Clifford F. Weil

Clifford F. Weil Profile Picture

Associate Professor-Department of Agronomy
Ph.D., Cornell University, 1984

Contact Info:

Training Group(s):
Chromatin and Regulation of Gene Expression
Plant Biology

Active Mentor - currently hosting PULSe students for laboratory rotations and recruiting PULSe students into the laboratory; serves on preliminary exam committees

Current Research Interests:

Transposons and DNA repair in maize, Arabidopsis and yeast The Genetics of Genetics: genes controlling meiotic recombination in plants Identifying Genetic networks by Mutant-Assisted Gene Identification and Characterization (MAGIC) Mutational redesign of maize starch: better health and biofuels The Maize TILLING Project: reverse genetics for crop functional genomicsTransposons and DNA repair in maize, Arabidopsis and yeast. We are interested in better understanding how plants organize, maintain and express their genomes. Our work examines how plant cells repair DNA breaks, a question that also addresses how genes introduced into plants can be targeted to their homologous chromosomal sites and how chromosomes recombine during meiosis. Transgenes generally incorporate at essentially random sites (often in the wrong chromosomal context) through a process of non-homologous DNA end-joining (NHEJ). A homologous recombination mechanism also works at very low levels in plants (though at higher levels in other organisms). We want to know how cells choose one mechanism over the other and how that choice might be manipulated so that maize and other crops can be modified in a more controlled manner. Our approach has been to study how NHEJ repairs the damage created when Ac/Ds transposons move in maize and Arabidopsis. We have also developed a system in which Ac/Ds transposons are mobile in yeast and other fungi; the damage they cause in yeast is also repaired by NHEJ, and we use yeast NHEJ genes and mutants to better understand the process in plants. Two key observations drive this research. 1) comparisons among datasets and with those from other plant species show that maize genome rearrangement and DNA repair have features unlike any other eukaryote. Deletion and mutation of bases is less severe in maize than in other species, suggesting maize has evolved more effective DNA repair responses to the presence of the active transposons maintained in its genome by human selection. We are using this difference in a comparative genomics study of NHEJ repair in plants, using Arabidopsis, maize, the maize progenitor teosinte, rice, tomato, barley and other species. We are also examining the effects of DNA repair mutations in our yeast transposition assay system. 2) When an Ac/Ds element excises, the host DNA flanking the transposon forms a DNA hairpin structure, with the backbone of one strand of the double helix covalently bound to the backbone of the complementary strand. This structure is the same one formed when vertebrate immunoglobulin gene segments rearrange to make antibody-encoding genes. Plants do not have homologs of some of the genes essential to this process in vertebrates, yet they repair DNA hairpins very effectively. We want to know what these differences can teach us about how to treat particular forms of immune disease in animals. The Genetics of Genetics: genes controlling meiotic recombinationMeiotic recombination is another important aspect of DNA breaking and rejoining. In maize, most recombination events (“crossovers”) occur within or very near genes rather than in the repetitive retroelements that comprise 80% of the maize genome. In addition, meiotic crossovers are generally limited to one per chromosome arm through a poorly understood process called crossover interference. An interesting correlation is also that transposons such as Ac/Ds insert preferentially into the same regions where recombination events take place. As part of two collaborative efforts involving six other institutions, we have employed a forward genetic screen to identify over 100 mutants in maize that increase the frequency of recombination events, that decrease recombination, and that reduce crossover interference, a well as a reverse genetic screen to look at mutations in maize and Arabidopsis homologs of known recombination genes. We want to determine whether mutants identified in these screens are global or affect only specific regions of the genome, what effects these mutations have on the number and distribution of the protein machinery that carries out crossover events, (“recombination nodules”), and whether the distribution and frequency of transposon insertion is altered. Identifying Genetic Networks by Mutant-Assisted Gene Identification and Characterization (MAGIC)Geneticists have long noticed that a mutation crossed into different genetic backgrounds show a range of expression levels. These so-called “background effects” are often a complication in characterizing new mutations. However, the differences in expression also reflect interactions between the mutation in question and other genes in the genome, the very genetic networks that a lot of