|Gramene Newsletter||Gramene News Archive||Past and Upcoming Outreach|
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The Panzea project (NSF DBI 0321467) is a five-year NSF project headed by John Doebley, and involves eight additional investigators at seven institutions (University of Wisconsin, Cornell University, North Carolina State University, University of Missouri, University of California-Irvine, Cold Spring Harbor Laboratory and USDA-ARS). Our overall objectives are to address two major questions: 'How has selection shaped molecular diversity?' and 'How does this molecular diversity relate to functional trait variation?' We have completed our objectives relating to our first major question, and you can read more about the results to date from this project (and from its five-year forerunner) at http://www.panzea.org/lit/publication.html.
Now we are devoting our focus to the characterization of functional diversity in both teosinte and maize. We are engaged in QTL and association mapping experiments both in modern maize and in crosses between teosinte and maize. We are currently working with two teosinte association mapping populations, three teosinte-maize backcross QTL mapping populations, a maize association mapping population and a maize 'Nested Association Mapping' (NAM) population.
The maize NAM population is the centerpiece of our project - we expect this population to be the most significant to the maize research community. Nested Association Mapping is a powerful new method for localizing QTL which uses a multifamily RIL mapping population derived from crosses to a common parent (i.e., B73) in order to perform a joint QTL and association analysis. By employing a genomic scan of common parent-specific SNPs in the progeny RILs combined with high density genotyping (or sequencing) of the parental lines, the NAM strategy captures the best of both worlds: the statistical power of QTL analysis is combined with the high chromosomal resolution of association analysis.
We are pioneering the NAM approach in maize. Our NAM population consists of >5000 RILs from 25 families, with 200 RILs per family, all being genotyped at 1500 SNP loci. It forms a permanent QTL mapping resource for the benefit of the maize and grass communities. The families were generated by crossing 25 diverse maize inbred lines with B73 as the common parent, and the well-known IBM mapping population is included as the 26th family. Finally, a collection of 280 diverse maize inbreds from around the world has been included to serve as an association mapping platform for maize. We have recently demonstrated the power of our NAM population for detecting higher order epistatic interactions among QTL, using simulated data based upon actual SNP genotypes from our 25 NAM parents (Stich et al., Genetics 176:563-70, 2007).
Measuring Traits @ Aurora Field near Ithaca, NY. Back row (L-R): Zhiwu Zhang, Sara Larsson, Mike Gore, Nick Lepak, Dallas Kroon, Peter Bradbury. Front row (L-R): Jason Peiffer, Elhan Ersoz, Ed Buckler
|This summer we planted out all of these RILs in three locations (Raleigh, NC; Aurora, NY; Champaign-Urbana, IL). The parental lines are being sequenced over the next year and a half – making it possible to analyze all populations as one unified experiment, potentially with gene-level QTL resolution.
We are scoring a several obvious agronomic and developmental traits in these populations, but are unable to score some of the more complex traits. We are hoping that maize and grass researchers working on complex, specialty traits will score their own phenotypes of interest in one or more of our NAM 'Fields of Dreams'. We also have extensive experience in creating barcoding tools for phenotyping, and can provide help with this. For further details or to arrange your phenotyping visit(s), please contact Ed Buckler, Jim Holland or Torbert Rocheford. Our only stipulation is that your data set must be deposited in our project database, Aztec, where it will be held privately for two years (members of the Panzea group will not be allowed to analyze it either, without prior permission from you), and then released to the public via www.panzea.org.
If you are unable to make it to one of our fields this summer, do not fret! Plans are afoot to have public grow-outs of the NAM population for as many as four more years, but at this point funding support is guaranteed only through the summer of 2008. For educators focusing primarily on undergraduate teaching, the NAM resource provides an ideal opportunity for research involving undergraduate or Masters students, potentially funded via the NSF's 'Research Opportunity Awards'. Resources from these awards could potentially be pooled with those from other sources to fund one or more future 'public' grow-outs of the NAM population. In addition, for researchers interested in growing out all or part of the NAM population themselves, seed from the entire, fully-genotyped NAM population will be available from the Maize Stock Center in 2008.
Meet the amazing team of researchers who set a high standard of excellence for future geneticists, here pictured in front of their field house in 1929, the building that still stands next to the Pounder Heritage Garden in the Cornell Plantations.
Charles Burnham (1903-1989)
Burnham was a maize cytogeneticist and breeder. He came to Cornell as a postdoctoral fellow to work with Emerson and McClintock. Later, he spent 34 years as a faculty member at University of Minnesota and authored 255 scientific papers.
