Abstract
Besides phenotypic data from field trials and molecular data from lab experiments, modern plant breeding programs generate a wide variety of data, for instance pedigree, randomization, geostatistical or climate data. Due to the lack of an integrated database system, breeders generally exploit only part of these data for selection decisions or retrieve only part of the information present in the data. Most approaches in genomics, however, develop their full power only when they are based on analyses of large numbers of genotypes from multiple crosses and current as well as past generations. We have developed a flexible data management and -analyses system for storage and quality control of plant breeding data. It is implemented using the PostgreSQL database management system and linked to the R software environment for integrated statistical analyses of phenotypic and genomic data. The database structure is capable of managing the following types of data observed in breeding programs of all major crops: (a) germplasm data of any species including pedigree data, (b) phenotypic data of any trait and trait complexity, (c) trial management data for any field and trial design, (d) molecular marker data for all common types of markers, as well as (e) project and study management data.
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References
Agrobase a database management and analysis system for agronomists, plant breeders, and plant researchers (http://www.agronomix.mb.ca/) Cited, 30.11.2006
Heckenberger M, Muminović J, Büchse A, Frisch M, Maurer HP, Melchinger AE, Möhring J, Piepho H-P, Reif JC, Stich B, Utz HF, Lichert F, Braun A, Breun J, Dreyer F, Ebmeyer E, Knopf E, Lübeck J, Schechert A, Stelling D, Streng S, Zacharias A, Wortmann H (2006) GABI-BRAIN: development and implementation of innovative statistical concepts and computational tools for integrating genomics research and applied plant breeding programs. Poster presented at the status seminar of the GABI-Community, 15/16th Feb 2006. Postdam, Germany
Heckenberger M, Muminović J, Van Der Voort JR, Peleman J, Bohn M, Melchinger AE (2006) Identification of essentially derived varieties obtained from biparental crosses of homozygous lines. III. AFLP data from maize inbreds and comparison with SSR data. Mol Breed 17:111–125
Lee JM, Davenport GF, Marshall D, Ellis THN, Ambrose MJ, Dicks J, Van Hintum TJL, Flavell AJ (2005) GERMINATE. A generic database for integrating genotypic and phenotypic information for plant genetic resource collections. Plant Physiol 139:619–631
Maurer HP, Melchinger AE, Frisch M (2007) Population genetical simulation and data analysis with Plabsoft. Euphytica (in press). doi:10.1007/s10681-007-9493-7
Piepho HP, Büchse A, Truberg B (2006) On the use of multiple lattice designs and α-designs in plant breeding trials. Plant Breed 125:523–528
Piepho HP, Möhring J, Melchinger AE, Büchse A (2007) BLUP for phenotypic selection in plant breeding and variety testing. Euphytica (in press). doi:10.1007/s10681-007-9449-8
Piepho HP, Möhring J (2006) On weighting in two-stage analysis of series of experiments. Biuletyn Oceny Odmian (awaiting approval by collaborating breeders of GABI-BRAIN)
PostgreSQL – (http://www.postgresql.org/) Cited 30. Nov (2006)
R Development Core Team (2004) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria, ISBN 3–900051-07-0, URL http://www.R-project.org
Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reif JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111:723–730
Stich B, Maurer HP, Melchinger AE, Frisch M, Heckenberger M, Van Der Voort JR, Peleman J, Sorensen AP, Reif JC (2006) Comparison of linkage disequilibrium in elite European maize inbred lines using AFLP and SSR markers. Mol Breed 17:217–226
Stich B, Melchinger AE, Piepho H-P, Heckenberger M, Maurer H, Reif J (2006) A new test for family-based association mapping with inbred lines from plant breeding programs. Theor Appl Genet 113:1121–1130
Utz HF (2001) Plabstat, ein Computerprogramm zur statistischen Analyse von pflanzenzüchterischen Experimenten, Version 2P vom 14. Juli 2001 (in German). Universität Hohenheim, Germany
Zhao W, Canaran P, Jurkuta R, Fulton T, Glaubitz J, Buckler E, Doebley J, Gaut B, Goodman M, Holland J, Kresovich S, McMullen M, Stein L, Ware D (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic acids res 34:752–757
Acknowledgements
The development of the Plabsoft database was funded by the German Federal Ministery of Education and research, Grant No. (0313126) “GABI-BRAIN” within the German genome research initiative “GABI”.
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Heckenberger, M., Maurer, H.P., Melchinger, A.E. et al. The Plabsoft database: a comprehensive database management system for integrating phenotypic and genomic data in academic and commercial plant breeding programs. Euphytica 161, 173–179 (2008). https://doi.org/10.1007/s10681-007-9478-3
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DOI: https://doi.org/10.1007/s10681-007-9478-3