The Cassava Genome: Current Progress, Future Directions

Prochnik, Simon; Marri, Pradeep Reddy; Desany, Brian; Rabinowicz, Pablo D.; Kodira, Chinnappa; Mohiuddin, Mohammed; Rodriguez, Fausto; Fauquet, Claude; Tohme, Joseph; Harkins, Timothy; Rokhsar, Daniel S.; Rounsley, Steve

doi:10.1007/s12042-011-9088-z

The Cassava Genome: Current Progress, Future Directions

Journal Article · Thu Jan 05 00:00:00 EST 2012 · Tropical Plant Biology

DOI:https://doi.org/10.1007/s12042-011-9088-z· OSTI ID:1816627

Prochnik, Simon ^[1]; Marri, Pradeep Reddy ^[2]; Desany, Brian ^[3]; Rabinowicz, Pablo D. ^[4]; Kodira, Chinnappa ^[3]; Mohiuddin, Mohammed ^[3]; Rodriguez, Fausto ^[5]; Fauquet, Claude ^[6]; Tohme, Joseph ^[7]; Harkins, Timothy ^[8]; Rokhsar, Daniel S. ^[9]; Rounsley, Steve ^[10]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); OSTI
Univ. of Arizona, Tucson, AZ (United States). BIO5 Inst.
454 Life Sciences (Roche), Branford, CT (United States)
Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Inst. for Genome Sciences (IGS)
Johns Hopkins Univ., Baltimore, MD (United States)
Donald Danforth Plant Science Center, St. Louis, MO (United States). ILTAB
CIAT, Recta Cali-Palmira (Colombia)
Life Technologies Corp, Carlsbad, CA (United States)
Univ. of California, Berkeley, CA (United States). Dept. of Moelcular and Cell Biology
Dow Agrosciences, Indianapolis, IN (United States)

The starchy swollen roots of cassava provide an essential food source for nearly a billion people, as well as possibilities for bioenergy, yet improvements to nutritional content and resistance to threatening diseases are currently impeded. A 454-based whole genome shotgun sequence has been assembled, which covers 69% of the predicted genome size and 96% of protein-coding gene space, with genome finishing underway. The predicted 30,666 genes and 3,485 alternate splice forms are supported by 1.4 M expressed sequence tags (ESTs). Maps based on simple sequence repeat (SSR)-, and EST-derived single nucleotide polymorphisms (SNPs) already exist. Thanks to the genome sequence, a high-density linkage map is currently being developed from a cross between two diverse cassava cultivars: one susceptible to cassava brown streak disease; the other resistant. An efficient genotyping-by-sequencing (GBS) approach is being developed to catalog SNPs both within the mapping population and among diverse African farmer-preferred varieties of cassava. These resources will accelerate marker-assisted breeding programs, allowing improvements in disease-resistance and nutrition, and will help us understand the genetic basis for disease resistance.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1816627

Journal Information:: Tropical Plant Biology, Journal Name: Tropical Plant Biology Journal Issue: 1 Vol. 5; ISSN 1935-9756

