Emerging Model Organisms

Maize (Zea mays): A Model Organism for Basic and Applied Research in Plant Biology

Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA

¹Corresponding author (mjs298{at}cornell.edu).

INTRODUCTION

Zea mays ssp. mays is one of the world’s most important crop plants, boasting a multibillion dollar annual revenue. In addition to its agronomic importance, maize has been a keystone model organism for basic research for nearly a century. Within the cereals, which include other plant model species such as rice (Oryza sativa), sorghum (Sorghum bicolor), wheat (Triticum spp.), and barley (Hordeum vulgare), maize is the most thoroughly researched genetic system. Several attributes of the maize plant, including a vast collection of mutant stocks, large heterochromatic chromosomes, extensive nucleotide diversity, and genic colinearity within related grasses, have positioned this species as a centerpiece for genetic, cytogenetic, and genomic research. As a model organism, maize is the subject of such far-ranging biological investigations as plant domestication, genome evolution, developmental physiology, epigenetics, pest resistance, heterosis, quantitative inheritance, and comparative genomics. These and other studies will be advanced by the completed sequencing and annotation of the maize gene space, which will be realized during 2009. Here we present an overview of the use of maize as a model system and provide links to several protocols that enable its genetic and genomic analysis.

BACKGROUND INFORMATION

Zea mays L. ssp. mays, commonly referred to as maize or corn, belongs to the grass tribe Andropogoneae of the family Gramineae (Poaceae). The grasses originated 55-70 million years ago (mya) and subsequently diversified to include all the major cereal crop species in addition to nearly 10,000 nondomesticated relatives (Fig. 1A ; Kellogg 2001; Bolot et al. 2009). The maize genome originated 4.8 mya via the segmental allotetraploidization of two progenitor genomes that themselves diverged from a sorghum progenitor ~11.9 mya (Gaut and Doebley 1997; Swigonova et al. 2004). Although they differ in ploidy and overall genome size, cereal genomes exhibit a relatively high degree of genic colinearity and sequence conservation (Gale and Devos 1998; Bennetzen and Ma 2003). Much of the size variation within the cereal genomes is attributed to genome duplication and the expansive amplification of transposable elements (SanMiguel et al. 1996, 1998; Bennetzen 2000).

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Figure 1. Evolutionary relationships of maize to cereal crops and within the genus Zea. (A) A partial phylogeny of the cereals with Arabidopsis as an outgroup. Divergence of the major cereal crop progenitors is estimated to have occurred within the past 50 mya. Maize and rice diverged ~50 mya, whereas maize and sorghum diverged more recently, ~9 mya. (Reprinted, with permission, from Bolot et al. 2009. © 2009 Elsevier.) (B) A phylogeny of the genus Zea. After diverging from the genus Tripsacum, the ancestral genus Zea underwent a relatively recent radiation to give rise to four extant species and at least four subspecies. Molecular data indicate Z. mays ssp. parivglumis is the closest relative to modern maize (Z. mays ssp. mays) and that the two diverged ~9000 yr ago (*). (Reprinted, with permission, from Vollbrecht and Sigmon 2005. © 2005 The Biochemical Society.)

Deciphering the genetic history of maize in light of its domestication is pivotal to an understanding of its natural history (for review, see Doebley 2004). The closest wild relatives of domesticated maize are the teosintes, the annual and perennial grasses of the genus Zea that are indigenous to Mexico and Central America (Fukunaga et al. 2005). The teosintes include four species: Z. luxurians, Z. diploperennis, Z. perennis, and Z. mays, with Z. mays composed of at least four subspecies (ssp. mays, ssp. mexicana, ssp. parviglumis, and ssp. huehuetenangensis) (Fig. 1B; Fukunaga et al. 2005; Vollbrecht and Sigmon 2005). Genetic studies of maize domestication have identified Z. mays ssp. parviglumis as the direct ancestor of modern maize, and, complemented by archeological data (Piperno and Flannery 2001), estimate that maize diverged from its teosinte ancestor between 6000 and 9000 years ago (Matsuoka et al. 2002). In that same study, Matsuoka and colleagues (2002) postulate a single domestication event, which likely occurred in southern Mexico’s central Balsas River region. The subsequent diversification of maize took place in the Mexican highlands between Oaxaca and Jalisco provinces. Dispersal of modern maize then proceeded along two principle routes: a northern route stretching from northwestern Mexico, through the southwestern United States, and into the eastern United States and Canada; and a southern route ranging from Mexico’s southwestern lowlands into Guatemala, the Caribbean, and South America (Matsuoka et al. 2002). Zea mays ssp. mays produced a multibillion dollar revenue from the 157 million hectares harvested globally in 2007 (http://faostat.fao.org).

