Maize doubled haploid (DH) technology provides fixed, pure lines from a donor parent. Protocols for breeding of DH lines are available for over 250 crop species, and over 300 DH-derived cultivars have been developed in 12 species worldwide (Forster and Thomas, 2005). In maize, methods for inducing, selecting and doubling haploid plants are advanced and are in widespread use. In a haploid plant, expression of positive or deleterious effects of genes for seed development, plant growth and function is unmasked, and plants that function effectively will have a better chance to grow to maturity and set seeds. Haploid plants that show good vigor in a natural environment will usually perform well as DH progenies under environmental stress. When doubled and brought to normal genetic balance, DH lines can be selected for agronomic traits, and testing can more accurately estimate yield potential and yield stability under different environments. The DH genome with its pure genetic makeup may still be challenged by environment in the absence of prior selective pressure. The characteristics of DH lines in theory are fixed and stable, and no further inbreeding depression should be observed from generation to generation, although spontaneous mutation or genomic changes caused by transposable elements cannot be avoided (Stadler 1951; Messing 2005).

Early genetic analyses of maize were rooted in genetic mapping, and mapping continues to be an important tool for contemporary maize geneticists. Mapping is extraordinarily easy in maize; consequently many maps have been made. The first genetic map published for maize in 1935 contained 62 loci defined by morphological variants. Current genetic maps contain thousands of loci defined by morphological, biochemical, cytogenetic, and molecular polymorphic variants. These maps serve critically important functions in linking genes to traits, facilitating comparative evolutionary studies, enabling positional cloning, and anchoring the physical map for genome sequencing. Sequencing in turn now makes it possible to derive the map locations of sequenced genes by matching to genomic sequences that have been anchored to the physical map.

Background Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required for BAC contig assembly from 80 to 50 percent. Finally, they validate assemblies based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy in combination with a high-throughput PCR-based screening method to anchor the maize genetic and physical maps. Results A total of 110,592 maize BAC clones (~ 6x haploid genome equivalents) were pooled into six different matrices, each containing 48 pools of BAC DNA. The quality of the BAC DNA pools and their utility for identifying BACs containing target genomic sequences was tested using 254 PCR-based STS markers. Five types of PCR-based STS markers were screened to assess potential uses for the BAC pools. An average of 4.68 BAC clones were identified per marker analyzed. These results were integrated with BAC fingerprint data generated by the Arizona Genomics Institute (AGI) and the Arizona Genomics Computational Laboratory (AGCoL) to assemble the BAC contigs using the FingerPrinted Contigs (FPC) software and contribute to the construction and anchoring of the physical map. A total of 234 markers (92.5%) anchored BAC contigs to their genetic map positions. The results can be viewed on the integrated map of maize [ 1 , 2 ]. Conclusion This BAC pooling strategy is a rapid, cost effective method for genome assembly and anchoring. The requirement for six replicate positive amplifications makes this a robust method for use in large genomes with high amounts of repetitive DNA such as maize. This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information.

Seventy-five years ago, a convincing demonstration that the genes were physically aligned along the chromosome was lacking. Harriet Creighton (1909-2004) and Barbara McClintock (1902-1992) [Creighton, H. B. & McClintock, B. (1931) Proc. Natl. Acad. Sci. USA 17, 492-497] showed by an elegantly simple experiment in 1931 that exchange between genes was accompanied by exchange of cytological, i.e., physical, parts of chromosomes. The work has been acclaimed as one of the great experiments in biology. Creighton's doctoral dissertation under McClintock's mentorship provided the basis for the landmark paper, which was unique in merging cytological with genetic data. A companion paper by McClintock, printed and bound back-to-back with the joint paper, set the essential stage with data on the cytological and genetic features that Creighton applied. Following directly from this work, and leading to today's recognition that the genome is a graspable entity, was the knowledge that the genes could be studied as components of a linear structure, the chromosome. Here, we review the data surrounding the Creighton and McClintock paper and provide a perspective on the significance of their findings.

