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The National Academies
500 5th St NW - KWS 502
Washington, DC 20001
Tel: (202) 334-2800
Fax: (202) 334-2139
Phase 3 (2007 Deadline)
Integrated Genetic/Physical Mapping of Gossypium
Andrew Paterson, University of Georgia, Athens
Mehboob-ur-Rahman, National Institute for Biotechnology and Genetic Engineering, Faisalabad
Pakistani Funding (MoST): $140,000 (not yet paid)
US Funding (State): $160,000
Project Dates on US Side: July 1, 2008 - June 30, 2012
This project is focused on the creation of an integrated genetic/physical map of the Gossypium D genome (cotton species of New World origin). The US lab has produced a high-quality bacterial artificial chromosome (BAC) library for the D genome and has begun both fingerprinting the library and anchoring to a leading cotton reference genetic map also made in the US lab. Major activities on the project include targeted bridging of gaps in the current contig map of the D genome and targeted anchoring of rogue unanchored contigs by genetic mapping of BAC-end derived simple sequence repeats (in Pakistan) using DNA from the reference map provided by the US lab. Pakistani scientists have received interdisciplinary training in genetic, molecular, and computational methodologies at the University of Georgia, although progress has been significantly hindered by the lack of funding from MoST.
- Enriched the integration of genetic and physical maps for cotton (Gossypium) that are being used in guiding assembly of the genome sequence by an international consortium led by the US principal investigator and including the Pakistani principal investigator
- Hosted visits of 6-9 months by the Pakistani principal investigator and two of his graduate students (a third is pending) at the University of Georgia, after which one of the students, Ms. Nabila Tabassam, independently established a plant genomics lab at the National Institute for Genomics and Advanced Biotechnology in Islamabad
- Augmented the sets of DNA markers in use at NIBGE, which is adopting tools and resources gained from the project in its germplasm characterization and genetic improvement programs
- Catalyzed scientific collaborations with additional Pakistani and US scientists, one of whom was awarded a grant under Phase 4 of the Pakistan-US S&T Cooperation Program to study cotton begomoviruses
The partners remain in regular contact and continue to focus on mapping additional DNA markers to the G. raimondii map and further refining the physical map. Four manuscripts on the results have been published and a fifth (a joint review of cotton genetic resources) is in press in the journal Agronomy for Sustainable Development. Dr. Shahid Mansoor, a researcher from NIBGE, was awarded a Fulbright grant and arrived in Dr. Paterson's lab in late September 2011 for a one-year stay. Meanwhile, Dr. Paterson continues to serve as informal advisor via e-mail to Pakistani graduate students at NIBGE. Prospects for continuation of linkages between NIBGE and the University of Georgia are excellent, given the recent funding of the Phase 4 project involving Dr. Mansoor and another Georgia researcher, Dr. Peng Chee. As of April 2012, the project is essentially complete on the U.S. side; however, the funds remain pending on the Pakistani side.
Progress Report Summaries
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2012 Download final report
2011 Show summary || Hide summary|| Download full report
A visiting scientist from the Pakistani lab, M. Kashif Shahzad Sarwar, completed a survey of additional SSR markers and mapped a subset of the markers on the D-genome reference population. He finished his six-month visit in June 2011 and returned to Pakistan, where he continues to work on analyzing the data collected during his stay at the University of Georgia. Meanwhile, Dr. Paterson has received word that Ms. Nabila Tabassam, who trained in his lab during the first year of the project, has now established an independent plant genetics lab at the National Institute for Genomics and Advanced Biotechnology in Islamabad. Another Pakistani scientist, Muhammed Atif Iqbal, arrived May, 2011 and has been an active participant in field and lab work related to cotton population development and genetic mapping, slated to return to Pakistan in October, 2011. Dr. Shahid Mansoor, a researcher from NIBGE, has been awarded a Fulbright grant and arrived in Dr. Paterson's lab in late September, 2011, for one year. The Pakistani side has not received funding from MoST in 2011. A no-cost extension requested by Dr. Paterson has been issued through June 30, 2012. Nevertheless, Dr. Paterson reports that the collaboration has been productive and has so far resulted in publication of an article in Nature, two co-authored book chapters, and submission of a preproposal to the National Science Foundation. Appreciable progress toward integrated genetic and physical mapping of Gossypium has been made during the year.
Although the Pakistani partner’s institute still has not received any funding from MoST in 2010, Drs. Paterson and Mehboob-ur-Rahman have made appreciable progress toward integrated genetic and physical mapping of Gossypium through the three major activities described above. The Pakistani graduate student has conducted mapping on the reference cross used in the U.S. lab. In addition, the mapping in the U.S. lab is also involving a visiting Pakistani scientist, M. Kashif Shahzad Sarwar, who arrived in December 2010 for a 6-month training. The principal researchers on both sides remain in regular e-mail contact. As of December 2010, Dr. Paterson has served as external evaluator for six Pakistani dissertations. Dr. Shahid Mansoor was awarded a Fulbright grant and plans to visit Dr. Paterson’s lab for one year, once he obtains a visa (currently pending). At the same time, Drs. Paterson and Rahman continue to seek funding opportunities for the project. In the coming year, they will focus on mapping additional DNA markers to the G. raimondii map.
