects, geographic distribution and economic value
journal, January 2008
- Nassar, Nagib M. A.; Hashimoto, D. Y. C.; Fernandes, S. D. C.
- Genetics and Molecular Research, Vol. 7, Issue 1
Draft genome sequence of the rubber tree Hevea brasiliensis
journal, January 2013
- Rahman, Ahmad Yamin Abdul; Usharraj, Abhilash O.; Misra, Biswapriya B.
- BMC Genomics, Vol. 14, Issue 1
Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland
journal, April 2020
- Furtwängler, Anja; Rohrlach, A. B.; Lamnidis, Thiseas C.
- Nature Communications, Vol. 11, Issue 1
Thai elite cassava genetic diversity was fortuitously conserved through farming with different sets of varieties
journal, July 2014
- Fu, Yong-Bi; Wangsomnuk, Preeya P.; Ruttawat, Benjawan
- Conservation Genetics, Vol. 15, Issue 6
Genomic selection in plant breeding: from theory to practice
journal, February 2010
- Jannink, J. -L.; Lorenz, A. J.; Iwata, H.
- Briefings in Functional Genomics, Vol. 9, Issue 2
A framework for variation discovery and genotyping using next-generation DNA sequencing data
journal, April 2011
- DePristo, Mark A.; Banks, Eric; Poplin, Ryan
- Nature Genetics, Vol. 43, Issue 5
SNPs, SSRs and inferences on cassava’s origin
journal, November 2004
- Olsen, Kenneth M.
- Plant Molecular Biology, Vol. 56, Issue 4
Conservation of the genetic resources of cassava (Manihot Esculenta) Determination of wild species localities with emphasis on probable origin
journal, July 1978
- Nassar, Nagib M. A.
- Economic Botany, Vol. 32, Issue 3
Archaeological manioc (Manihot) from Coastal Peru
journal, January 1986
- Ugent, Donald; Pozorski, Shelia; Pozorski, Thomas
- Economic Botany, Vol. 40, Issue 1
Unlocking the potential of tropical root crop biotechnology in east Africa by establishing a genetic transformation platform for local farmer-preferred cassava cultivars
text, January 2013
- Nyaboga, Evans; Njiru, Joshua; Nguu, Edward
- ETH Zurich
Population Structure and Eigenanalysis
journal, January 2006
- Patterson, Nick; Price, Alkes L.; Reich, David
- PLoS Genetics, Vol. 2, Issue 12
High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding
journal, June 2014
- Rabbi, Ismail Y.; Hamblin, Martha T.; Kumar, P. Lava
- Virus Research, Vol. 186
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
journal, October 2003
- Haas, B. J.
- Nucleic Acids Research, Vol. 31, Issue 19
AFLP assessment of genetic variability in cassava accessions ( Manihot esculenta ) resistant and susceptible to the cassava bacterial blight (CBB)
journal, April 1999
- Sanchez, Gilda; Restrepo, Silvia; Duque, Myriam-Cristina
- Genome, Vol. 42, Issue 2
Genetic Mapping Using Genotyping-by-Sequencing in the Clonally Propagated Cassava
journal, January 2014
- Rabbi, Ismail; Hamblin, Martha; Gedil, Melaku
- Crop Science, Vol. 54, Issue 4
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
text, January 2015
- Putnam, Nicholas H.; O'Connell, Brendan; Stites, Jonathan C.
- arXiv
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
journal, June 2014
- Wu, G. Albert; Prochnik, Simon; Jenkins, Jerry
- Nature Biotechnology, Vol. 32, Issue 7
Cassava genome from a wild ancestor to cultivated varieties
journal, October 2014
- Wang, Wenquan; Feng, Binxiao; Xiao, Jingfa
- Nature Communications, Vol. 5, Issue 1
Cytogenetics of Manihot esculenta Crantz (cassava) and eight related species
journal, June 2002
- De Carvalho, Reginaldo; Guerra, Marcelo
- Hereditas, Vol. 136, Issue 2
Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava
journal, June 2015
- Ceballos, Hernán; Kawuki, Robert S.; Gracen, Vernon E.