The origin of maize as a model organism traces back to early studies performed in 1869 by Gregor Mendel, where maize was used to corroborate the more renowned breeding experiments he performed previously in Pisum (pea) (Rhoades 1984; Coe 2001). Like pea, maize is a large plant, making it well-suited for phenotypic analysis and thereby conferring a decided advantage in genetic analysis of morphological mutants. Some 30 years later, Correns and de Vries utilized maize extensively in their investigations on xenia--the dominant influence exerted by the pollen parent on the phenotype of the endosperm. The results from these studies complemented and extended Mendel’s original genetic studies and were integral to the rediscovery of Mendel’s landmark work.

While Correns and de Vries were among the early pioneers of maize research, R. A. Emerson of Cornell University and his thesis advisor E. M. East of Harvard University are widely regarded as the founding fathers of modern maize genetics. Emerson served as mentor to an astoundingly energetic and influential first generation of maize geneticists, including George Beadle, Charles Burnham, Marcus Rhoades, and Barbara McClintock. Throughout the 1920s and 1930s, the Cornell group established a solid foundation in transmission genetics and cytology that provided a framework for the use of maize as a model genetic system. Detailed historical perspectives on this foundational research in maize genetics are provided in articles by Rhoades (1984) and Coe (2001).

SOURCES AND HUSBANDRY

The Maize Genetics Cooperation Stock Center (MGCSC) located at the University of Illinois at Urbana-Champaign, is a primary source for maize mutant stocks used in research (Table 1). As a free service to the maize community, the MGCSC obtains, maintains, and disseminates seed stocks internationally and is a repository for information regarding all known allelic and cytological variations in maize. The MGCSC collection contains over 100,000 pedigrees, including several hundred gene mutants and alleles (Neuffer et al. 1997). Also included in the collection are stocks harboring chromosome aberrations and aneuploidy, inbred-specific ethyl methane sulfonate (EMS) mutant stocks, and a prodigious collection of well-characterized transposable element stocks that are a hallmark of maize genetic research (see "Genetics and Genomics").

Owing to its exceptional genetic diversity, maize is highly adaptable and responsive to selective pressure. As a result, maize has been cultivated from the tropics to southern Canada, a wide biogeographical range that encompasses tremendous diversity in soil composition, climate, day length, and elevation (Neuffer 1982). The length of the growing period and the quality of ambient light are the major determinants of the geographical ranges suitable for field cultivation of specific maize inbred lines.

Although hundreds of maize inbred lines are described, B73, Mo17, and W22 are the most widely used laboratory accessions. These lines require a growing period of ~100 d; planting to pollination spans 60-70 d, after which ~40 d are required for seed development and desiccation. In the continental United States, the summer climate allows for field cultivation, whereas winter stocks must be raised in light-supplemented greenhouses. In addition, growing maize at lower latitudes during the winter months permits the propagation of two large field crops per calendar year. For specific protocols and advice on pollinating and growing maize, see "Technical Approaches."

Most field-grown maize in the continental United States (i.e., under long-day conditions) is predominately day-neutral with respect to floral induction (Galinat and Naylor 1951). That is, after the vegetative meristem initiates a fixed number of vegetative nodes, it converts to floral or tassel development (Fig. 2 ). Therefore, for the majority of maize lines, floral induction occurs in response to a developmental cue rather than day length. However, floral induction in some maize lines can be influenced by environmental signals (Russell and Stuber 1983). Indeed, photoperiod limits the latitudinal range of some tropical lines of maize, which are classified as quantitative short-day plants.