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity Bredeson, Jessen V.; Lyons, Jessica B.; Prochnik, Simon E. Nature Biotechnology, Vol. 34, Issue 5 https://doi.org/10.1038/nbt.3535	journal	April 2016
Cassava genome from a wild ancestor to cultivated varieties Wang, Wenquan; Feng, Binxiao; Xiao, Jingfa Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6110	journal	October 2014
Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation Ramu, Punna; Esuma, Williams; Kawuki, Robert Nature Genetics, Vol. 49, Issue 6 https://doi.org/10.1038/ng.3845	journal	April 2017
Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta Kayondo, Siraj Ismail; Pino Del Carpio, Dunia; Lozano, Roberto Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-19696-1	journal	January 2018
Physiological and proteomic analysis on long-term drought resistance of cassava (Manihot esculenta Crantz) Shan, Zhongying; Luo, Xinglu; Wei, Maogui Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-35711-x	journal	December 2018
Nutritional quality of fritters produced from fresh cassava roots, high-quality cassava and soy flour blends, and consumer preferences Oladeji, Alamu Emmanuel; Pheneas, Ntawuruhunga; Prisca, Chileshe Cogent Food & Agriculture, Vol. 5, Issue 1 https://doi.org/10.1080/23311932.2019.1677129	journal	January 2019
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome Piližota, Ivana; Train, Clément-Marie; Altenhoff, Adrian Bioinformatics, Vol. 35, Issue 7 https://doi.org/10.1093/bioinformatics/bty772	journal	September 2018
GREENC: a Wiki-based database of plant lncRNAs Paytuví Gallart, Andreu; Hermoso Pulido, Antonio; Anzar Martínez de Lagrán, Irantzu Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1215	journal	November 2015
Cassava brown streak disease: a threat to food security in Africa Kanju, Edward; Legg, James P.; Patil, Basavaprabhu L. Journal of General Virology, Vol. 96, Issue 5 https://doi.org/10.1099/vir.0.000014	journal	May 2015
First assembly of the gene‐space of Lolium multiflorum and comparison to other Poaceae genomes Knorst, Verena; Yates, Steven; Byrne, Stephen Grassland Science, Vol. 65, Issue 2 https://doi.org/10.1111/grs.12225	journal	December 2018
Why mosaic? Gene expression profiling of African cassava mosaic viru s-infected cassava reveals the effect of chlorophyll degradation on symptom development: Gene expression profiling of virus-infected cassava leaves Liu, Jiao; Yang, Jun; Bi, Huiping Journal of Integrative Plant Biology, Vol. 56, Issue 2 https://doi.org/10.1111/jipb.12133	journal	January 2014
Production of very‐high‐amylose cassava by post‐transcriptional silencing of branching enzyme genes Zhou, Wenzhi; Zhao, Shanshan; He, Shutao Journal of Integrative Plant Biology, Vol. 62, Issue 6 https://doi.org/10.1111/jipb.12848	journal	September 2019
Rooting for cassava: insights into photosynthesis and associated physiology as a route to improve yield potential De Souza, Amanda P.; Massenburg, Lynnicia N.; Jaiswal, Deepak New Phytologist, Vol. 213, Issue 1 https://doi.org/10.1111/nph.14250	journal	October 2016
Gene expression atlas for the food security crop cassava Wilson, Mark C.; Mutka, Andrew M.; Hummel, Aaron W. New Phytologist, Vol. 213, Issue 4 https://doi.org/10.1111/nph.14443	journal	January 2017
Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes Lyu, Haomin; He, Ziwen; Wu, Chung-I New Phytologist, Vol. 217, Issue 1 https://doi.org/10.1111/nph.14784	journal	September 2017
Chromosome-scale pseudomolecules refined by optical, physical and genetic maps in flax You, Frank M.; Xiao, Jin; Li, Pingchuan The Plant Journal, Vol. 95, Issue 2 https://doi.org/10.1111/tpj.13944	journal	May 2018
Genomic Signatures of Specialized Metabolism in Plants Chae, L.; Kim, T.; Nilo-Poyanco, R. Science, Vol. 344, Issue 6183 https://doi.org/10.1126/science.1252076	journal	May 2014
Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration Saithong, Treenut; Rongsirikul, Oratai; Kalapanulak, Saowalak BMC Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1752-0509-7-75	journal	January 2013
The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies O’Rourke, Jamie A.; Fu, Fengli; Bucciarelli, Bruna BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1718-7	journal	July 2015
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts Vilperte, Vinicius; Lucaciu, Calin Rares; Halbwirth, Heidi BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6247-3	journal	November 2019
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars Kuon, Joel-E.; Qi, Weihong; Schläpfer, Pascal BMC Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12915-019-0697-6	journal	September 2019
Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots Lentz, Ezequiel Matias; Kuon, Joel-Elias; Alder, Adrian Plant Methods, Vol. 14, Issue 1 https://doi.org/10.1186/s13007-018-0340-5	journal	August 2018
Proteomic analysis of injured storage roots in cassava (Manihot esculenta Crantz) under postharvest physiological deterioration Qin, Yuling; Djabou, Astride Stéphanie Mouafi; An, Feifei PLOS ONE, Vol. 12, Issue 3 https://doi.org/10.1371/journal.pone.0174238	journal	March 2017
New opportunities and challenges to engineer disease resistance in cassava, a staple food of African small-holder farmers Bart, Rebecca S.; Taylor, Nigel J. PLOS Pathogens, Vol. 13, Issue 5 https://doi.org/10.1371/journal.ppat.1006287	journal	May 2017
Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis Pinard, Desre; Mizrachi, Eshchar; Hefer, Charles A. BioMed Central https://doi.org/10.14288/1.0221467	text	January 2015
Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis Pinard, Desre; Mizrachi, Eshchar; Hefer, Charles A. BioMed Central https://doi.org/10.14288/1.0223782	text	January 2015
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts Vilperte, Vinicius; Lucaciu, Calon Rares; Halbwirth, Heidi London : BioMed Central https://doi.org/10.15488/9330	other	January 2019
Genome-Wide Identification and Expression Analysis of the KUP Family under Abiotic Stress in Cassava (Manihot esculenta Crantz) Ou, Wenjun; Mao, Xiang; Huang, Chao Frontiers in Physiology, Vol. 9 https://doi.org/10.3389/fphys.2018.00017	journal	January 2018
Genomics-Assisted Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB) Friedmann, Michael; Asfaw, Asrat; Anglin, Noelle Agriculture, Vol. 8, Issue 7 https://doi.org/10.3390/agriculture8070089	journal	June 2018
Genome‐Wide Association and Prediction Reveals Genetic Architecture of Cassava Mosaic Disease Resistance and Prospects for Rapid Genetic Improvement Wolfe, Marnin D.; Rabbi, Ismail Y.; Egesi, Chiedozie The Plant Genome, Vol. 9, Issue 2 https://doi.org/10.3835/plantgenome2015.11.0118	journal	July 2016
Genome‐Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content Rabbi, Ismail Y.; Udoh, Lovina I.; Wolfe, Marnin The Plant Genome, Vol. 10, Issue 3 https://doi.org/10.3835/plantgenome2016.09.0094	journal	November 2017
Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response Anjanappa, Ravi B.; Mehta, Devang; Okoniewski, Michal J. ETH Zurich https://doi.org/10.3929/ethz-b-000219480	text	January 2017
First assembly of the gene‐space of Lolium multiflorum and comparison to other Poaceae genomes Verena, Knorst,; Steven, Yates,; Stephen, Byrne, ETH Zurich https://doi.org/10.3929/ethz-b-000309533	text	January 2019
Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response Anjanappa, Ravi B.; Mehta, Devang; Okoniewski, Michal J. Wiley-Blackwell Publishing, Inc. https://doi.org/10.5167/uzh-145948	text	January 2018

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454-sequencing
59 BASIC BIOLOGICAL SCIENCES
Cassava
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Genotyping by sequencing
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The Cassava Genome: Current Progress, Future Directions

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