Clifford F Weil Clifford F Weil

Professor of Agronomy

Department: Agronomy
Phone: 765.496.1917
Fax: 765.496.2926
Office: Lilly 2-349
Area of Expertise: Maize Genetics, Genomics, Value-Added Traits​

Curriculum Vitae​


Dr. Cliff Weil earned his bachelor’s degree in Genetics from UC Davis in 1978. He earned his doctoral degree in Genetics and Development from Cornell University in 1984. Cliff serves on the faculty at Purdue University. He teaches an undergraduate Introductory Genetics course, and graduate courses in Advanced Plant Genetics and in Genomics. He is also a member of the Whistler Center for Carbohydrate Research, a group including food chemists, engineers, and biophysicists working with food and ingredient companies around the world to bring advances in carbohydrate research to bear on food and industrial problems, improvements and development.

Dr. Weil's lab works on using genetics and genomics for cereal crop improvement, largely in maize and sorghum.  He and his lab team are primarily interested in understanding how to improve the digestibility of the starch and protein in the grain for food and feed uses.  They are also looking at the basic genetic controls that determine how, when and where sugars move throughout the plant, a central question for both development and yield.  As part of these projects they have been involved in developing some of the world’s largest-scale genetic mutant resources in both maize and sorghum for deployment to these communities worldwide.  These have allowed them, and others, to begin looking at a wide range of biological questions (nutritional quality, morphology, metabolism, development, signaling, just to name a few) using a combination of forward and reverse genetic approaches. Developing extensive catalogues of all the mutations in all the genes of these lines is providing a platform both for understanding gene function and for understanding the genetic diversity available to breeders for these genes in diverse materials around the world.

Current Research Interests

Transposons 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 recombination
Meiotic 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 biofuels 
We 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.


Purdue Division of Genetics
Purdue Plant Biology Program, PULSe Chromatin and Gene Expression Training Group, PULSe Plant Biology Training Group

Recent Publications

Weil, C. F. and R. Kunze (2000). Transposition of maize Ac/Ds transposable elements in the yeast Saccharomyces cerevisiae. Nature Genet. 26: 187-190 

Giedt, C.D. and C.F. Weil (2000) Developmental control of Ac/Ds transposition by the LAG1-O mutation in maize. Plant J. 24:815

Kunze, R and C.F. Weil.  (2002) The hAT and CACTA superfamilies of plant transposons. In Mobile DNA II, N. Craig, R. Craigie, M. Gellert and A. Lambowitz eds., ASM Press, Washington, DC, pp.565-610

Yu, J.-H., K. Marshall, M. Yamaguchi, J.E. Haber and C.F. Weil. (2004) Microhomology-dependent end-joining and repairof transposon-induced DNA hairpins by host factors in yeast. Molec. Cell. Biol. 24:1351

Weil, C. F., R. Monde, B. Till, L. Comai and S. Henikoff (2005) Mutagenesis and functional genomics in maize. Maydica 50:415-424

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

Groth, D., R. Helms, B. Hamaker, L. Mauer and C. Weil.  A high-throughput assay reveals mutants that alter digestion rates of corn starch, (submitted to Starch)

Waterworth, W., Ç. Altun. K. Young, S. Armstrong, C. Weil, C. Bray, C. West (2006) A plant homolog for Nbs1, the signaling component of the Mre11 DNA repair/recombination complex, (submitted to PNAS)

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

Johal, G., P. Balint-Kurti and C. Weil (2008) Mining and harnessing natural variation - current approaches and a little MAGIC. Crop Sci. 48:2066-2073   


Undergraduate Introductory Genetics (AGRY 320)
Graduate Advanced Plant Genetics (AGRY 630)
Graduate Genomics (AGRY 600/BIOL 595W)

Positions Held

Associate Professor, Dept. of Agronomy, Purdue University, 2001-present
Associate Professor, Dept. of Biological Sciences, University of Idaho, 1998-2001
Assistant Professor, Dept. of Biological Sciences, University of Idaho, 1992-1998
Postdoctoral Research Associate, University of Georgia, 1988-1992
Postdoctoral Research Associate, Ohio State University, 1984-1988

Awards and Honors

NIH Predoctoral Training Grant, 1982-1984
University of Idaho Alumni Award for Teaching Excellence, 1998 (student nominated)
Seeds of Success Research Award, Purdue University, 2003, 2006
Elected Fellow, American Association for the Advancement of Science, 2006
Editorial Board, Plant Genomes and Systems Biology, 2006-2008
Editorial Board, BioEnergy Research, 2007-present
Scientific Advisory Board, NSF Plant Genome: Maize Inflorescence Project, 2008


B.S., University of California-Davis, 1978
Ph.D., Cornell University, 1984

Date joined staff:  2001