team make pilgrimages to vast corn-growing regions of the American Midwest and Mexico, looking for mutants that are the products of natural variation.

Learning from mutations is a time-honored procedure in research, and one with immense implications for genetics. “Going all the way back to Mendel, plant breeding has led the way in our efforts to understand the secrets of development and the underlying princi- ples of inheritance,” Jackson observes. Perhaps the most famous of CSHL’s plant breeders was Barbara McClintock, who grew corn next to Carnegie Library in the 1930s and ’40s en route to her Nobel-winning dis- covery of bits of DNA that propagated themselves, seemingly at random, across the — what she called “jumping ” and others later called transposons.

RESEARCH PROFILE Technology has dramatically changed what happens after interesting specimens are gathered from the field. “Until recently, we’ve been very focused on finding interesting genes, one by one,” says Jackson. For David Jackson example, a in corn called TILLERED1. In 2007, Jackson discovered that it encodes a protein that regu- lates other genes, which turn out to be responsible for how and when branching takes place. TILLERED1 was notable because Jackson’s team found that it responds to light, suggesting one way in which adjust to Studies in plant genetics are environmental conditions. teaching us about how Like many of the discoveries his lab is making, the organisms develop TILLERED1 insights have potentially interesting applica- tions in agriculture. Those possibilities can be expected It’s a late summer afternoon and many members of the to multiply as new tools, especially new imaging tech- faculty at Cold Spring Harbor Laboratory are busy at nologies and very fast gene sequencers, “are now their computers or huddled over experiments in fluores- enabling us to see how groups of genes work together,” cent-lit laboratories. David Jackson and several of his according to Jackson. postdocs are no less engrossed in their work, yet we find them outdoors on this beautiful day, in the middle Gene interactions play a fundamental developmental of a sun-drenched field just up the road, beyond the role in all organisms. Jackson’s work on plant architec- mudflats of the lower harbor. They are carefully exam- ture therefore is only an aspect of a diverse body of ining specimens of Zea mays — maize, a.k.a. corn work that has also provided insights about how devel- — planted in long, ruler-straight rows. opmental signals are propagated in plants, particularly in the inflorescences that give rise to the seeds valued Jackson, a member of the CSHL faculty for a dozen by agriculturalists and upon which billions of the planet’s years and a professor since 2006, studies genes that hungry people depend. influence the shapes that plants take. Finding odd- looking ears and tassels in maize – respectively, the ‘Taking things to pieces’ plant’s female and male floral structures, or inflores- cences — has proven a productive jumping-off point. Dave Jackson loved nature as a child, and could often Each year, in fact, Jackson and a few members of his be found hiking the English countryside on the outskirts

HARBOR TRANSCRIPT WINTER 2009

Going all the way back to “Mendel, plant breeding has led the way in our efforts to understand the secrets of Lancaster, in the northwest, where he grew up. He took inspiration from his father, an engineer with a big of development and the underlying workshop at home. “In the basement there were tools principles of inheritance. everywhere and we used to fix things — or, in my David Jackson case, take them to pieces and not be able to fix them ” again,” Jackson remembers. “I always wanted to know how things worked.”

He was an undergraduate at the University of Leeds in the mid-1980s, interested in biotechnology, although not specifically in plants until hearing a talk atthe Royal Society, at which the doctoral thesis of a student named Robert Martienssen was discussed. Ten years later, Martienssen would be instrumental in bringing Dave Jackson to CSHL, following Jackson’s Ph.D. at John Innes Institute, the center of plant genetics research in England, and a fruitful period of postdoctoral research at U.C. Berkeley.

At Berkeley, Jackson became involved in work on a maize gene called KNOTTED1. His mentor, Sarah Hake, had succeeded in showing the gene was involved in development of the maize plant, but also

