Projects

Current Grants

GEPR: The genetic basis of transgressive variation in rice

Using wild ancestors to make rice more resilient to increasingly unpredictable water availability

  • Funding: BBSRC - SCPRID
  • Principal Investigators: Ian Graham (Univ. York, UK); CoPI’s- S. McCouch, and 8 others
  • Location of Project: University of York (UK), Cornell University (USA), Cuttack Central Rice Research Institute (India)
  • Grant Term: 06/01/2012 - 05/31/2016

Enhancing utilization of crop wild relatives: Capturing genetic value from ancestral populations of wild rice

  • Funding: Global Crop Diversity Trust
  • Principal Investigators: Susan McCouch (Cornell); CoPI’s- K. McNally, R. Hamilton (IRRI)
  • Location of Project: Cornell University (USA), IRRI (Philippines)
  • Grant Term: 12/31/2011 - 05/31/2015

Dissecting the Genetic, Molecular and Physiological Basis of Aluminum Tolerance in Rice: Implications for Cereal Improvement

  • The generation of cultivars adapted to acid soils, where Al toxicity is a major limitation, is a key aspect in sustainable crop production. Rice is the most Al tolerant cereal crop, providing a good model to identify Al tolerance genes and mechanisms. Our goal is to enable the development of crops with superior performance on acid soils, based on a comprehensive understanding of the physiological mechanisms underlying Al tolerance, the genetic variation in key Al tolerance loci and how this variation contributes to the phenotypic diversity in rice.
  • Funding: USDA – NIFA grant #2013-67013-21379
  • Principal Investigators:  Lyza Maron, Leon Kochian and Susan McCouch
  • Location of Project: : Cornell University and Robert W Holley Center for Agriculture and Health, USDA-ARS
  • Grant Term: 09/01/2013 – 08/31/2016

Rice Climate Resilience

  • We aim to use U.S. rice production as a model system to identify genomic signatures associated with rice climate resilience. We will model rice yield distributions conditional on weather, location, and genome-wide genetic information using farm and county level yields in the four major rice-growing states in the U.S.
  • Funding: USDA-AFRI 2013-0441:  Characterization of genomic signatures for rice crop resilience in response to climate change in the U.S.
  • Principal Investigators:  Susan McCouch, Joshua Woodard, Anna McClung, Lewis Ziska, David Lobell
  • Team Members: Diane R Wang, Lingxiao Hu
  • Collaborators: Steven Linscombe
  • Grant Term: 10/2013 - 10/2015

Other Collaborations

Enhancing Education and Research in Breeding for Plant Disease Resistance

  • "As we transition to sustainable agricultural systems that focus on local production and prepare for the consequences of global warming, a clear imperative emerges to invest in plant breeding for biotic stress resistance in the northeastern United States. The faculty in the Department of Plant Breeding and Genetics at Cornell University are in a unique position to leverage investments in genomics for crop improvement in this region. We propose to build on our existing programs to train future plant breeders that are able utilize genomic tools, navigate a wealth of data with bioinformatics and synthesize research perspectives from both vegetable and grain breeding as part of their modern skillset."
  • Funding: USDA-AFRI 0220914: Enhancing Education and Research in Breeding for Plant Disease Resistance
  • Principle Investigators: Michael Mazourek (lead), Mark Sorrells, Martha Mutschler, Walter De Jong, Lukas Mueller, Rebecca Nelson, Phillip Griffiths, Susan McCouch, Mary Kreitinger
  • Grant Term: 3/1/2010 - 2/28/2014

Previous Grant Support

Development of a high resolution SNP chip (600K) and genotyping of 850 diverse rice (Oryza sp.) accessions

  • This project aims to generate one of the largest and most useful databases of diversity information for any crop in the world. By providing a large repository of information about the precise location of 1M single nucleotide polymorphisms (SNPs) in rice, as well as the occurrence of SNP alleles in 850 diverse rice samples, and an additional 1440 rice samples from IRRI, it will enable breeders to readily select sub-sets of informative SNPs for use on smaller, in-house platforms for immediate applications in marker-assisted or genomic selection and help drive basic research aimed at unraveling phenotype-genotype associations in rice.
  • Project website: Ricesnp.org
  • Funding: USDA-AFRI 2009-65300-05698: Development of a high resolution SNP chip (600K) for genotyping of 850 diverse rice (Oryza sp.) accessions, and additional funding from IRRI under the GRiSP program
  • Principle Investigators: Susan McCouch
  • Team Members: Chih-Wei Tung, Mark (Koni) Wright
  • Location of Project: Cornell University
  • Grant Term: 1/1/2009 - 2/28/2013

Genotyping of 1440 Rice Samples using the 1M SNP Array Developed at Cornell University as Part of the Rice SNP Consortium.