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Figure 2. Zea mays ssp. mays. (A) The adult maize plant is comprised of the above-ground shoot and the underground root. Nodes mark points of leaf attachment along the stem; the internode is the stem segment between successive nodes. The tassel, a branched male inflorescence found at the apex of the stem, contains the staminate flowers. Pistillate flowers are located in the ear, which terminates a short branch found in the axis of leaves near the middle of the stem. The strap-like foliar leaf, a lateral appendage positioned at each node on the stem, has two distinct parts--the distal blade and the proximal sheath that encircles the stem at its insertion. Shoot-borne crown and brace roots are formed from consecutive basal nodes. Adventitious roots form the bulk of the root system and give rise to highly branched secondary roots. (B) Tassel branches bear an ordered arrangement of small flower-producing branches called spikelets. Two spikelets are initiated at each branch point, and each spikelet produces two functional florets--a pedicellate floret borne on a moderate stem and a sessile floret borne on a short stem. Anthers, forced out of the flower at anthesis, dangle downward and shed pollen. (C) Unlike the unequal spikelets of the tassel, ear spikelets are equivalent in size, and only one floret per spikelet develops to maturity. The mature ear floret contains a single ovary terminated in an elongated style, or silk. During pollination, pollen shed from the anthers germinates on the silk and travels through the growing pollen tube to the ovule. The ovary enlarges after fertilization to produce the kernel, a one-seeded fruit. (D) A husk leaf is attached at each node on the stem of the ear shoot. (E) The mature kernel contains the embryo and is enclosed in the pericarp, a transparent tissue layer of maternal origin. Pigmented cells are localized to the aleurone, which form the outermost cell layer of the endosperm. At maturity, the embryo harbors five or six tiny leaf primordia and a primary root. The endosperm accumulates starch reserves that are mobilized upon germination and transmitted through the scutellum to the growing seedling. (Original illustration by Dr. Walton Galinat; used with artist’s permission.)

RELATED SPECIES

Enabled by the extensive synteny among cereal genomes, comparative studies provide a powerful tool for gene discovery and analyses of genome evolution in the grasses (Bennetzen and Ma 2003; Devos 2005). This extensive colinearity of gene order and orientation between maize, sorghum, rice, wheat, and barley is often exploited to circumvent experimental barriers inherent to one or more of these species. The maize genome is moderately sized (~2.5 gigabase pairs [Gbp]) compared to many of its grass relatives such as rice (0.4 Gbp), sorghum (0.75 Gbp), barley (6 Gbp), and wheat (17 Gbp) (Mullet et al. 2002; Rabinowicz and Bennetzen 2006). In addition, maize offers decided genetic advantages in mutant stock collections, cytogenetics, transposon mutagenesis, and ease of controlled pollinations (see "Technical Approaches"). Advantages of rice include a relatively small, sequenced genome and more efficient transformation technologies. As the first grass genome to be fully sequenced (Goff et al. 2002), rice has been used extensively during annotation of the emerging maize genomic sequence.

USES OF MAIZE AS A MODEL SYSTEM

Like many other grasses, maize is wind pollinated and a natural cross-pollinator. However, maize is particularly amenable to genetic analysis owing to its monoecious floral development, wherein unisexual male and female flowers are borne on separate stems. Male (staminate) flowers develop in the tassel, a branched inflorescence that is positioned at the top of the main stem. Female (pistillate) flowers are found in the ear, a compact inflorescence borne at the ends of reduced lateral branches and located at the midpoint of the stem ~five to six nodes below the tassel (Fig. 2). In maize, sexual identity is acquired through the programmed cell death of stamen primordia in female flowers and the corollary abortion of carpel primordia in male florets (Cheng et al. 1983). The developmental partitioning of male and female flowers has implications for the discovery of genes controlling sex determination in maize (Delong et al. 1993; Chuck et al. 2007, 2008). Moreover, this physical separation of male and female flowers greatly facilitates controlled pollinations, in that ear and tassel shoots can be easily covered to prevent pollen contamination and to collect pollen, respectively. Crossing maize is not only simple, but also highly productive: Several hundred seed can be produced from a single pollinated ear. This feature sets maize apart from other cereals as an advantageous genetic system--genetic crosses in other cereals require emasculation, a laborious procedure that yields a single seed per flower.