2009 Show summary || Hide summary || Download full report
Dr. Paterson reported that the collaboration had been very productive and resulted in publication of an article in Nature, two co-authored book chapters, and submission of a preproposal to the National Science Foundation Partnerships in International Research and Education Program to expand their joint work. Although the Pakistani partner’s institute did not receive their grant, Drs. Paterson and Mehboob-ur-Rahman made appreciable progress toward integrated genetic and physical mapping of Gossypium through the following specific activities:
- Selected low-copy DNA probes were applied to a series of BAC libraries for A, D, AD, F genomes of Gossypium and the outgroup Gossypioides kirkii. The Pakistani participants were integrally involved in all aspects of this procedure—Ms. Tabassam was responsible for data interpretation and computational processing. These data will be incorporated into a publication (including the Pakistani participants as co-authors) describing the suite of BAC resources available for Gossypium genomics.
- From initial analysis of agarose-based contigs, 18,432 BACs that were terminal to the largest contigs (two BACs per end) were identified, rearrayed using the Genetix QBOT and fingerprinted using high-information-content fingerprinting methods. Analysis will begin soon. In addition, separate funds were available for end-sequencing a subset of the BACs, which has recently been completed, and analysis is in progress.
- Work continued on identifying simple sequence repeats (SSRs) that are diagnostic of large-insert clones. From the fosmid end-sequences provided by the Joint Genome Institute (JGI), the participants identified a modest sampling of SSRs and the Pakistani graduate student conducted mapping on the reference cross used in the US lab. This work expanded in 2009, using additional sources of SSRs that include BAC end-sequences and new sequences from the JGI.
2008 Show summary || Hide summary || Download full report
During much of the first year of the project, the Pakistani principal investigator Dr. Rahman and his graduate student N. Tabassam made a nine-month visit to Dr. Paterson’s lab in Georgia. Dr. Rahman had originally intended to stay until April 2009, but due to financial and political complications back home at his institute he returned to Pakistan in November 2008.
Publications Show || Hide
Paterson, Andrew H., John E. Bowers, Rémy Bruggmann, Inna Dubchak, Jane Grimwood, Heidrun Gundlach, Georg Haberer, Uffe Hellsten, Therese Mitros, Alexander Poliakov, Jeremy Schmutz, Manuel Spannagl, Haibao Tang, Xiyin Wang, Thomas Wicker, Arvind K. Bharti, Jarrod Chapman, F. Alex Feltus, Udo Gowik, Igor Grigoriev, Eric Lyons, Christopher A. Maher, Mihaela Martis, Apurva Narechania, Robert Otillar, Bryan W. Penning, Asaf Salamov, Yu Wang, Lifang Zhang, Nicholas C. Carpita, Michael Freeling, Alan R. Gingle, C. Thomas Hash, Beat Keller, Patricia Klein, Stephen Kresovich, Maureen C. McCann, Ray Ming, Daniel G. Peterson, Mehboob-ur-Rahman, Doreen Ware, Peter Westhoff, Klaus F.X. Mayer, Joachim Messing, Daniel S. Rokhsar. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556.
Rahman, M., Y. Zafar, and A. H. Paterson. 2009. Gossypium DNA markers: types, numbers, and uses. Chapter 5 in A. H. Paterson, Genetics and Genomics of Cotton. New York: Springer.
Rahman, M., and A. H. Paterson. In press, 2010. Comparative genomics. In S. M. Jain and D. S. Brar (eds.), Molecular Techniques for Crop Improvement, Second Edition. New York: Springer.
Lifeng Lin, Gary Pierce, John E. Bowers, James C. Estill, Rosana O. Compton, Lisa K Nelson, Changsoo Kim, Cornelia Lemke, Junkang Rong, Haibao Tang, Xiyin Wang, Michele Braidotti, Amy H. Chen, Kristi Collura, Ethan Epps, Wolfgang Golser, Corrinne Grover, Kristen L. Herrick, Jennifer Ingles, Santhosh Karunakaran, Dave Kudrna, Jaime Olive, Nabila Tabassam, Eareana Um, Marina Wissotski, Yeisoo Yu, Andrea Zuccolo, Mehboob-ur-Rahman, Daniel G. Peterson, Rod A. Wing, Jonathan F. Wendel, and Andrew H. Paterson. 2010. A Draft Physical Map of a D-genome Cotton Species (G. ramondii). BMC Genomics 11:395.
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