Channels of communication

Since 2005, Jackson and colleagues have made some interesting discoveries about those tiny conduits, the plasmodesmata. They’ve revealed that the KN1 protein, encoded by KNOTTED1, has not two but at least three potential destinations in plant stem cells located in meristems. A portion of the KN1 protein’s structure called a homeo- domain enables it to bind specific DNA sequences, accounting for its function as a regulator of developmental genes. KN1 can also bind to its own RNA and enter plasmodesmata, acting as a signal. And when it interacts with a protein called MBP2C, it becomes anchored in the cytoplasm, preventing it from acting as a signal (presumably in response to a developmental cue). that it acted, in a manner not yet understood, as a signal. In its developmental role, KNOTTED1 was a This spring, Jackson led a team that discovered a gene called GAT1 transcription factor that encoded a protein, KN1, that instructs cells to produce a protein found mainly in meristems. which moved into the cell nucleus to regulate other The protein, an antioxidant, relieves cellular stress; its impact in genes. What made it interesting, says Jackson, was its meristem cells is to improve the flow of traffic through the tiny separate role in signaling between cells. He wanted to plasmodesmata. It’s a mechanism, says Jackson, by which the study that role. channels change their structure in response to environmental cues as development unfolds. This work continued after Jackson was brought to Cold Spring Harbor Laboratory by Martienssen and Winship Herr, the founding dean of CSHL’s Watson School of

11 Biological Sciences, in 1997. In tracing the path of the KN1 signal, Jackson’s attention was drawn to tiny channels called plasmodes- mata which connect plant cells. These minuscule conduits — num- Creating new imaging tools bering in the hundreds or thou- sands in each cell — carry nutrients Jackson and colleagues have made important contributions to the between cells and serve as path- broader research community by developing genetic tools that provide ways for . the means with which to observe processes not previously seen in living plants. Under an NSF grant, Jackson is creating 100 maize Inside the meristem plant lines that express fluorescent proteins across the full spectrum of cellular “compartments.” These have yielded images that are not only beautiful to behold but also productive of new knowledge about how His work in the intervening years plant cells work. The recent Science poster on the maize (see has brought to light new knowl- p. 13) includes a Jackson image (below) revealing proteins called edge about the plasmodesmata, expansins (green) being expressed in the wall of maize meristem cells particularly about their previously (red) just as those cells prepare to grow out into new organs. unrecognized importance in sig- naling. Using maize and another plant, a cress called Arabidopsis, as models, Jackson and colleagues have focused on communities of stem cells in plants called meri- stems, situated at the growing tips of shoots and roots. In maize, the shoot meristem, which gives rise to leaves and flowers (tassels and ears), is a niche containing hun- dreds of stem cells. It’s where KNOTTED1 expresses the protein KN1. It’s also where a gene called RAMOSA3 is expressed, a gene first identified, by Jackson, several years ago.

RAMOSA3 is remarkable because it encodes an enzyme that has proved to have a very important role in maize development — it controls branching in inflores- cences. What makes this extraordi- nary is the fact that the encoded enzyme was known son. “But now we’re doing the interesting part: trying previously for a very ordinary function: the removal of to figure out how this thing is working — how this ordi- phosphate groups from sugar molecules. “The fact that nary enzyme gained such a vital function. Finding this gene could be controlling something so important something unexpected like this is what keeps us going as plant morphology was really incredible,” says Jack- in science.” Peter Tarr

HARBOR TRANSCRIPT WINTER 2009 Maize milestone

A major multi-institutional effort in which three CSHL of an extensive reference manual that will help guide future scientists played important roles culminated in late Novem- research. Ware also co-led a parallel effort simultaneously ber with publication in Science of a reference genome for reported in Science to generate the first haplotype map of maize. (Part of an accompanying informational poster is maize. The HapMap gauges diversity in the maize genome reproduced below.) Doreen Ware, Rob Martienssen and by comparing 27 distinct maize lines with the reference Richard McCombie were co-principal investigators on the version; it sheds new light on subjects ranging from the project, which Ware calls “a landmark.” Ware’s lab of maize and other plants to the adaptation of focused on annotation of the genome, the rough equivalent maize to environmental changes, including global warming.