Meiosis in maize is synchronized, such that the relative size of developing maize anthers correlates with the meiotic stage of the microsporocytes within. This useful feature, coupled with the relatively large physical size of maize chromosomes, has placed maize at the forefront of plant cytogenetic research. Chromosomal characteristics such as knobs facilitate the tracking of chromosome pairing and segregation. Because of these traits, uncovering meiotic mutants in maize has been relatively straightforward. In addition, chromosomal aberrations including translocations, inversions, and deficiencies were used to assign genes to chromosomal locations (see, e.g., Rhoades 1984). For example, the waxy-marked translocation stocks link this observable endosperm marker to each arm of the ten haploid chromosomes in maize, thereby facilitating the placement of genes to chromosome arm (Laughnan and Gabay-Laughnan 1994). Recent, more sophisticated approaches to cytogenetic analysis, such as the development of single-copy fluorescence in situ hybridization (FISH) and fiber-FISH technologies, have revolutionized studies on maize genomic organization (Jiang et al. 2003; Kato et al. 2004; Wang et al. 2006).

Maize kernel morphology and composition are quantitative traits of immense agronomic and nutritional importance. A single-seeded fruit, the large and prominent maize kernel has been the focus of hundreds of genetic analyses of morphological and biochemical mutants. Barbara McClintock’s pioneering research on transposable elements exploited genetically mosaic sectors induced via transposable element activity in the aleurone, the anthocyanin-enriched outer cell layer of the maize endosperm (McClintock 1950; Dooner and Kermicle 1971). Mutations affecting the development of the embryo or the accumulation of storage proteins and starch in the endosperm are especially abundant, and have contributed to our understanding of developmental and biosynthetic pathways operating in the maize kernel (Laughnan 1953; Scanlon et al. 1994).

As a predominantly out-crossing species, maize has an extraordinary level of genotypic diversity. The frequency of nucleotide polymorphism observed when comparing the genomes of any two modern maize inbred lines is equivalent to the sequence diversity between chimpanzees and humans (Buckler et al. 2006). Pivotal to the success of maize domestication, this nucleotide diversity continues to be exploited in modern breeding programs. For example, the native heterozygosity of the maize genome is exploited in association mapping strategies, wherein correlations between phenotypic and genetic diversity are identified in analyses of complex, natural populations (Yu and Buckler 2006). Such studies have identified candidate genes associated with complex traits, such as flowering time (Thornsberry et al. 2001), starch biosynthesis (Wilson et al. 2004), and seed carotenoid content (Harjes et al. 2008), which can be manipulated by breeders for agronomic and nutritional improvement of maize varieties.

GENETICS AND GENOMICS

A comprehensive, standardized gene nomenclature for maize was established in the late 1990s. Guidelines for the naming of nuclear and organellar genes and gene products, allelic and nonallelic designations, transposon-induced mutations, chromosomal rearrangements, and molecular genetic marker loci are outlined on the Maize Genome and Genetics Database website (http://www.maizegdb.org/maize_nomenclature.php).

