Genome Sequence for Phaseolus - PURDUE UNIVERSITY

Recipient Organization
PURDUE UNIVERSITY
(N/A)
WEST LAFAYETTE,IN 47907

Performing Department
Agronomy

Non Technical Summary
We will sequence the genome of common bean (Phaseolus vulgaris) using traditional and new sequencing methodologies. The DNA sequence will help advance the genetics and breeding of this important food and feed source and will affect both US growers and consumers around the world. Having the DNA sequence will enable scientists to find genes underlying key traits and will expedite the use of those traits for breeding. The sequence will be completely public and freely available.

Animal Health Component

(N/A)

Research Effort Categories

Basic

100%

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1410	1080	50%
201	1411	1080	50%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1410 - Beans (dry); 1411 - Beans (fresh, fresh-processed);

Field Of Science
1080 - Genetics;

Keywords

Goals / Objectives
The goal of this project is to develop a sequence map of common bean using next generation sequencing technology coupled with limited Sanger sequencing of larger insert clones and additional BAC-end sequencing. This effort will be complemented by the development of a high-density map of common bean that will enable the genome sequence to be integrated with genetic maps. All of this builds on a previous USDA/NRI grant that supported the development of a BAC-based physical map for common bean derived from BAC end sequencing and clone fingerprinting. We plan to extend that sequence map and populate it with high-density common bean sequences generated by next generation sequencing to create a reference genome sequence for common bean. This resource will be validated for quality, genes and repeats annotated and delivered to the public.

Project Methods
DNA sequencing will be performed using both Sanger-based sequencing as well as Next Generation Sequencing. DNA assembly will be done at HudsonAlpha using internally developed software.

Progress 09/01/09 to 08/31/13

Outputs
Target Audience: The genome sequencing of Phaseolus vulgaris was done to provide tools to the common bean breeding community to more rapidly and efficiently develop and release improved cultivars. In addition to this, the data has been of use to those working on the evolution and domestication of common bean in the Central America to South American regions. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Two female PhD students were trained as part of this project. One is now in industry, the other in a postdoctoral position. How have the results been disseminated to communities of interest? Several publications listed in this report as well as dozens of conference presentations and data that that is available at phytozome.org. The major genome paper should be accepted for publication soon. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? A genome sequence was produced of very high quality and is available at phytozome.org and has been integrated into other crop and comparative databases such as soybase.org.

Publications

Type: Journal Articles Status: Under Review Year Published: 2013 Citation: Schmutz, J., P. McClean, S. Mamidi, G.A. Wu, S.B. Cannon, J. Grimwood, J. Jenkins, S. Shu. Q. Song, C. Chavarro, V.Geffroy, S. Moghaddam, D. Gao, B. Abernathy, K. Barry, M. Blair, M. Brick, M. Chovatia, P. Gepts, D.M. Goodstein, M. Gonzales, U. Hellsten, D.L. Hyten, G. Jia, J.D. Kelly, D. Kudrna, R. Lee, M.M.S. Richard, P. Miklas, J. Osorno, J. Rodriguez, V. Thareau, C.A. Urrea, M. Wang, Y. Yu, M. Zhang, R.A. Wing, P.B. Cregan, D.S. Rokhsar and S.A. Jackson. 2013. A reference genome and domestication of common bean. Nature Genet. in review.
Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Gao, D., B. Abernathy, D. Rohksar, J. Schmutz and S.A. Jackson. 2013. Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris). Frontiers in Plant Genet and Genomics in press.
Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: ORourke, J.A., L.P. Iniguez, F. Fu, B. Bucciarelli, S.S. Miller, S.A. Jackson, P.E. McClean, P.X. Zhao, G. Hernandez and C.P. Vance. 2013. An RNA-seq analysis of the common bean transcriptome. Plant Physiol. in press.
Type: Journal Articles Status: Published Year Published: 2013 Citation: Iwata, A., A. Tek; M. Richard, B. Abernathy, A. Fons�ca, J. Schmutz, N. Chen, V. Thareau, G. Magdelenat, Y. Li, M. Murata, A. Pedrosa-Harand, V. Geffroy, K. Nagaki, S.A. Jackson. 2013. Identification and characterization of functional centromeres of common bean. Plant J. DOI: 10.1111/tpj.12269.
Type: Journal Articles Status: Published Year Published: 2013 Citation: ORourke, J.A., L.P. Iniguez, B. Bucciarelli, J. Roessler, J. Schmutz, P.E. McClean, S.A. Jackson, G. Hernandez, M.A. Graham, R.M Stupar and C.P. Vance. 2013. A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar. Front Plant Science 4:210.
Type: Journal Articles Status: Published Year Published: 2013 Citation: Iwata, A., C. Greenland and S.A. Jackson. 2013. Cytogenetics of legumes. The Plant Genome. doi: 10.3835/plantgenome2013.03.004
Type: Journal Articles Status: Published Year Published: 2013 Citation: Manon, R., N.W. G. Chen, V. Thareau, S. Pflieger, S. Blanchet, A. Pedrosa-Harand, A. Iwata, C. Chavarro, S.A. Jackson, V. Geffroy. 2013. The subtelomeric khipu satellite repeat from Phaseolus vulgaris: lessons learned from the genome analysis of the Andean genotype G19833. Front. Plant Sci. 4:109. doi: 10.3389/fpls.2013.00109