From Gene Discovery to Application Early explorers of the Americas took maize back to Europe during the 16th century. Since then, maize has spread globally and is now a major world crop. Yields have increased steadily over the past The Maize Genome century as maize became an important source of food, feed, fiber and, more recently, biofuels. During this period, scientists, breeders, growers, and seed companies worked together to translate basic research in maize genetics into practical applications. One event of particular impact was the demonstration of hybrid vigor, or heterosis, which results when two parental varieties, both showing The Domestication of Maize reduced stature caused by inbreeding, are crossed to produce more robust hybrid offspring. Vigorous hybrids increase crop productivity dramatically and are now used for nearly all Corn, also known as maize (from the Spanish commercial corn production. Geneticists are still unraveling maíz), was first domesticated nearly 10,000 years the underlying molecular basis of heterosis and the ago from teosinte, a wild grass that looked quite sequencing of maize will provide new insights different from our modern crop. Teosinte grew in into its mechanisms. Genomics resources will also speed Mexico and Central America as a bushy plant with the identification of genes conferring useful traits that many spikes, the precursor to our familiar ear of Soon after the discovery of heterosis, can be incorporated into breeding programs. corn. The small teosinte spikes had only two rows corn yields began to increase steadily of nearly inedible kernels, or seeds, each enclosed (Graph: ers.usda.gov). by a hard covering. These seeds separated individually at maturity and were dispersed widely. A cross between two smaller inbred plants (left and right) produces more vigorous and productive In probably less than a thousand years, the tiny Zea mays ssp. parviglumis, descendent hybrid offspring (center; Image: Jun Cao and Patrick S. spikes of ancestral teosinte transformed into larger from the original teosinte, shown here Schnable, Iowa State University, reprinted by permission ears with edible kernels that remained on the cob growing in Ames, IA (Image: David from Springer-Plant Sciences). for easy harvest. How these dramatic changes Cavagnaro, Decorah, IA). occurred has been a puzzle for over a century. Geneticists are now convinced that humans living in the Balsas River region of Mexico were foraging teosinte seeds when they noticed rare aberrations—likely caused by random mutations— that increased spike size dramatically. Seeds were propagated from these bigger spikes, and thus The shrunken2 mutation causes a block in starch synthesis: sugar the remarkable events of domestication began. precursors accumulate in the milky fluid of the kernel, making By studying the maize genome, researchers have sweeter tasting corn. The kernels deflate when the ear dries, as now confirmed that mutations in single genes, such above (Image: William F. Tracy, University of Wisconsin-Madison). as Teosinte glume architecture1 (Tga1), alter kernel and plant structure and that changes in many genes influence complex developmental traits, such as the The opaque2 mutation was used by breeders in time to flowering. As human populations migrated Improved hybrids, combined with advances in crop Africa and at CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo) to develop lines, throughout the Americas, new varieties of maize were management, contributed to increased yields. (Scale bar = called Quality Protein Maize (left), with selected to grow in local environments. Some varieties People standing to left of freshly harvested corn; Image: Patrick S. Schnable, Iowa State University). increased quantities of the amino acids were maintained as so-called landraces, each growing lysine and tryptophan (Image: Brian A. Larkins, in ecological niches in Mexico and . Now, University of Arizona). these varieties and landraces hold a wealth of genetic diversity, which is being tapped for both basic research The cradle of maize domestication was Teosinte and as traits for crop breeding. in the Balsas River basin, marked with pin (Image: iStockphoto.com/KeithBinns).