- Theoretical and Applied Genetics, Vol. 128, Issue 9
Sketching algorithms for genomic data analysis and querying in a secure enclave
journal, March 2020
- Kockan, Can; Zhu, Kaiyuan; Dokmai, Natnatee
- Nature Methods, Vol. 17, Issue 3
Origin and Domestication of Native Amazonian Crops
journal, January 2010
- Clement, Charles; De Cristo-Araújo, Michelly; Coppens D’Eeckenbrugge, Geo
- Diversity, Vol. 2, Issue 1
AFLP assessment of genetic variability in cassava accessions (Manihot esculenta) resistant and susceptible to the cassava bacterial blight (CBB)
journal, January 1999
- Sanchez, Gilda; Restrepo, Silvia; Duque, Myriam-Cristina
- Genome, Vol. 42, Issue 2
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
journal, April 2014
- Kajitani, Rei; Toshimoto, Kouta; Noguchi, Hideki
- Genome Research, Vol. 24, Issue 8
Some evidence on the genetic structure of present-day raspberry varieties and some possible implications for further breeding
journal, July 1963
- Jennings, D. L.
- Euphytica, Vol. 12, Issue 2
Microsatellite variation in cassava ( Manihot esculenta , Euphorbiaceae) and its wild relatives: further evidence for a southern Amazonian origin of domestication
journal, January 2001
- Olsen, Kenneth M.; Schaal, Barbara A.
- American Journal of Botany, Vol. 88, Issue 1
Evidence on the origin of cassava: Phylogeography of Manihot esculenta
journal, May 1999
- Olsen, K. M.; Schaal, B. A.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 10
Unlocking the potential of tropical root crop biotechnology in east Africa by establishing a genetic transformation platform for local farmer-preferred cassava cultivars
journal, January 2013
- Nyaboga, Evans; Njiru, Joshua; Nguu, Edward
- Frontiers in Plant Science, Vol. 4
BROADENING THE GENETIC BASE OF CASSAVA, Manihot esculenta Crantz, BY INTERSPECIFIC HYBRIDIZATION
journal, July 1989
- Nassar, Nagib M. A.
- Canadian Journal of Plant Science, Vol. 69, Issue 3
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
journal, July 2010
- McKenna, A.; Hanna, M.; Banks, E.
- Genome Research, Vol. 20, Issue 9
Domestication and Diversity in Manioc ( Manihot esculenta Crantz ssp. esculenta , Euphorbiaceae)
journal, December 2008
- Rival, Laura; McKey, Doyle
- Current Anthropology, Vol. 49, Issue 6
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011
- Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi
- PLoS ONE, Vol. 6, Issue 5, Article No. e19379
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
journal, March 1999
- Morgenstern, B.
- Bioinformatics, Vol. 15, Issue 3
Molecular Markers and Their Application to Cassava Breeding: Past, Present and Future
journal, December 2011
- Ferguson, Morag; Rabbi, Ismail; Kim, Dong-Jin
- Tropical Plant Biology, Vol. 5, Issue 1
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
The Cassava Genome: Current Progress, Future Directions
journal, January 2012
- Prochnik, Simon; Marri, Pradeep Reddy; Desany, Brian
- Tropical Plant Biology, Vol. 5, Issue 1
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
journal, February 2016
- Putnam, Nicholas H.; O'Connell, Brendan L.; Stites, Jonathan C.
- Genome Research, Vol. 26, Issue 3
Works referencing / citing this record:
De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
journal, February 2017
- Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat
- Scientific Reports, Vol. 7, Issue 1
Comparison of leaf transcriptomes of cassava “Xinxuan 048” diploid and autotetraploid plants
journal, May 2018
- Yin, Ling; Qu, Junjie; Zhou, Huiwen
- Genes & Genomics, Vol. 40, Issue 9
Rooting for cassava: insights into photosynthesis and associated physiology as a route to improve yield potential
journal, October 2016
- De Souza, Amanda P.; Massenburg, Lynnicia N.; Jaiswal, Deepak
- New Phytologist, Vol. 213, Issue 1
Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops
journal, January 2020
- Price, Elliott J.; Drapal, Margit; Perez‐Fons, Laura
- The Plant Journal, Vol. 101, Issue 6
Genomics-Assisted Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB)
journal, June 2018
- Friedmann, Michael; Asfaw, Asrat; Anglin, Noelle
- Agriculture, Vol. 8, Issue 7
QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert
journal, July 2017
- Masumba, E. A.; Kapinga, F.; Mkamilo, G.