Progress 09/01/11 to 08/31/12

Outputs
OUTPUTS: An updated genome sequence has been released at Phytozome.org. This release includes more than 7,000 SNP markers that were developed as part of this project and in collaboration with a separately funded Coordinated AGriculture Project. These SNPs were used to collapse the sequence contigs and scaffolds into 11 pseudomolecules that are represented at phytozome.org. This resource is publicly available and we are working on the primary publication. PARTICIPANTS: Phil McClean, North Dakota State University Perry Cregan, USdA-ARS Jeremy Schmutz, HudsonAlpha, Arkansas Dan Rohksar, DOE-JGI TARGET AUDIENCES: Molecular biologists sequencing phaseolus PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Eleven pseudomolecules that capture more than 95% of the sequence were assembled and annotated and made available to the public at Phytozome.org. This resource is being used widely to develop additional markers, clone genes, analyze gene families and understand evolution within the legume family.

Publications

Varshney, R.K., C. Song, R. Saxena, S. Azam, S. Yu, A.G. Sharpe, S. Cannon, J. Baek, B Taran, T. Millan, X. Zhang, B. Rosen, L.D. Ramsay, A. Iwata, Y. Wang, W. Nelson, A.D. Farmer, P. M. Gaur, C. Solderlund, R.V. Penmetsa, C. Xu, A. Bharti, W. He, P. Winters, S. Zhao, J.K. Hane, N. Carrasquilla-Garcia, J.A. Condie, H. Upadhyaya, M. Luo, N.P. Sing, J. Lichtenzveig, K.K. Gali, J. Rubio, N. Nadarajan, M. Thudi, J. Dolezel, K. Bansal, X. Xu, D. Edwards, G. Zhang, G. Kahl, J. Gil, K.B. Singh, S.K. Datta, S.A. Jackson, J. Wang and D. Cook. 2012. Draft Genome sequence of Kabuli chickpea (Cicer arietinum): genetic structure and breeding constraints for crop improvement. Nature Biotech. Submitted.
Melmaiee, K., A. Todd, P. McClean, R. Lee, J. Schlueter, S.A. Jackson, and V. Kalavacharla. 2012. Identification of Molecular Markers Associated with the Deleted Region in Common Bean (Phaseolus vulgaris) ur-3 Mutants. Australian J. of Crop Sci. in press.
Varshney, R.K., W. Chen, Y. Li, A.K. Bharti, RK Saxena, JA Schlueter, MT.A. Donoghue, S. Azam, G. Fan, A.M. Whaley, A. Farmer, R. Tuetja, R.V. Penmetsa, W. Wu, H. Upadhyaya, S-P. Yang, T. Shah, K.B. Saxena, E. Ward, T. Michael, W. R. McCombie, B. Yang, J.D.G. Jones, C. Spillane, D.R. Cook, G.D. May, X. Xu, S.A. Jackson. 2011. Genome sequence for pigeonpea. Nature Biotech. doi:10.1038/nbt.2022

