PeanutMap: an online genome database for comparative molecular maps of peanut
© Jesubatham and Burow; licensee BioMed Central Ltd. 2006
Received: 07 April 2006
Accepted: 11 August 2006
Published: 11 August 2006
Molecular maps have been developed for many species, and are of particular importance for varietal development and comparative genomics. However, despite the existence of multiple sets of linkage maps, databases of these data are lacking for many species, including peanut.
PeanutMap http://peanutgenetics.tamu.edu/cmap provides a web-based interface for viewing specific linkage groups of a map set. PeanutMap can display and compare multiple maps of a set based upon marker or trait correspondences, which is particularly important as cultivated peanut is a disomic tetraploid. The database can also compare linkage groups among multiple map sets, allowing identification of corresponding linkage groups from results of different research projects. Data from the two published peanut genome map sets, and also from three maps sets of phenotypic traits are present in the database. Data from PeanutMap have been incorporated into the Legume Information System website http://www.comparative-legumes.org to allow peanut map data to be used for cross-species comparisons.
The utility of the database is expected to increase as several SSR-based maps are being developed currently, and expanded efforts for comparative mapping of legumes are underway. Optimal use of these data will benefit from the development of tools to facilitate comparative analysis.
Molecular maps are an important part of the genomics revolution. The use of DNA markers has expanded our knowledge of genetic linkage relationships considerably by removing the need for linkage to phenotypic markers. DNA-based maps were first developed in the 1980s , and have since expanded to encompass thousands of markers in some species [2–4]. Two RFLP-based maps of peanut have been published [5, 6], and the recent development of SSRs for peanut [7–10] is expected to result in rapid generation of additional maps.
Genetic markers have been developed for selection of qualitative traits and QTLs in multiple species. In peanut, DNA-based markers have been developed for nematode resistance, and were used for selection during of the final two generations of development of the variety 'NemaTAM' . In addition to being useful in selection programs, markers are useful for identification of biological relationships among accessions and species, and are an integral part of gene isolation by positional cloning  and ordered gene sequencing .
One of the most-important insights from genomics is the discovery of synteny among species of the same botanical family and, to a lesser extent, among different families. Comparative maps using genetic markers have demonstrated considerable similarity in chromosome structure and gene order among species in the same botanical family, with Poaceae being a striking example [14, 15]. Marker analysis of several legume species has also provided evidence for the conservation of gene order in Fabaceae . Conservation of gene order has been used in attempts to clone genes based on comparative information between species , and given insights into genome structure.
One of the limitations of genomics has been the lack of informatics resources for analysis of the large amounts of data produced, and for comparison of data among species. Databases exist for species of interest as model systems or having the greatest economic value, but are lacking in other species, including peanut. Among legumes, genome databases exist only for Glycine  and Medicago . As awareness of the significance of comparative genomics has increased, there is a trend towards databases encompassing data from multiple species. Gramene has incorporated data from maize and rice , and a cross-legume database, called the Legume Information System, is currently being developed to combine data from species-specific databases and permit cross-legume comparisons .
A large amount of the older species-specific data were held in either the AceDB-type databases  or proprietary databases. AceDB had the advantage that it was a database developed specifically for genomic data; however, the lack of structured query language and tools for comparative maps have made this type of database problematic for comparative genomics. Proprietary databases make use of commercial software, such as Oracle ; such databases are very powerful, but software licencing is prohibitively expensive for all but the largest research projects, and the software lacks built-in tools for genomics. Recently, the USDA and NIH have co-sponsored development of the GMOD  suite of open-source programs for genomics. This software runs on open-source databases such as MySQL  or PostGresSQL , and on multiple operating systems, including the open-source Linux operating system. Parts of the Gramene  and LIS  databases are utilizing or migrating to the GMOD-based software. The component of this software for maps is called CMAP .
One hindrance to the advancement of peanut genomics has been the lack of a genome database. Development of such a database would assist in the dissemination of genomic data, accelerate genomic research and varietal development, and foster comparative genomics with other legumes. In this paper, we present a new map database for peanut, called PeanutMap.
Construction and content
The installation of PeanutMap was done on a PC with SCSI hard drives set up for Ultra 160 RAID 1 mirroring, and running the Redhat Linux Advanced Server v. 3.0 operating system . The following software was installed before installing CMAP, with current versions listed after the software: libgd 2.0 , MySQL database v.4.0.20 , Perl v.5.8.0 , CPAN modules v. 1.390 , and Apache v. 2.0.46 . Libgd is the C graphics library used by CMAP. The MySQL structured query language database was installed as binaries, and serves as the relational database system for data storage and retrieval. The Perl programming language is needed for execution of CMAP. The CPAN shell was installed and used to download all the required CPAN Perl modules. The CPAN shell was allowed to check automatically for dependencies among Perl modules; however, modules that the CPAN shell failed to install were installed manually. The Apache Web Server was installed as binaries, and scripts that came packaged with Apache are used to start and stop the web server.