- Theoretical and Applied Genetics, Vol. 130, Issue 10
Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize
journal, January 2019
- Gonzalez-Segovia, Eric; Pérez-Limon, Sergio; Cíntora-Martínez, G. Carolina
- PeerJ, Vol. 7
Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut
journal, January 2018
- Zou, Zhi; Huang, Qixing; Xie, Guishui
- Scientific Reports, Vol. 8, Issue 1
QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii
journal, July 2017
- Nzuki, Inosters; Katari, Manpreet S.; Bredeson, Jessen V.
- Frontiers in Plant Science, Vol. 8
A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia
journal, September 2019
- Alves‐Pereira, Alessandro; Clement, Charles R.; Picanço‐Rodrigues, Doriane
- Evolutionary Applications, Vol. 13, Issue 2
Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval
journal, July 2018
- Cai, Liming; Xi, Zhenxiang; Amorim, André M.
- New Phytologist, Vol. 221, Issue 1
Divergent Regulation of CBF Regulon on Cold Tolerance and Plant Phenotype in Cassava Overexpressing Arabidopsis CBF3 Gene
journal, December 2016
- An, Dong; Ma, Qiuxiang; Yan, Wei
- Frontiers in Plant Science, Vol. 7
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
- Beyene, Getu; Solomon, Felix R.; Chauhan, Raj D.
- Plant Biotechnology Journal, Vol. 16, Issue 6
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
- Gomez, Michael A.; Lin, Z. Daniel; Moll, Theodore
- Plant Biotechnology Journal, Vol. 17, Issue 2
Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava
journal, January 2018
- Hummel, Aaron W.; Chauhan, Raj Deepika; Cermak, Tomas
- Plant Biotechnology Journal, Vol. 16, Issue 7
Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation
journal, February 2019
- Burgarella, Concetta; Barnaud, Adeline; Kane, Ndjido Ardo
- Frontiers in Plant Science, Vol. 10
Identification and characterization of drought-responsive CC-type glutaredoxins from cassava cultivars reveals their involvement in ABA signalling
journal, December 2018
- Ruan, Meng-Bin; Yang, Yi-Ling; Li, Kai-Mian
- BMC Plant Biology, Vol. 18, Issue 1
Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta
journal, January 2018
- Kayondo, Siraj Ismail; Pino Del Carpio, Dunia; Lozano, Roberto
- Scientific Reports, Vol. 8, Issue 1
A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data
journal, December 2018
- Chan, Ariel W.; Williams, Amy L.; Jannink, Jean-Luc
- BMC Bioinformatics, Vol. 19, Issue 1
A rapid virus-induced gene silencing (VIGS) method for assessing resistance and susceptibility to cassava mosaic disease
journal, March 2017
- Beyene, Getu; Chauhan, Raj Deepika; Taylor, Nigel J.
- Virology Journal, Vol. 14, Issue 1
A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus
journal, August 2017
- Amuge, T.; Berger, D. K.; Katari, M. S.
- Scientific Reports, Vol. 7, Issue 1
Overexpression of Arabidopsis FLOWERING LOCUS T (FT) gene improves floral development in cassava (Manihot esculenta, Crantz)
journal, July 2017
- Adeyemo, O. Sarah; Chavarriaga, Paul; Tohme, Joe
- PLOS ONE, Vol. 12, Issue 7
PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting
other, January 2019
- Erkes, Anett; Mücke, Stefanie; Reschke, Maik
- San Francisco, CA : Public Library of Science (PLoS)
Genomic prediction applied to high-biomass sorghum for bioenergy production
journal, April 2018
- de Oliveira, Amanda Avelar; Pastina, Maria Marta; de Souza, Vander Filipe
- Molecular Breeding, Vol. 38, Issue 4
Genetic Correlation, Genome-Wide Association and Genomic Prediction of Portable NIRS Predicted Carotenoids in Cassava Roots
journal, December 2019
- Ikeogu, Ugochukwu N.; Akdemir, Deniz; Wolfe, Marnin D.