Marcus Rhoades (1903-1991)
Rhoades made important contributions to the fields of maize genetics and cytogenetics. He unselfishly shared unpublished information, exchanged seed stocks, and revealed new techniques in order to advance the knowledge of maize genetics. Dr. Rhoades was also interested in non-Mendelian genetics, and made several breakthroughs in this subject. George Beadle (1903-1989)
Beadle worked with R.A. Emerson and L.W. Sharp as a graduate student. He studied Mendelian asynapsis in maize, and received his Ph.D. for this work. The Sixth International Genetics Congress was held in August of 1932 in Ithaca, NY. Here, over 800 people attended, 101 members of which were from other countries of the world, including some of the most famous geneticists of the time. At the congress, scientific abstracts were presented, social activities organized, and a variety of exhibits presented. [Reference: J. Heredity 23:355-360 (1932)]
George Beadle (1903-1989)
Beadle worked with R.A. Emerson and L.W. Sharp as a graduate student. He studied Mendelian asynapsis in maize, and received his Ph.D. for this work.
The Sixth International Genetics Congress was held in August of 1932 in Ithaca, NY. Here, over 800 people attended, 101 members of which were from other countries of the world, including some of the most famous geneticists of the time. At the congress, scientific abstracts were presented, social activities organized, and a variety of exhibits presented. [Reference: J. Heredity 23:355-360 (1932)]
Outside the plant breeding shed near Cornell's Ag Quad in 1929 are (standing, from left) researchers Chares R. Burnham and Marcus Rhoades, Professor Rollins A. Emerson, and Barbara McClintock, later a Nobel laureate. Kneeling is George W. Beadle, also to be a Nobel laureate, with Emerson's dog Pudgie.
Barbara McClintock (1902-1992)
McClintock was a leader in the field of maize cytogenetics with her studies on the changes of maize chromosomes during reproduction. This made it possible for her to develop techniques to visualize the chromosomes and demonstrated fundamental genetic ideas such as recombination by chromosomes crossingover during meiosis.
Rollins Adams Emerson (1873-1947)
Emerson published many papers on maize including the following topics: sex expression, plant color inheritance, quantitative inheritance and mutations. Founded the Maize Genetics Cooperation, an organization which sponsored a newsletter and a mutant stock center.
75 years of Mapping the Maize Genome - Emerson's map of Chromosome 1 (on left), showing the approximate locations of 11 genes, compared to a modern-day map.
Map image contributed by Immanuel Yap, Gramene
Polyploids, genome halving and phylogeny. Sankoff D, Zheng C, Zhu Q. Bioinformatics. 2007 Jul 1;23(13):i433-i439.
Are source and sink strengths genetically linked in maize plants subjected to water deficit? A QTL study of the responses of leaf growth and of Anthesis-Silking Interval to water deficit. Welcker C, Boussuge B, Bencivenni C, Ribaut JM, Tardieu F.. Journal of experimental botany, 2007, vol. 58, pp. 339-349.
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY. Plant Physiol. 2007 Feb;143(2):587-99. Epub 2006 Dec 1.
Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. Gomez-Porras JL, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B. BMC Genomics. 2007 Aug 1;8(1):260.
Molecular and pathotypic characterization of new Xanthomonas oryzae strains from West Africa. Gonzalez C, Szurek B, Manceau C, Mathieu T, Séré Y, Verdier V. Mol Plant Microbe Interact. 2007 May;20(5):534-46.
Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Mariac C, Luong V, Kapran I, Mamadou A, Sagnard F, Deu M, Chantereau J, Gerard B, Ndjeunga J, Bezançon G, Pham JL, Vigouroux Y. Theor Appl Genet. 2006 Dec;114(1):49-58. Epub 2006 Oct 18.
Lincoln Stein, PI
Susan McCouch, Co-PI
Doreen Ware, Co-PI
Pankaj Jaiswal, Co-PI, Curator
Ed Buckler, Co-PI
Chengzhi Liang, Coordinator
Junjian Ni, Curator
Immanuel Yap, Curator
Anu Pujar, Curator
Dean Ravenscroft, Curator
Chih-Wei Tung, Curator
Ken Youens-Clark, Developer
Shulamit Avraham, Developer
Liya Ren, Developer
William Spooner, Developer
Payan Canaran, Developer
Sharon Wei, Developer
Terry Casstevens, Developer
Jim Thomason, Developer
Claire Hebbard, Outreach