CMAP version 0.10 was installed as the core of the PeanutMap system; CMAP is a cgi (computer gateway interface) application written entirely in Perl The CMAP software  is open source, originally written for the Gramene project and is now part of GMOD . The locations for the cache, templates, and html documents were specified in the CMAP configuration file. Tables were then created for housing the CMAP data, using scripts that came with CMAP. A cronjob was written to remove the images from the cache folder on a daily basis.
The current data files were made in a multistage process. Linkage map data were entered in a Lotus 1-2-3 spreadsheet with columns in the order specified for CMAP. The data were exported in comma-separated variable format, and converted to tab-delimited ASCII files. The script supplied with the program was used to import the map data.
The datasets in PeanutMap have been made available to the Legume Information System, which is compiling map data from different legume species . This will permit data held in different legume databases to be used for comparison of synteny in gene order among different species.
PeanutMap is a useful addition to the tools for genetic mapping of peanut. It is the only peanut-specific genome database known to the authors. Several map sets are already present and available for use for mapping and for phenotypic analysis. It is expected that additional maps will be forthcoming, especially as SSR and SNP-based markers are mapped. We plan to update the database with additional genomic information as it becomes available.
Use of the SQL-formatted CMAP software will allow interoperability and data exchange with other genome databases, facilitating comparative mapping of peanut with other legumes and perhaps species outside the family. Incorporation of data from PeanutMap into the Legume Information System are an example of this.
PeanutMap is a graphics-oriented database that makes the current peanut map data available in a web-accessible format, and allows comparative mapping of linkage data. This will undoubtedly accelerate the pace and usefulness of mapping the peanut genome, and will further allow integration of different peanut maps and facilitate comparison of peanut and other legumes.
Availability and requirements
Bacterial Artificial Chromosome
Generic Model Organism Database
Legume Information Systems
National Institute for Health
Quantitative Trait Locus
Single Nucleotide Polymorphism
Single Sequence Repeats
Restriction Fragment Length Polymorphism
United States Department of Agriculture
Yeast Artificial Chromosome
This work was supported by an award "Accelerating Development of Peanut Varieties through Molecular Markers" from the National Peanut Board to M. B.
- Botstein D, White RL, Skolnick M, Davis RW: Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980, 32: 314–331.PubMed CentralPubMedGoogle Scholar
- Hudson TJ, Stein LD, Gerety SG, Ma J, Castle AB, Silva J, Slonim DK, Baptista R, Kruglyak L, Xu SH, Hu X, Colbert AME, Rosenberg C, Reeve-Daly MP, Rozen S, Hui L, Wu X, Vestergaard C, Wilson KM, Bae JS, Maitra S, Ganiatsas S, Evans CA, DeAndelis MM, Ingalls KA, Nahf RW, Horton LT Jr, Anderson MO, Collymore AJ, Ye W, Kouyoumjian V, Zemsteva IM, Tam J, Devine R, Courtney DF, Reynaud MT, Nguyen H, O'Connor TJ, Fizames C, Faur S, Gyapay G, Dib C, Morissette J, Orlin JB, Birren BW, Goodman N, Weissenbach J, Hawkins TL, Foote S, Page DC, Lander ES: An STS-based map of the human genome. Science 1995, 270: 1945–1954.View ArticlePubMedGoogle Scholar
- Menz MA, Klein RR, Mullet JE, Obert JA, Unruh NC, Klein PE: A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP, RFLP, and SSR markers. Plant Mol Biol 2002, 48: 483–499. 10.1023/A:1014831302392View ArticlePubMedGoogle Scholar
- Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, DelMonte TA, Ding X, Garza JJ, Marler BS, Park CH, Pierce GJ, Rainey KM, Rastogi VK, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao X, Zhu L, Paterson AH: A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission, and evolution of cotton ( Gossypium ). Genetics 2004, 166: 389–417. 10.1534/genetics.166.1.389PubMed CentralView ArticlePubMedGoogle Scholar
- Halward T, Stalker HT, Kochert G: Development of an RFLP linkage map in peanut species. Theor Appl Genet 1993, 87: 379–394. 10.1007/BF01184927View ArticlePubMedGoogle Scholar