IN the early 1920s, the Maize Genetics Cooperation (MGC) began in an informal way among R. A. Emerson and his students. His ethical and cooperative spirit paved the way for an expanded network of maize researchers who freely shared their materials and unpublished research, thus resulting in rapid progress in fundamental genetic research (Coe 2001; Kass and Bonneuil 2004). The first letter summarizing both published and unpublished maize linkage data was compiled by Emerson and his student George Beadle and sent to students of maize genetics on April 12, 1929. This communication was an outcome of a “cornfab” held in Emerson's hotel room in December 1928, during the annual American Association for the Advancement of Science (AAAS) meetings. The “Historical Notes on Maize Cooperation” identifies Emerson's 1929 communication as the first Maize Genetics Cooperation News Letter (MNL; Emerson 1940). Beadle was the first secretary of the MGC and he solicited material for additional summaries of linkage data, which were distributed in two parts in 1930. Rhoades succeeded Beadle as secretary and continued to summarize and publish the reports of cooperators in the MNL, which continues to be published annually. The cooperators met at the Sixth International Congress of Genetics (ICG) at Ithaca in 1932 and organized a committee to establish the maize stock center at Cornell University and to seek funding for their enterprise. Emerson's grant application to the National Research Council (NRC) was denied and he was encouraged to apply immediately to the Rockefeller Foundation (RF), who granted him funds to support his information and supply network in 1934. The work of Barbara McClintock in cooperation with Beadle, Rhoades, Creighton, Burnham, and others at Cornell between 1928 and 1934 resulted in a definitive correlation of chromosomes and linkage groups in maize—ultimately published in 1935 by Emerson et al. The cytogenetics of maize was also reviewed in that year (Rhoades and McClintock 1935). The exhibits that Emerson submitted to support his Rockefeller Foundation grant included a historical summary of the MGC and MNL. These documents allowed us to reconstruct the events that established these important resources for the maize genetics community. Emerson's legacy lives on in the cooperative spirit of maize researchers and in the News Letter he founded 75 years ago. At the 1932 ICG held in Ithaca, New York, Rollins Adams Emerson (Nelson 1993), Head of the Department of Plant Breeding at Cornell University, gave an opening address titled, “The Present Status of Maize Genetics.” In his introduction he declared, “I cannot refrain from noting here a very real advantage experienced by students of maize genetics … I am aware of no other group of investigators who have so freely shared with each other not only their materials but even their unpublished data. The present status of maize genetics, whatever of noteworthy significance it presents, is largely to be credited to this somewhat unique, unselfishly cooperative spirit of the considerable group of students of maize genetics” (Emerson 1932, p. 141; Kass 2001). During this Congress, Emerson called a meeting of ∼45 students of maize genetics and formalized what would soon be called the Maize Genetics Cooperation. Following their meeting Emerson and his graduate student Marcus Rhoades issued on October 5, 1932, what has long been considered the first Maize Genetics Cooperation News Letter (Rhoades 1932a). Our research (Bonneuil and Kass 2001; Coe 2001; Kass and Bonneuil 2004; E. H. Coe and L. B. Kass, unpublished results), which we offer in keeping with the long tradition of maize cooperation, provides a historical perspective on the actual origin of the MGC and the beginnings of the MNL, which was first issued in 1929. We present here the history of Emerson's successful negotiations with the Rockefeller Foundation to fund his cooperative enterprise at Cornell University following his unsuccessful attempt to obtain funding from the NRC. Future Nobel laureates George Beadle, Emerson's student, and Barbara McClintock, Lester W. Sharp's student and Beadle's collaborator, freely submitted their results to the MNL; this laid the groundwork for a similar publication, the Drosophila Information Service, for the Drosophila geneticists in March 1934 (Bridges and Demerec 1934) and for the Worm Breeders Gazette, the community newsletter of the roundworm biologists (Edgar 1975; Cohen 1995), among others. We rejoice in the founding of Emerson's ideal and celebrate the 75th anniversary of the MNL.