current work is trying to reveal. Collaborating with Guri Johal at Purdue and Peter Balint-Kurti of the USDA-ARS, we are characterizing these genetic networks by taking advantage of the fact that diverse maize inbred lines differ at, on average, ~1.5% of their sequence. The Panzea Project has identified 25 maize inbred lines that, among them, represent >80% of the genetic diversity known in maize. Furthermore, sets of 200 recombinant inbred lines (RILs) have been made for each of these lines crossed to the sequenced, reference B73 inbred line. The 5000 resulting lines, known as the Nested Association Mapping (NAM) panel, have been and continue to be genotyped extensively; these data are publicly available. The RILs partition the genomes of each diverse parent into well-characterized segments. Crossing known mutations in the B73 inbred to the 25 NAM founder lines, we examine progeny for enhanced or suppressed expression of the mutant phenotype. For any founder lines where we observe genetic modifiers of our starting mutation, we go back and cross the mutation to the 200 RILs derived from that parent, again screening progeny for the same enhanced or suppressed phenotype we observed with the diverse parent line of these RILs. The segments of the diverse parent that those RILs have in common then identify candidate regions for the modifiers. We call this approach Mutant-Assisted Gene Identification and Characterization (MAGIC) and have been able to demonstrate its utility using the dominant lesion mimic mutation Rp1D21, as well as recessive alleles of tie-dyed1 (tdy1), tdy2 and sucrose export defective1 (sxd1), which are unable to move sucrose out of the leaves effectively after photosynthesis (a collaboration with David Braun at Univ. of Missouri). Additional studies are looking at modifiers of kernel starch and protein as well as kernel development mutants.  Mutational redesign of maize starch: better health and biofuelsWe are using a combined genetic, biochemical and protein structural approach to look at how specific mutations in maize alter starch digestibility. Cornstarch that digests more slowly in its cooled form and therefore releases glucose into the bloodstream over a longer period than normal cornstarch can be valuable in combating obesity and diseases related to it, as well as Type II diabetes. Conversely, starch that digests rapidly without the need for cooking can improve the efficiency of producing biofuels such as ethanol and butanol. We have identified ~100 mutant lines that alter starch digestibility, including those that decrease digestibility and those that increase digestibility. We are initiating more detailed characterization of these mutations and, in collaboration with the Whistler Center for Carbohydrate Research (located at Purdue), characterizing what they do to starch fine structure, to the interaction of starch with other cellular components and to the ultrastructure and development of the starch granule. Additional biofuels projects include modifying maize kernel architecture and developing maize lines that accumulate sugars in the stalk. The Maize TILLING Project, one of the most powerful tools available for understanding gene function is to analyze the effects of mutating that gene. We operate the Maize TILLING Project, an NSF-supported resource, as a service to the international maize community. TILLING is a technology, originally developed for Arabidopsis, that allows us to screen through the DNAs of a large, EMS mutagenized population of maize and quickly identify any individuals in that population that have a mutation in a user’s gene of interest. We then sequence the mutations we find and return this information, the predicted effects of the mutations and, most importantly, seed carrying the mutations to the person who initiated the request. These mutants can then be analyzed further to better understand gene function. We are developing projects that apply this technique to other crops as well, including soybean, sorghum, marigold, switchgrass and ryegrass, and welcome inquiries into its application to other crops. 

Selected Publications:

Yang, G., C. F. Weil and S. R. Wessler (2006) A rice Tc1/mariner- like element transposes in yeast. Plant Cell 18:2469-2478

Waterworth, W., Ç. Altun. K. Young, S. Armstrong, C. Weil, C. Bray, C. West (2007) A plant homolog for Nbs1, the signaling component of the Mre11 DNA repair/recombination complex, Plant J 52:41-52.

Weil, C. F. and R. Monde (2007) Getting the point—mutations in maize. Crop Sci 47: S-60-67

Dooner, H. K. and C. F. Weil (2007) Give-and-take: Interactions between DNA transposons and their host plant genomes, Curr. Opin. Gen. Dev 17:486-492.

Kim, H.-S., S. Vijayakumar, M. Reger, J. Harrison, J. E. Haber, C. Weil, and J. H .J. Petrini (2008) Functional interactions between Sae2 and the Mre11 complex. Genetics (in press)

Groth, D., J. Santini, B. Hamaker, L. Mauer and C. Weil. (2008) A high-throughput assay reveals mutants that alter digestion rates of corn starch, (accepted pending revisions at Starch)

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