Diverse ears of corn can be seen at a market in Pisaq, Peru (far left; Image: Candice Gardner, The tiny spike of teosinte The Future USDA/ARS). (left) gave rise to the Two maize genomes sequenced recently were B73, an A statue of an Aztec maize elite inbred line grown in the Midwestern United States (right; large edible corn ear of Maize has adapted through domestication to nearly every climate across the globe, and many societies deity (left), holding corn ears today (right) (Image: Hugh The Dynamic Image: Ruth Swanson-Wagner and Patrick S. Schnable, Iowa State in hand, shows the significance Iltis). University, reprinted by permission from Springer-Plant Sciences), and now depend on maize to feed expanding populations of people and livestock. Although breeders of maize in the lives of Palomero toluqueño, a popcorn landrace grown in the highlands of and agronomists have increased crop yields over the past century, the world’s growing population Mesoamericans (Image: The Mexico (left; Image: Jaime Padilla, Irapuato, Guanajuato, Mexico). strains global food production as climate patterns are disrupted, arable land diminishes, and Dolan DNA Learning Center, Cold Maize Genome nonrenewable energy supplies dwindle. Solutions will be made possible by global cooperation Spring Harbor Laboratory). in which scientific and technological progress translates basic discoveries into practical Maize has a strikingly dynamic genome: two maize varieties show applications. To this end, the genome sequences of maize and other crops are as much DNA sequence variation as that observed between two significantly enhancing established breeding efforts. Soon it will be possible different species. Also, genes present in one maize variety may to reconstruct and fully understand the genetic basis for maize growth be absent in another. Such and development; new tools will permit researchers to pinpoint functions variation is evidence and study interactions of gene products and plant metabolites with of rapid genome the environment. This basic information change that can be used to tailor maize varieties, occurred during through molecular breeding, to thrive the evolution in new environments, generate new of maize. The products, and increase yields. Other grass lineage that advances include the use of transgenes includes maize and that help maintain crop yields despite teosinte diverged from environmental pressures from drought, Maize Genetics in the 20th Century rice and wheat approximately insects, pathogens and weeds. Maize also 50 million years ago. Subsequently, the full serves as a model grass to develop methods for Maize emerged as a model research plant in the early 20th complement of chromosomes doubled in A farmer tends her crop. Maize Maize geneticists at optimizing plant-based biofuel production. The maize century partly because its domesticated traits were ideal number in the ancestor of teosinte. Analysis can be modified to suit local in the early 1920s included (left to environments and to satisfy genome sequence thus enables researchers to make right) Charles R. Burnham, Marcus M. for genetics experiments. Controlled genetic crosses were of the sequenced genome of the Midwestern possible because the male tassel was separate from the cultural needs (Photo: Arjen van de targeted improvements, allowing us to keep pace with a Rhoades, Rollins A. Emerson, Barbara variety, B73, demonstrates that this ancestral Merwe). future as dynamic as the maize genome itself. McClintock, and (crouching) George female ear. Also, genes controlling seed and plant colors duplicated genome underwent significant W. Beadle. McClintock was awarded were ideal markers for studying patterns of inheritance. rearrangement, with pieces of chromosomes inverted, a for her discovery of Geneticists developed methods to observe the distinctive exchanged, transposed, further duplicated, or lost. Transposons Tools are being developed to take advantage of the transposons in maize. (Image: MaizeGDB meiotic chromosomes of maize, ushering in a new scientific maize genome and to meet the needs of the future. and with permission of W. B. Provine). contributed substantially to genome variation. Some classes of discipline: . For the first time, researchers could transposons cluster near , while others are found This is being accomplished through the use of new study behavior and could associate genes near genes that lack the chemical modification of methylation. sequencing, proteomic, metabolomic and cellular level with individual chromosomes using visible cytogenetic Most, however, are located in heavily methylated, intergenic technologies. The sample below shows just a few of the markers. The discovery of transposons—pieces of mobile regions, contributing to the distinctive genome of each inbred functional genomics resources being developed. DNA—revolutionized the field of genetics and demonstrated variety. Comparative genomics studies are useful to identify A genetic map from 1937 the dynamic nature of the maize genome. By the second genes in maize that are similar to those found in other plant displays the 10 maize half of the 20th century, maize geneticists had studied species. Using these methods, study of the genome of the chromosomes. Mutants are used hundreds of mutants, mapped gene locations, cloned the Mexican maize landrace, Palomero toluqueño, identified genes to map and study genes and first plant genes, and identified transposon-induced genome Maize develop traits for breeding maize under selection homologous to those that are suspected to be as a commercial crop. Sample rearrangements among closely related maize varieties. involved in metal processing. Genome analysis demonstrates mutants and chromosomal Meanwhile, a physical map of the maize genome was that landraces and worldwide varieties are highly diverse, positions are shown below. populated with markers and was integrated with the maize Sequence analysis of the maize variety, B73, shows the making preservation of their unique molecular heritage (Image: MaizeGDB). genetic map. These tools, combined with gene expression dynamic nature of the maize genome. The outer rings are maize important for cultural, scientific, and agricultural reasons. profiles and other resources, provided the necessary chromosomes (labeled 1 to 10) with duplicate regions connected UniformMu: An inbred transposon foundation to sequence the maize genome. by ribbons, showing the large related segments derived from population is used for functional Genome databases, such as the maize