Resources for maize genetics and genomics exist in great depth and breadth. They can be brought to bear on its productivity, on selected properties, and on studies of genetic functions, mechanisms Of inheritance, phylogeny, and processes of change during domestication. Genetic materials available include the trait variations in tens Of thousands of diverse germplasm collections, and a readily accessible, 75-year collection of mutant variations. Descriptions of germplasms as well as of Mutant variations are available online. Maps of genes in diagrammatic and in tabulated form, accompanied by linked supportive data, have been updated recently. high-resolution genetic maps with molecular markers undergird physical mapping, anchoring and orienting contigs to the chromosomes. Physical mapping has progressed to the point that minimum tiling paths can be defined for the genome, the gene space is largely encompassed, and sequencing of the genome is ready to proceed.

The molecular basis of hybrid vigor (heterosis) has remained unknown despite the importance of this phenomenon in evolution and in practical breeding programs. To formulate a molecular basis of heterosis, an understanding of gene expression in inbred and hybrid states is needed. In this study, we examined the amount of various transcripts in hybrid and inbred individuals (B73 and Mo17) to determine whether the quantities of specific messenger RNAs were additive or nonadditive in the hybrids. Further, we examined the levels of the same transcripts in hybrid triploid individuals that had received unequal genomic contributions, one haploid genome from one parent and two from the other. If allelic expression were merely the additive value in hybrids from the two parents, the midparent values would be observed. Our study revealed that a substantial number of genes do not exhibit the midparent value of expression in hybrids. Instead, transcript levels in the diploid hybrids correlate negatively with the levels in diploid inbreds. Although transcript levels were clearly nonadditive, transcript levels in triploid hybrids were affected by genomic dosage.

Data retrieval, comprehension and sharing within and between plant-based databases are essential to exploit comparative genomic information to elucidate functional aspects of plant biology and to conduct studies of synteny and homology. However, the functionality is often hampered by the variability of terms used to describe comparable objects. The Zea mays Plant Structure Ontology database is designed to overcome this problem via the provision of a controlled vocabulary that facilitates knowledge sharing. It comprises international botanical terms, references, synonyms, and phylogenetic information and is open-source.

MOTIVATION Because of the unique biological features, a bioinformatic platform for the integrated genetic and physical map of maize is required for storing, integrating, accessing and visualizing the underlying data. RESULTS The goal of the Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display this integrated map, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer) and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers and bacterial artificial chromosome (BAC) contigs. The database also contains integrated information produced by applying a set of anchoring rules to assign BAC contigs to specific locations on the genetic map. The iMap Viewer and iMap Search functions are combined in the user interface to allow viewing and retrieving many types of genetic and physical map data. The iMap Viewer features side-by-side chromosome-based displays of the genetic map and associated BAC contigs. For each genetic locus, information about marker type or contig can be viewed via pop-up windows that feature links to external data resources. Searches can be conducted for genetic locus, probe or sequence accession number; search results include relevant map positions, anchored BAC contigs and links to the graphical display of relevant chromosomes. iMap can be accessed at http://www.maizemap.org AVAILABILITY The iMap utility package is available for non-commercial use upon request from the authors.

UNLABELLED:cMap, a www comparative genetic map graphical utility, has a search capability and provides comparison of two genetic maps within or between species with dynamic links to data resources and text lists of the shared loci, running in a relational database environment. Currently, maps from three species (maize 'Zea mays L.', rice 'Oryza sativa L.', and sorghum 'Sorghum bicolor L.'), representing over 13,800 distinct loci, are available for comparison at http://www.agron.missouri.edu/cMapDB/cMap.html. AVAILABILITY:cMap source code is available without cost on request for non-commercial use.

MOTIVATION:The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, researchers need an efficient way to interact with genetic mapping software and with data files from automated DNA sequencing. They also need ways to manage primer data for mapping and sequencing and provide views of the integrated physical and genetic map and views of genetic map comparisons.RESULTS:The MMP-LIMS system has been used successfully in a high-throughput mapping environment. The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers have been entered and verified via MMP-LIMS. The system is flexible, and can be easily modified to manage data for other species. The software is freely available.AVAILABILITY:To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.