Maize research has benefited from a vast collection of genetic mutants (Neuffer et al. 1997). Over the past decade, high-throughput mutagenesis programs were launched to both expand this inventory of maize mutants and expedite the distribution of mutants to the research community (Table 1). For example, the Maize TILLING (Targeting Induced Local Lesions IN Genomes) project is a reverse-genetics approach utilizing gene-targeted screening of EMS-mutagenized inbred populations (Till et al. 2004; Weil and Monde 2007). A second project involves the use of the Activator (Ac)/Dissociation (Ds) transposable element system in a strategy of targeted, regional mutagenesis. Exploiting the propensity of Ac and Ds to transpose short distances, this strategy aims to saturate specific chromosomal regions adjacent to mapped Ac/Ds transposons in an effort to generate new insertional mutations in genes closely linked to existing transposons (Bai et al. 2007). Once identified, new Ac/Ds insertional mutations generate a molecular tag that is utilized for cloning targeted genes (Pohlman et al. 1984). Imprecise transposon excision/insertion events can create "footprint" alleles, which generate allelic variation and contribute to genome evolution (Chen et al. 1987; Kolkman et al. 2005; Bai et al. 2007). Characterized by an increased transposon copy number and a correspondingly elevated mutation rate, the Mutator (Mu) transposable element system has emerged as a popular method for mutagenesis among maize geneticists. The Maize-Targeted Mutagenesis (MTM) project utilizes a polymerase chain reaction (PCR)-based reverse genetic strategy to identify gene-specific, germinal transposon insertions in a population of ~44,000 plants that are enriched for mobilized Mu elements. Following mutagenesis, Mu activity in the MTM lines is epigenetically silenced by crossing to Mu killer (Slotkin et al. 2003), a strategy that eliminates new Mu transpositions in the progeny (May et al. 2003). Importantly, Mu silencing effectively eliminates new somatic Mu insertions, which are not transmitted to the progeny and can lead to confounding false positives in PCR screens (May et al. 2003). A steady-state mutagenesis system is utilized in the UniformMu collection, a forward- and reverse-genetic strategy wherein active Mu transposons are introgressed into the W22 inbred line and insertion mutations are identified by massively parallel sequence technology (McCarty et al. 2005). Despite these outstanding genetic resources, maize research is slowed by the lack of cost-efficient, high-throughput approaches for genetic transformation, a technology that is still relatively slow and technically challenging in maize (Frame et al. 2002).

A diverse toolkit for genomic analyses is readily available to the maize research community. The intermated B73 x Mo17 recombinant inbred lines (IBMRIL; Lee et al. 2002) and their subsequent saturation with molecular markers, such as restriction fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs; Sharopova et al. 2002), insertion/deletion polymorphisms (IDPs; Fu et al. 2006), and single-nucleotide polymorphisms (SNPs), have greatly increased the resolution of the maize genetic map. Capitalizing on the extensive heterogeneity within the maize gene pool, the maize nested associated mapping (NAM) population comprises 5000 RILs developed from crosses between B73 and each of 25 diverse maize inbred lines (Yu and Buckler 2006). The NAM population captures much of the natural allelic variation present in Zea mays ssp. mays and represents a powerful tool for the fine-scale resolution and molecular dissection of genes contributing to complex traits in maize. Positional cloning is emerging as the most powerful tool for gene identification in maize, a procedure that is greatly enhanced by the genomic sequencing effort (Bortiri et al. 2006). Links to these tools and other related maize resources are summarized in Table 1.

Genomic sequencing of the maize inbred line B73 is nearing completion; full release of the genome sequence is expected during 2009. B73 was selected as the reference genome because it performs well throughout much of the continental United States, exhibits high yield, and is the most utilized inbred line in basic research laboratories. Consequently, B73 is the source of the majority of the maize expressed sequence tags (ESTs) and commercially important germplasm, as well as the vast collection of bacterial artificial chromosome (BAC) libraries (Bennetzen et al. 2001). Presently, annotation of the maize genome is incomplete. Annotation efforts are driven by the maize research community, and maize gene predictions are extensively derived from models of rice orthologs.

TECHNICAL APPROACHES

Maize genetic research is greatly facilitated by the physical separation of male and female flowers, making controlled pollinations simple and highly productive. A detailed protocol for maize pollination, complete with video demonstrations, helpful tips, and required materials can be accessed from the website "Controlled Pollinations of Maize" (http://www.maizegdb.org/IMP/WEB/pollen.htm). An efficient protocol for the isolation of maize DNA suitable for use in restriction digests, small-insert (i.e., 25 kb or less) cloning, and PCR analysis has been developed by Dr. Stephen Dellaporta and colleagues (http://www.agron.missouri.edu/mnl/57/25dellaporta.html). Maize has been extensively utilized in the development of advanced cytogenetic protocols, including genomic in situ hybridization (GISH), single copy FISH (Wang et al. 2006), chromosome painting (Kato et al. 2004), and extended fiber FISH (Jiang et al. 2003). Protocols for GISH and fiber FISH can be accessed from Dr. Jiming Jiang’s laboratory (http://www.hort.wisc.edu/jjiang/protocols_1.htm). Maize is also the first organism utilized for in situ hybridization of small RNA transcripts (21-24 nucleotides) utilizing locked nucleic acid (LNA) hybridization probes, as described by Drs. Catherine Kidner and Marja Timmermans (http://schnablelab.plantgenomics.iastate.edu/docs/resources/protocols/pdf/in_situ_protocol.2007.04.01.pdf); Kidner and Timmermans 2006).