- Frontiers in Plant Science, Vol. 10
PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting
journal, July 2019
- Erkes, Annett; Mücke, Stefanie; Reschke, Maik
- PLOS Computational Biology, Vol. 15, Issue 7
Identification of FT family genes that respond to photoperiod, temperature and genotype in relation to flowering in cassava (Manihot esculenta, Crantz)
journal, December 2018
- Adeyemo, Oluwabusayo Sarah; Hyde, Peter T.; Setter, Tim L.
- Plant Reproduction, Vol. 32, Issue 2
Genomic prediction applied to high-biomass sorghum for bioenergy production
journal, April 2018
- de Oliveira, Amanda Avelar; Pastina, Maria Marta; de Souza, Vander Filipe
- Molecular Breeding, Vol. 38, Issue 4
Genome‐Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content
journal, November 2017
- Rabbi, Ismail Y.; Udoh, Lovina I.; Wolfe, Marnin
- The Plant Genome, Vol. 10, Issue 3
Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins
journal, March 2019
- Ciska, Malgorzata; Hikida, Riku; Masuda, Kiyoshi
- Journal of Experimental Botany, Vol. 70, Issue 10
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
journal, September 2018
- Piližota, Ivana; Train, Clément-Marie; Altenhoff, Adrian
- Bioinformatics, Vol. 35, Issue 7
Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis
journal, January 2019
- Mateus, Ivan D.; Masclaux, Frédéric G.; Aletti, Consolée
- The ISME Journal, Vol. 13, Issue 5
Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots
text, January 2018
- Lentz, Ezequiel M.; Kuon, Joel‑Elias; Alder, Adrian
- ETH Zurich
Effect of temperature on development and reproduction of the carmine spider mite, Tetranychus cinnabarinus (Acari: Tetranychiae), fed on cassava leaves
journal, March 2018
- Zou, Zhiwen; Xi, Jianfei; Liu, Ge
- Experimental and Applied Acarology, Vol. 74, Issue 4
Symplasmic phloem unloading and radial post-phloem transport via vascular rays in tuberous roots of Manihot esculenta
text, January 2019
- Rabih, Mehdi,; E., Lamm, Christian; B., Anjanappa, Ravi
- ETH Zurich
Genome-wide identification and expression of GRAS gene family members in cassava
journal, January 2020
- Shan, Zhongying; Luo, Xinglu; Wu, Meiyan
- BMC Plant Biology, Vol. 20, Issue 1
Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation
journal, April 2017
- Ramu, Punna; Esuma, Williams; Kawuki, Robert
- Nature Genetics, Vol. 49, Issue 6
Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
journal, October 2018
- Zhang, Jisen; Zhang, Xingtan; Tang, Haibao
- Nature Genetics, Vol. 50, Issue 11
Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection
journal, December 2019
- Wolfe, Marnin D.; Bauchet, Guillaume J.; Chan, Ariel W.
- Genetics, Vol. 213, Issue 4
Genomic Diversity of Three Brazilian Native Food Crops Based on Double-Digest Restriction Site-Associated DNA Sequencing
journal, June 2019
- Alves-Pereira, Alessandro; Novello, Mariana; Dequigiovanni, Gabriel
- Tropical Plant Biology, Vol. 12, Issue 4
Accelerated ex situ breeding of GBSS - and PTST1 -edited cassava for modified starch
journal, September 2018
- Bull, Simon E.; Seung, David; Chanez, Christelle
- Science Advances, Vol. 4, Issue 9
PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting
other, January 2019
- Erkes, Anett; Mücke, Stefanie; Reschke, Maik
- San Francisco, CA : Public Library of Science (PLoS)
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
journal, September 2019
- Kuon, Joel-E.; Qi, Weihong; Schläpfer, Pascal
- BMC Biology, Vol. 17, Issue 1
A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus
journal, August 2017
- Amuge, T.; Berger, D. K.; Katari, M. S.