Maize ( Zea mays ) is among the most important crop plants in the world. For any crop plant, an integrated genetic and physical map serves as the foundation for numerous studies, especially those aimed at improving the agronomic characteristics of the plant. Once a phenotypically defined locus

MaizeDB (http://www.agron.missouri.edu/) has existed since the early 90's as a genomespecific database that is grounded in genetic maps, their documentation and annotation. The database management system is robust and has continuously been Sybase. In this brief review we provide an introduction to the database as a functional genomics tool and new accesses to the data: 1) probe tables by bin location 2) BLAST access to map data 3) cMap, a comparative map graphical tool.

Crop plant research is poised to make revolutionary strides including the following: cloning target genes based on their function and/or their position in the genome; documenting all genes and their interplay; defining and exploring all the existing genetic diversity in a species; and using

Following several years of vigorous communication with co-workers in maize, Emerson et al. (1935) presented the first comprehensive maps, linkage data, and genetic descriptions for maize. Sharing of data and stocks, i.e., maize genetics cooperation, enabled M.M. Rhoades to construct the first linkage maps (Emerson et al., p. 71). These maps included phenotypic variants and a few reciprocal translocations. One pest resistance gene (rpl, resistance to Puccinia sorghi) had been placed to chromosome arm by deletion analysis, but no biochemically defined loci were yet identified. Accretion of sixty years of data on the 1935 foundation is reflected in the genetic linkage maps in Mutants of Maize (Neuffer et al. 1997).

Early geneticists, and generations since, have been drawn to maize to study basic questions, its curious phenomena and its practical applications. Part of the allure of this unique crop plant lies in the collegiality of the Maize Genetics Cooperation, extending all the way from the 'roaring twenties' of genetics to today.

For maize, we have analyzed conjointly the map locations reported to-date of genes for growth, development, and stress response. We find that these genes associate into functional clusters, 10–30 cM long, distributed non-randomly along all ten chromosomes. These clusters comprise the loci for environmental and hormonal sensors, the growth machinery genes (e.g., genes for the enzymes of hormone synthesis, mutations disturbing sporophyte and gametophyte development, or genes for programmed cell death) and the master genes presiding over the spatial and temporal transitions in cell growth and differentiation (e.g., genes expressing transcription factors). Taking into consideration mapping accuracy, the putative associations of developmental genes generally coincide with the location of homeotic genes mapped with cDNA probes. The majority of over 800 quantitative trait loci (QTLs) for plant architecture, growth and development in vivo and in vitro, the grain yield as the integer of growth, and ABA accumulation and effects, also map within these clusters. Several physiologically different quantitative traits of plant development and yield are often mapped by one and the same molecular probe. The clusters are redundant, apparently due to several duplication events in the course of maize evolution. We presume that these clusters are the functional units of genes expressed in concert to contribute toward regulating plant development and, apparently, some of the plant responses to abiotic stress. The major QTLs for plant height, earliness and grain yield are visible manifestations of the developmental clusters. The evolutionary and cytogenetic evidence seems to support the adaptive significance of functional gene networks for development. The physiological advantage of the close association of functionally related genes in the clusters may rely on compartmentation and tunneling of signal molecules, which helps to cooperatively recruit the transcription factors into multicomponent regulatory modules of high specificity.

Publisher SummaryThe U.S. Congress appropriated funds in 1991 for the USDA Plant Genome Research Program, four years after its initial conception in 1987. The goal of the USDA Plant Genome Research Program is to improve plants (agronomic, horticultural, and forest tree species) by locating marker DNA or genes on chromosomes, determining gene structure, and transferring genes to improve plant performance with accompanying reduced environmental impact to meet marketplace needs and niches. The Plant Genome Research Program is one program with two parts: National Research Initiative and Plant Genome Database (PGD). The PGD is now a real and functioning information and data resource for agricultural and other plant science genome researchers, and it is in the public domain. Additional progress is given according to major plant groups. The PGD is a suite of several information products produced at the National Agricultural Library (NAL) in collaboration with the Agricultural Research Service and Forest Service species coordinators.

Genetic and biotechnological knowledge in maize, and its applications, will be enhanced by prompt availability of data in personal databases and in the Maize Genome Database. Guidelines are offered for systematic documentation of descriptions for mutant variations (i.e., stages affected, body parts, and expressions), and of mapping data.