- Burow MD, Simpson CE, Starr JL, Paterson AH: Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut ( Arachis hypogaea L.): broadening the gene pool of a monophyletic polyploid species. Genetics 2001, 159: 823–837.PubMed CentralPubMedGoogle Scholar
- Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD, Kresovich S: Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Sci 1999, 39: 1243–1247.View ArticleGoogle Scholar
- He G, Meng R, Newman M, Gao G, Pittman RN, Prakash CS: Microsatellites as DNA markers in cultivated peanut ( Arachis hypogaea L.). BMC Plant Biol 2003, 3: 3–8. 10.1186/1471-2229-3-3PubMed CentralView ArticlePubMedGoogle Scholar
- Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S: Microsatellite identification and characterization in peanut. ( A. hypogaea L.). Theor Appl Genet 2004, 108: 1064–1070. 10.1007/s00122-003-1535-2View ArticlePubMedGoogle Scholar
- Moretzsohn M, de Carvalho, Hopkins MS, Mitchell S, Kresovich S, Valls JFM, Ferreira ME: Genetic diversity of peanut ( Arachis hypogaea L ) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biology 2005, 4: 11–20. 10.1186/1471-2229-4-11View ArticleGoogle Scholar
- Simpson CE, Starr JL, Church GL, Burow MD, Paterson AH: Registration of 'NemaTAM' peanut. Crop Sci 2003, 43: 1561.View ArticleGoogle Scholar
- Martin GB, de Vicente MC, Tanksley SD: High-resolution linkage analysis and physical characterization of the Pto bacterial resistance locus in tomato. Mol Plant Microb Interact 1993, 6: 26–34.View ArticleGoogle Scholar
- The Arabidopsis Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2002, 408: 796–815. 10.1038/35048692View ArticleGoogle Scholar
- Moore G, Devos KM, Wang Z, Gale MD: Cereal genome evolution. Grasses, line up and form a circle. Curr Biol 1995, 5: 737–9. 10.1016/S0960-9822(95)00148-5View ArticlePubMedGoogle Scholar
- Bennetzen JL, Freeling M: The unified grass genome: synergy in synteny. Genome Res 1997, 7: 301–306.PubMedGoogle Scholar
- Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR: Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 2004, 101: 15289–15294. 10.1073/pnas.0402251101PubMed CentralView ArticlePubMedGoogle Scholar
- Miftahudin, Chikmawati T, Ross K, Scoles GJ, Gustafson JP: Targeting the aluminum tolerance gene Alt3 region in rye, using rice/rye micro-colinearity. Theor Appl Genet 2005, 906–913. 10.1007/s00122-004-1909-0Google Scholar
- Grant D, Imsande MI, Shoemaker RC: SoyBase, the USDA-ARS soybean genome database.2003. [http://soybase.agron.iastate.edu] verified Sept. 13, 2005Google Scholar
- Lamblin A-FJ, Crow JA, Johnson JE, Silverstein KAT, Kunau TM, Kilian A, Benz D, Stromvik M, Endré G, VandenBosch KA, Cook DR, Young ND, Retzel EF: MtDB: database for personalized data mining of the model legume Medicago truncatula transcriptome. Nucl Acids Res 2003, 31: 196–201. 10.1093/nar/gkg119PubMed CentralView ArticlePubMedGoogle Scholar
- Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L: Gramene: a resource for comparative grass genomics. Nucl Acids Res 2002, 30: 103–105. 10.1093/nar/30.1.103PubMed CentralView ArticlePubMedGoogle Scholar
- Gonzales MD, Archuleta E, Farmer A, Kajendran K, Grant D, Shoemaker R, Beavis WD, Wright ME: The Legume Information System (LIS) : an integrated information resource for comparative legume biology. Nucl Acids Res 2005, 33: D660-D665. 10.1093/nar/gki128PubMed CentralView ArticlePubMedGoogle Scholar
- Durbin R, Mieg JT: A C. elegans database. 1991. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.govGoogle Scholar
- Garcia GM, Stalker HT, Shroeder E, Kochert G: Identification of RAPD, SCAR, and RFLP markers tightly linked to nematode resistance genes introgressed from Arachis cardenasii into Arachis hypogaea . Genome 1996, 39: 836–845.View ArticlePubMedGoogle Scholar
- Burow MD, Starr JL, Simpson CE, Paterson AH: Identification of RAPD markers in peanut ( Arachis hypogaea ) associated with root-knot nematode resistance derived from A. cardenasii . Mol Breeding 1996, 2: 307–319. 10.1007/BF00437915View ArticleGoogle Scholar
- Choi K, Burow MD, Church G, Burow G, Paterson AH, Simpson CE, Starr J: Genetics and mechanism of resistance to Meloidogyne arenaria in peanut germplasm. J Nematol 1999, 31: 283–290.PubMed CentralPubMedGoogle Scholar
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