- Scientific Reports, Vol. 7, Issue 1
Genome-Wide Identification, Expression, and Functional Analysis of the Sugar Transporter Gene Family in Cassava (Manihot esculenta)
journal, March 2018
- Liu, Qin; Dang, Huijie; Chen, Zhijian
- International Journal of Molecular Sciences, Vol. 19, Issue 4
Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz)
journal, May 2017
- Wang, Bin; Guo, Xin; Zhao, Pingjuan
- PLOS ONE, Vol. 12, Issue 5
Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots
text, January 2018
- Lentz, Ezequiel M.; Kuon, Joel‑Elias; Alder, Adrian
- ETH Zurich
Symplasmic phloem unloading and radial post-phloem transport via vascular rays in tuberous roots of Manihot esculenta
journal, June 2019
- Mehdi, Rabih; Lamm, Christian E.; Bodampalli Anjanappa, Ravi
- Journal of Experimental Botany, Vol. 70, Issue 20
Proteomic analysis of injured storage roots in cassava (Manihot esculenta Crantz) under postharvest physiological deterioration
journal, March 2017
- Qin, Yuling; Djabou, Astride Stéphanie Mouafi; An, Feifei
- PLOS ONE, Vol. 12, Issue 3
Genome-wide identification and expression of GRAS gene family members in cassava
journal, January 2020
- Shan, Zhongying; Luo, Xinglu; Wu, Meiyan
- BMC Plant Biology, Vol. 20, Issue 1
Physiological and proteomic analysis on long-term drought resistance of cassava (Manihot esculenta Crantz)
journal, December 2018
- Shan, Zhongying; Luo, Xinglu; Wei, Maogui
- Scientific Reports, Vol. 8, Issue 1
Identification and validation of mutation points associated with waxy phenotype in cassava
journal, April 2020
- do Carmo, Cátia Dias; Sousa, Massaine Bandeira e.; dos Santos Silva, Priscila Patrícia
- BMC Plant Biology, Vol. 20, Issue 1
Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific
journal, October 2018
- Benucci, Gian Maria Niccolò; Bonito, Victor; Bonito, Gregory
- Microbial Ecology, Vol. 78, Issue 1
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
journal, August 2017
- Moll, Karen M.; Zhou, Peng; Ramaraj, Thiruvarangan
- BMC Genomics, Vol. 18, Issue 1
Genome-Wide Identification and Expression, Protein–Protein Interaction and Evolutionary Analysis of the Seed Plant-Specific BIG GRAIN and BIG GRAIN LIKE Gene Family
journal, October 2017
- Mishra, Bhuwaneshwar S.; Jamsheer K., Muhammed; Singh, Dhriti
- Frontiers in Plant Science, Vol. 8
A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia
journal, September 2019
- Alves‐Pereira, Alessandro; Clement, Charles R.; Picanço‐Rodrigues, Doriane
- Evolutionary Applications, Vol. 13, Issue 2
Cassava yield traits predicted by genomic selection methods
journal, November 2019
- Andrade, Luciano Rogério Braatz de; Sousa, Massaine Bandeira e.; Oliveira, Eder Jorge
- PLOS ONE, Vol. 14, Issue 11
Reproductive biology in cassava: stigma receptivity and pollen tube growth
journal, January 2019
- Ramos Abril, L. N.; Pineda, L. M.; Wasek, I.
- Communicative & Integrative Biology, Vol. 12, Issue 1
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
text, January 2019
- Kuon, Joel‑Elias; Qi, Weihong; Schläpfer, Pascal
- ETH Zurich
Physiological and proteomic analysis on long-term drought resistance of cassava (Manihot esculenta Crantz)
journal, December 2018
- Shan, Zhongying; Luo, Xinglu; Wei, Maogui
- Scientific Reports, Vol. 8, Issue 1
Genome-wide comparison reveals divergence of cassava and rubber aquaporin family genes after the recent whole-genome duplication
journal, May 2019
- Zou, Zhi; Yang, Jianghua
- BMC Genomics, Vol. 20, Issue 1
Identification and characterization of drought-responsive CC-type glutaredoxins from cassava cultivars reveals their involvement in ABA signalling
journal, December 2018
- Ruan, Meng-Bin; Yang, Yi-Ling; Li, Kai-Mian
- BMC Plant Biology, Vol. 18, Issue 1
Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis
journal, January 2020
- Zhao, Yongguo; Kong, Hua; Guo, Yunling
- PeerJ, Vol. 8
Production of very‐high‐amylose cassava by post‐transcriptional silencing of branching enzyme genes
journal, September 2019
- Zhou, Wenzhi; Zhao, Shanshan; He, Shutao
- Journal of Integrative Plant Biology, Vol. 62, Issue 6
Divergence of duplicated genes by repeated partitioning of splice forms and subcellular localization
journal, October 2019
- Qiu, Yichun; Tay, Yii Van; Ruan, Yuan
- New Phytologist, Vol. 225, Issue 2
Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots
journal, August 2018
- Lentz, Ezequiel Matias; Kuon, Joel-Elias; Alder, Adrian
- Plant Methods, Vol. 14, Issue 1
De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
journal, February 2017
- Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat
- Scientific Reports, Vol. 7, Issue 1
The extent of adaptive wild introgression in crops
journal, October 2018
- Janzen, Garrett M.; Wang, Li; Hufford, Matthew B.