  • Current funding: IRRI (International Rice Research Institute)
  • Principle Investigator: Susan McCouch
  • Location of Project: Cornell University
  • Grant Term: 10/10/2010 - 12/31/2012

GEPR: Exploring the genetic basis of transgressive variation in rice

  • The Rice Diversity project is a collaborative effort to explore the genetic basis of variation in rice. The project evaluates genotypes and phenotypes in a diverse set of 400 rice accessions and uses association mapping to link genotype and phenotype. Our genotyping platforms are based on 44,000 SNP markers, from which a 44K Affymetrix SNP chip has been constructed. Our phenotyping efforts use controlled vocabularies to systematically describe a broad array of plant characteristics.
  • Funding: NSF Grant 0606461: Exploring the genetic basis of transgressive variation in rice. NSF Grant page
  • Principle Investigators: Susan McCouch (lead), Carlos Bustamante, Georgia Eizenga, Anna McClung
  • Team Members: Liakat Ali, Joshua Cobb, Lauri Dahl, Stefan Einarson, Adam Famoso, Francine Jasper, Janelle Jung, D.H. Goodall, Teresa Hancock, Sandy Harrington, Hyunjung Kim, Heather Maupin, Gen (Fumio) Onishi, Badri Padhukasahasram (former), Jenny Kimball-Pevo (former), Lisa Polewczak (former), Andy Reynolds, Ellie Rice, Chih-Wei Tung, Wricha Tyagi (former), Diane Ran Wang, Daniel Wood, Koni Wright, Keyan Zhao
  • Collaborators: Jonathan Lynch, Ken McNally, Abdel Ismail, Michael Thomson, Melissa Fitzgerald, Adam Price, M. Rafiqul Islam
  • Location of Project: Cornell University, University of Arkansas, IRRI
  • Grant Term: 08/01/2006 - 07/31/2012
  • Project short-name: "NSF-TV"

TRPGR Gramene: A platform for comparative plant genomics

  • Project website: Gramene.org
  • Funding source: NSF subaward (CSHL- Lincoln Stein, PI) 
  • Principle Investigators: Susan McCouch; CoPI's-Pankaj Jaiswal, Ed Buckler
  • Location of Project: Cornell University, Cold Spring Harbor Laboratory
  • Grant Term: 10/01/2007 - 9/30/2012

Design and implementation of a “collaborator’s database”: protocols to facilitate sample tracking and data management as part of the International Rice Diversity Research Platform

  • Current funding: US-AID Linkage Grant (from IRRI)
  • Principle Investigators: Susan McCouch
  • Location of Project: Cornell University
  • Grant Term: 9/01/2011 - 8/31/2012

Investigations into the Genetics and Physiological Mechanisms of Aluminum Tolerance in Rice (USDA-AFRI)

  • Funding: USDA-CSREES-AFRI 002010
  • Principle Investigators: Leon Kochian (lead), CoPI: Susan McCouch
  • Location of Project: Cornell University
  • Grant Term: 09/01/2009 - 08/31/2012

Resequencing for SNP discovery across multiple indica and aus rice genomes

  • Funding: USAID Linkage Program (managed by IRRI, Philippines)
  • Principle Investigator: Susan McCouch
  • Location of Project: Cornell University
  • Grant Term:09/01/2009 - 08/31/2010

Advancing crop improvement through integration of new technologies

  • Funding: CSREES-USDA
  • Principle Investigators: Earle, Elizabeth CoPI's: Brutnell, Thomas; Buckler, Edward; Bustamante, Carlos; McCouch, Susan; Sorrells, Mark; Tanksley, Steven.
  • Location of Project: Cornell University
  • Grant Term: 11/15/2006 - 11/14/2011