U.S.A. 87, 9888 (1990). 87, Sci. U.S.A. Acad. Natl. Proc. each of the ancestral genomes (Image: From Schnable et al., Science genomics (Image: A. Mark Settles with genetics and genomics database, 326 (5956) (2009); DOI: 10.1126/science.1178437). Donald R. McCarty, Karen E. Koch, L mtmDB: Mutations, such as in synthesize and make accessible large and Curtis Hannah, University of Florida). branched silkless1 (bd1) shown increasingly complex datasets (Image: here, can be found using a MaizeGDB). transposon tagging resource (Image: Rob Martienssen, Cold Spring Harbor Laboratory). Maize Genomics Browsers and Genetics Resources Maize Stock Center Seed and Resources maizecoop.cropsci.uiuc.edu www.maizegdb.org Functional Genomics Resources maizesequence.org www.ars-grin.gov/cgi-bin/npgs/html/tax_search.pl?Zea www.panzea.org public.iastate.edu/~usda-gem magi.plantgenomics.iastate.edu maize.jcvi.org/cellgenomics/index.shtml ramosa1 (ra1) Mutations in Comparative Maize and Plant Genomics www.plantgdb.org/prj/AcDsTagging Educational Resources on Maize ra1 cause extra branching in www.gramene.org uniformmu.uf-genome.org www.agry.purdue.edu/ext/corn/index.html the ear early in development www.plantgdb.org mtm.cshl.org www.dnalc.org/resources/dnatoday (Image: Erik Vollbrecht, Iowa State synteny.cnr.berkeley.edu/CoGe maizecdna.org weedtowonder.org Panzea: Maize diversity is evident in a mapping population generated by crossing different University, and Rob Martienssen, Maize cell genomics: Maize meiotic chromosomes were www.phytozome.net/maize.php genome.purdue.edu/maizetilling www.extension.iastate.edu/hancock/info/corn.htm varieties with B73, ultimately producing distinct lines that serve as the “raw material” for Cold Spring Harbor Laboratory). Fluorescent tags mark proteins first visualized by Barbara McClintock www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html plantbio.berkeley.edu/~mukiller in cells, allowing for functional further maize improvement. Each row shows variation in one visible trait of plant height and others (upper middle, Image: Cold plantcentromeres.org Seed company resources are also available through studies (Image: From Mohanty Ds mutagenesis: A colored (Image: From McMullen et al., Science 325, 737 (2009); DOI: 10.1126/science.1174320). National and International Organizations Spring Harbor Laboratory Research maize-mapping.plantgenomics.iastate.edu individual company websites. et al. 2009. Plant sector in the tassel represents Ds glossy4 (gl4) Mutations in www.ncga.com Archives). Similar meiotic stages can Also see maizegdb.org/POPcorn for additional public 149:601-605. www.plantphysiol.org transposition, a tool for inducing gl4 affect waxes on juvenile www.cimmyt.org now be detected using antibodies resources Copyright American Society of Plant new mutations (Image: Thomas P. maize leaves so that water to proteins associated with the Biologists). Brutnell, Boyce Thompson Institute). droplets accumulate when the DNA (upper right, Image: R. Kelly Dawe, knotted1 (kn1) Mutations leaf is sprayed (Image: Sanzhen University of Georgia) and fluorescently Background maize kernels: Purple-colored sectors and in kn1 cause disorganized Liu and Patrick S. Schnable, Iowa labeled DNA probes identify regions spots demonstrate the phenotypic effects of chromosome growth of the leaf (Image: State University and reprinted by of interest in condensed somatic Sponsored By: MaizeGDB) permission from the Genetics Society breakage caused by activity of transposable elements maize chromosomes (left, Image: called Activator and Dissociation, in one of the earliest of America). Patrice S. Albert and James A. Birchler, examples of transposition (Corn ear from McClintock collection ) . grown in 1949, Cold Spring Harbor Laboratory. Image: Jim Duffy and Rob Martienssen, Cold Spring Harbor Laboratory). Teosinte and Maize drawings by Hugh Iltis; from Doebley et al., Doebley Hugh Iltis; from by drawings and Maize Teosinte

Poster content and text: Anne W. Sylvester, Patrick S. Schnable, and Rob Martienssen AAAS/Science Business Office Publication

Courtesy AAAS

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