Maize is a highly tractable system for developmental genetic and genomics. The relatively large size of maize organs, such as the leaf primordia and shoot apical meristem (SAM), renders them especially suitable for laser microdissection analyses. Laser microdissection permits the precise isolation of discrete cells, tissues, or organs from thin sections of fixed plant tissue immobilized on glass slides. RNA isolated from microdissected samples is suitable for use in expression analyses, such as quantitative real-time PCR (qRT-PCR), microarray hybridization, and massive parallel RNA sequencing (RNA-Seq). Provided here are links to detailed protocols from Dr. Patrick Schnable’s laboratory:

• growing maize seedlings in controlled environmental conditions suitable for genomic analyses (http://schnablelab.plantgenomics.iastate.edu/docs/resources/protocols/pdf/Growing_maize_seedlings.2007.04.01.pdf);
  
  
• tissue fixation, paraffin embedding, and microtome sectioning of maize shoots (http://schnablelab.plantgenomics.iastate.edu/docs/resources/protocols/pdf/Paraffin_sectioning_for_LCM.2007.10.19.pdf);
  
  
• cryosectioning of maize tissues (http://schnablelab.plantgenomics.iastate.edu/docs/resources/protocols/pdf/Cryosectioning_for_LCM.2007.04.01.pdf);
  
  
• linear amplification of microdissected RNA (http://schnablelab.plantgenomics.iastate.edu/docs/resources/protocols/pdf/RNA_amplification.2007.04.01.pdf);
  
  
• qRT-PCR analyses of maize cDNA (http://schnablelab.plantgenomics.iastate.edu/docs/resources/protocols/pdf/realtime_RT-PCR.2007.04.01.pdf);
  
  
• Maize Tissue Preparation and Extraction of RNA from Target Cells for Genotyping (Ohtsu and Schnable 2007a);
  
  
• T7-Based RNA Amplification for Genotyping from Maize Shoot Apical Meristem (Ohtsu and Schnable 2007b); and
  
  
• SNP Mining from Maize 454 EST Sequences (Ohtsu and Schnable 2007c).
  
  

ACKNOWLEDGMENTS

We acknowledge the vast contributions and friendly collegiality of the past and present community of maize researchers.

REFERENCES

Bai L, Singh M, Pitt L, Sweeney M, Brutnell TP. 2007. Generating novel allelic variation through Activator insertional mutagenesis in maize. Genetics 175: 981–992.[Abstract/Free Full Text]

Bennetzen JL. 2000. Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions. Plant Cell 12: 1021–1029.[Abstract/Free Full Text]

Bennetzen JL, Ma J. 2003. The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6: 128–133.[Medline]

Bennetzen JL, Chandler VL, Schnable PS. 2001. National Science Foundation-sponsored workshop report. Maize genome sequencing project. Plant Physiol 127: 1572–1578.[Free Full Text]

Bolot S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C, Salse J. 2009. The ‘inner circle’ of the cereal genomes. Curr Opin Plant Biol 12: 119–125.[Medline]

Bortiri E, Jackson D, Hake S. 2006. Advances in maize genomics: The emergence of positional cloning. Curr Opin Plant Biol 9: 164–171.[Medline]

Buckler ES, Gaut BS, McMullen MD. 2006. Molecular and functional diversity of maize. Curr Opin Plant Biol 9: 172–176.[Medline]

Chen J, Greenblatt LM, Dellaporta SL. 1987. Transposition of Ac from the P locus of maize into unreplicated chromosomal sites. Genetics 117: 109–116.[Abstract/Free Full Text]

Cheng PC, Greyson RI, Waldon DB. 1983. Organ initiation and the development of unisexual flowers in the tassel and ear of Zea mays. Am J Bot 70: 450–462.