Progress 09/01/10 to 08/31/11

Outputs
OUTPUTS: Sequencing and initial assembly is done. We are working with the CoPIs to get genetic mapping information in order to order the sequence scaffolds and create pseudo molecules. Annotation of the scaffolds is ongoing at the Joint Genome Institute and they have agreed to resequence a number of landraces in order to provide additional value for publication and to the community. Although we have not yet made an 'official' release, we have provided the sequence assemblies to those requesting it. A finalized assemble should be made public in the last few months of 2011. This will be done via phytozome.org and the Legume Information System. PARTICIPANTS: Jeremy Schmutz, Hudson Alpha Jane Grimwood, Hudson Alpha Scott Jackson, PUrdue University (now University of Georgia) Mirayada Torres-Torres, Purdue University Perry Cregan, USDA-ARS Phil McClean, North Dakota State Univ. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We have produced a genome sequence for Phaseolus vulgaris that is still be ordered and oriented. We have provided this data to anyone requesting it and will make a public release late 2011. More than 3000 genetic markers have been developed and another 3000 will be done in the next 30-60 days to help with the anchoring of the sequence scaffolds to the chromosomes of Phaseolus. The team is coordinating with an international group for analysis and eventual publication.

Publications

Jackson, S.A. A. Iwata, S-H Lee, J. Schmutz and R.C. Shoemaker. 2011. Sequencing Crop Genomes: Approaches and Applications. New Phyt. 191:915-925.
Varshney, R.K., W. Chen, Y. Li, A.K. Bharti, RK Saxena, JA Schlueter, MT.A. Donoghue, S. Azam, G. Fan, A.M. Whaley, A. Farmer, R. Tuetja, R.V. Penmetsa, W. Wu, H. Upadhyaya, S-P. Yang, T. Shah, K.B. Saxena, E. Ward, T. Michael, W. R. McCombie, B. Yang, J.D.G. Jones, C. Spillane, D.R. Cook, G.D. May, X. Xu, S.A. Jackson. 2011. Genome sequence for pigeonpea. Nature Biotech. In revision.

Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: According to our original timeline, the Fosmid end sequencing and BAC end sequencing and 454 sequencing should be done by the end of year one. However, when funded some of these activities (BES and FES) were split over years 1 and 2. All of these activities are proceeding as scheduled and, in fact, additional BESs are being done from a newly created BAC library to give us more large spanning clones for building better sequence scaffolds. Additional fosmid libraries are currently under construction at AGI and will be shipped to HudsonAlpha in the next months. The 454 data being done at JGI Walnut Creek will be completed by October, 2010 and has been doubled from 15 runs to 30-40 runs split between pairs and linear. For year two, all activities are on schedule. The SNP mapping being done by CoPIs Cregan and McClean are on schedule and it is likely that more SNPs will be mapped than originally projected. Our plan is to have a sequence assembly by the end of 2010 that would be made public. Additional refining and anchoring would continue into 2011 to provide chromosome-anchored sequence scaffolds. Below is the original timeline in the proposal and the revised timeline that reflects changes on funding and current progress. Original Timeline Activity 0-3 3-6 6-9 9-12 12-15 15-18 18-21 21-24 Fosmids x x x BESs X X 454 X X SNP mapping x x x x Assembly X X X X X Map integration X X X X annotation X X PARTICIPANTS: Scott jackson, Purdue University Jeremy Schmutz, HudsonAlpha Perry Cregan, USDA-ARS Phil McClean, North Dakota State Univ. Dan Rokhsar, DOE-JGI TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
SNPs have been called on a panel of diverse Phaseolus lines (CoPI Cregan) Fosmid ends have been sequenced and an additional BAC library has been made and additional BAC end sequences are being produce. An initial assembly based on 8x 454 sequence has been produced and is being used internally to asses the next phase of sequencing.

Publications

No publications reported this period