- New Phytologist, Vol. 221, Issue 3
A global overview of cassava genetic diversity
journal, November 2019
- Ferguson, Morag E.; Shah, Trushar; Kulakow, Peter
- PLOS ONE, Vol. 14, Issue 11
Cassava yield traits predicted by genomic selection methods
journal, November 2019
- Andrade, Luciano Rogério Braatz de; Sousa, Massaine Bandeira e.; Oliveira, Eder Jorge
- PLOS ONE, Vol. 14, Issue 11
TAL Effector Repertoires of Strains of Xanthomonas phaseoli pv. manihotis in Commercial Cassava Crops Reveal High Diversity at the Country Scale
journal, February 2021
- Zárate-Chaves, Carlos A.; Osorio-Rodríguez, Daniela; Mora, Rubén E.
- Microorganisms, Vol. 9, Issue 2
RNAi inhibition of feruloyl CoA 6′-hydroxylase reduces scopoletin biosynthesis and post-harvest physiological deterioration in cassava (Manihot esculenta Crantz) storage roots
text, January 2017
- Shi, Liu,; M., Zainuddin, Ima; Hervé, Vanderschuren,
- ETH Zurich
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
text, January 2019
- Kuon, Joel‑Elias; Qi, Weihong; Schläpfer, Pascal
- ETH Zurich
Photosynthesis across African cassava germplasm is limited by Rubisco and mesophyll conductance at steady state, but by stomatal conductance in fluctuating light
journal, October 2019
- De Souza, Amanda P.; Wang, Yu; Orr, Douglas J.
- New Phytologist, Vol. 225, Issue 6
The evolutionary significance of polyploidy
journal, May 2017
- Van de Peer, Yves; Mizrachi, Eshchar; Marchal, Kathleen
- Nature Reviews Genetics, Vol. 18, Issue 7
Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis
journal, January 2019
- Mateus, Ivan D.; Masclaux, Frédéric G.; Aletti, Consolée
- The ISME Journal, Vol. 13, Issue 5
Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola
journal, December 2018
- Malmberg, M. Michelle; Barbulescu, Denise M.; Drayton, Michelle C.
- Frontiers in Plant Science, Vol. 9
Genome‐Wide Association Study of Resistance to Cassava Green Mite Pest and Related Traits in Cassava
journal, July 2018
- Ezenwaka, Lydia; Carpio, Dunia Pino; Jannink, Jean-Luc
- Crop Science, Vol. 58, Issue 5
Genomic approaches for studying crop evolution
journal, September 2018
- Schreiber, Mona; Stein, Nils; Mascher, Martin
- Genome Biology, Vol. 19, Issue 1
Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut
journal, January 2018
- Zou, Zhi; Huang, Qixing; Xie, Guishui
- Scientific Reports, Vol. 8, Issue 1
A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality
journal, July 2019
- Carballo, J.; Santos, B. A. C. M.; Zappacosta, D.
- Scientific Reports, Vol. 9, Issue 1
Genetic diversity and SNP’s from the chloroplast coding regions of virus-infected cassava
journal, March 2020
- Rossitto De Marchi, Bruno; Kinene, Tonny; Krause-Sakate, Renate
- PeerJ, Vol. 8
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.