Chuck G, Meeley R, Irish E, Hajime S, Hake S. 2007. The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat Genet 39: 1517–1521.[Medline]

Chuck G, Meeley R, Hake S. 2008. Floral meristem initiation and meristem cell fate are regulated by the maize AP2 genes ids1 and sid1. Development 135: 3013–3019.[Abstract/Free Full Text]

Coe EH Jr. 2001. The origins of maize genetics. Nat Rev Genet 2: 898–905.[Medline]

DeLong A, Calderon-Urrea A, Dellaporta SL. 1993. Sex determination gene TASSELSEED2 of maize encodes a short-chain alcohol dehydrogenase required for stage-specific floral organ abortion. Cell 74: 757–768.[Medline]

Devos KM. 2005. Updating the ‘crop circle.’. Curr Opin Plant Biol 8: 155–162.[Medline]

Doebley J. 2004. The genetics of maize evolution. Annu Rev Genet 38: 37–59.[Medline]

Dooner HK, Kermicle JL. 1971. Structure of the R^r tandem duplication in maize. Genetics 67: 427–436.[Free Full Text]

Frame BR, Shou H, Chikwamba RK, Zhang Z, Xiang C, Fonger TM, Pegg SEK, Li B, Nettleton DS, Pei D, et al. 2002. Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system. Plant Physiol 129: 13–22.[Abstract/Free Full Text]

Fu Y, Wen TJ, Ronin YI, Chen HD, Gou L, Mester DI, Yang Y, Lee M, Korol AB, Ashlock DA, et al. 2006. Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics 174: 1671–1683.[Abstract/Free Full Text]

Fukunaga K, Hill J, Vigouroux Y, Matsuoka Y, Sanchez J, Liu K, Buckler ES, Doebley J. 2005. Genetic diversity and population structure of teosinte. Genetics 169: 2241–2254.[Abstract/Free Full Text]

Gale MD, Devos KM. 1998. Comparative genetics in the grasses. Proc Natl Acad Sci 95: 1971–1974.[Abstract/Free Full Text]

Galinat WC, Naylor AW. 1951. Relation of photoperiod to inflorescence proliferation in Zea mays L. Am J Bot 38: 38–47.

Gaut BS, Doebley JF. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci 88: 2060–2064.

Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100.[Abstract/Free Full Text]

Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, et al. 2008. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319: 330–333.[Abstract/Free Full Text]

Jiang J, Birchler JA, Parrott WA, Dawe RK. 2003. A molecular view of plant chromosomes. Trends Plant Sci 8: 570–575.[Medline]

Kato A, Lamb JC, Birchler JA. 2004. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci 101: 13554–13559.[Abstract/Free Full Text]

Kellogg EA. 2001. Evolutionary history of the grasses. Plant Physiol 125: 1198–1205.[Free Full Text]

Kidner C, Timmermans M. 2006. In situ hybridization as a tool to study the role of microRNAs in plant development. Methods Mol Biol 342: 159–179.[Medline]

Kolkman JM, Conrad LJ, Farmer PR, Hardeman K, Ahern KR, Lewis PE, Sawers RJH, Lebejko S, Chomet P, Brutnell TP. 2005. Distribution of Activator (Ac) throughout the maize genome for use in regional mutagenesis. Genetics 169: 981–995.[Abstract/Free Full Text]

Laughnan JR. 1953. The effect of the sh₂ factor on carbohydrate reserves in the mature endosperm of maize. Genetics 38: 485–499.[Free Full Text]

Laughnan JR, Gabay-Laughnan S. 1994. The placement of genes using waxy-marked reciprocal translocations. In The maize handbook (eds. M Freeling and V Walbot), pp. 255–257. Springer, New York.

Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A. 2002. Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol Biol 48: 453–461.[Medline]

Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley J. 2002. A single domestication for maize shown by microsatellite genotyping. Proc Natl Acad Sci 99: 6080–6084.[Abstract/Free Full Text]

May BP, Liu H, Volbrecht E, Senior L, Rabinowicz PD, Roh D, Pan X, Stein L, Freeling M, Alexander D, et al. 2003. Maize-targeted mutagenesis: A knockout resource for maize. Proc Natl Acad Sci 100: 11541–11546.[Abstract/Free Full Text]

McCarty DR, Settles AM, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier J, Avigne W, Lai J, et al. 2005. Steady-state transposon mutagenesis in inbred maize. Plant J 44: 52–61.[Medline]

McClintock B. 1950. The origin and behavior of mutable loci in maize. Proc Natl Acad Sci 36: 344–355.[Free Full Text]

Mullet JE, Klein RR, Klein PE. 2002. Sorghum bicolor--An important species for comparative grass genomics and a source of beneficial genes for agriculture. Curr Opin Plant Biol 5: 118–121.[Medline]

Neuffer MG. 1982. Growing maize for genetic purposes. In Maize for biological research (ed. WF Sheridan), pp. 19–30. University Press, University of North Dakota, Grand Forks, ND.

Neuffer MG, Coe EH, Wessler SR. 1997. Mutants of maize. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Ohtsu K, Schnable PS. 2007a. Maize tissue preparation and extraction of RNA from target cells for genotyping. Cold Spring Harb Protoc doi: 10.1101/pdb.prot4784.[Abstract/Free Full Text]

Ohtsu K, Schnable PS. 2007b. T7-based RNA amplification for genotyping from maize shoot apical meristem. Cold Spring Harb Protoc doi: 10.1101/pdb.prot4785.[Abstract/Free Full Text]

Ohtsu K, Schnable PS. 2007c. SNP mining from maize 454 EST sequences. Cold Spring Harb Protoc doi: 10.1101/pdb.prot4784.[Abstract/Free Full Text]

Piperno DR, Flannery KV. 2001. The earliest archaeological maize (Zea mays L.) from highland Mexico: New accelerator mass spectrometry dates and their implications. Proc Natl Acad Sci 98: 2101–2103.[Abstract/Free Full Text]

Pohlman RF, Fedoroff NP, Messing J. 1984. The nucleotide sequence of the maize controlling element Activator. Cell 37: 635–643.[Medline]

Rabinowicz PD, Bennetzen JL. 2006. The maize genome as a model for efficient sequence analysis of large plant genomes. Curr Opin Plant Biol 9: 149–156.[Medline]

Rhoades MM. 1984. The early years of maize genetics. Annu Rev Genet 18: 1–29.[Medline]

Russell WK, Stuber CW. 1983. Effects of photoperiod and temperatures on the duration of vegetative growth in maize. Crop Sci 23: 847–850.

SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, et al. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765–768.[Abstract/Free Full Text]

SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. 1998. The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43–45.[Medline]

Scanlon MJ, Stinard PS, James MG, Myers AM, Roberston DS. 1994. Genetic analysis of 63 mutations affecting maize kernel development isolated from Mutator stocks. Genetics 136: 281–294.[Abstract]

Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, et al. 2002. Development and mapping of SSR markers for maize. Plant Mol Biol 48: 463–481.[Medline]

Slotkin RK, Freeling M, Lisch D. 2003. Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays. Genetics 165: 781–797.[Abstract/Free Full Text]

Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, Bennetzen JL, Messing J. 2004. Close split of sorghum and maize genome progenitors. Genome Res 14: 1916–1923.[Abstract/Free Full Text]

Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28: 286–289.[Medline]

Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, et al. 2004. Discovery of induced point mutations in maize by TILLING. BMC Plant Biol 4: 12. doi: 10.1186/1471-2229-4-12.[Medline]

Vollbrecht E, Sigmon B. 2005. Amazing grass: Developmental genetics of maize domestication. Biochem Soc Trans 33: 1502–1506.[Medline]

Wang CJ, Harper L, Cande WZ. 2006. High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18: 529–544.[Abstract/Free Full Text]

Weil CF, Monde RA. 2007. Getting to the point--mutations in maize. Crop Sci 47: S60–S67.

Wilson LM, Whitt SR, Ibanez AM, Rocheford TM, Goodman MM, Buckler ES. 2004. Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16: 2719–2733.[Abstract/Free Full Text]

Yu J, Buckler ES. 2006. Genetic association mapping and genome organization of maize. Curr Opin Biotech 17: 155–160.[Medline]