Research Interest
Head: PD Dr. Renate Schmidt
Genetic analysis of seed traits in Arabidopsis thaliana
We are interested to study genetic factors with an impact on the trait seed yield in Arabidopsis thaliana. Populations of recombinant inbred lines and near-isogenic lines are used to determine characters such as seed weight, seed size, seed number per silique and seed yield per plant. Loci of importance for these traits are identified via the mapping of quantitative trait loci. In order to gain a first insight which factors may underlie the traits of interest, genome-wide transcript profiles at a defined stage of seed development were established for recombinant inbred lines and used for the identification of gene expression QTL. These activities contribute to the IPK research theme FSP4 “Growth and metabolism”.
Transgene silencing in Arabidopsis thaliana
Silencing of introduced genes is often observed in transgenic plants. A systematic analysis of transgene expression in Arabidopsis thaliana showed that post-transcriptional transgene silencing is triggered by excessive transcript levels (S-PTGS). The transgene expression level correlates with the probability that S-PTGS is initiated early in plant development. The study of progeny of plants with silenced transgenes showed that the silenced state is not transmitted to the next generation, instead silencing has to be established in each generation anew. In order to study the impact of natural variation on this process, sequence variation of genes involved in S-PTGS and/or other RNA silencing pathways is surveyed. Moreover, monitoring of S-PTGS in introgression lines is used for the identification and characterisation of silencing modulators in Arabidopsis thaliana accession genomes.
The impact of duplications in the oilseed rape genome
Polyploidy is widespread in the plant kingdom. We are therefore interested to trace the fate of duplicated regions in the course of evolution. We use the allopolyploid species Brassica napus (oilseed rape) to study the arrangement, structure and expression of duplicated genes in selected regions of the rapeseed genome. A PCR-based screening platform of an oilseed rape BAC library enables quick access to regions of interest in the rapeseed genome. Furthermore, we determine the allelic diversity of selected genes in a broad set of oilseed rape accessions.
Publications
Boudichevskaia A, Cao H X, Schmidt R:
Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach. Plant Cell Rep. 36 (2017) 1323-1332. https://dx.doi.org/10.1007/s00299-017-2157-5
Jiang Y, Schmidt R H, Zhao Y, Reif J C:
A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat. Nat. Genet. 49 (2017) 1741-1746. https://dx.doi.org/10.1038/ng.3974
Knoch D, Riewe D, Meyer R C, Boudichevskaia A, Schmidt R, Altmann T:
Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. J. Exp. Bot. 68 (2017) 1655-1667. https://doi.org/10.1093/jxb/erx049
Analysis of sense transgene-induced gene silencing in introgression lines reveals thepresence of silencing modulators in Arabidopsis thaliana accession genomes. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Naturwissenschaftliche Fakultät I Biowissenschaften (2017) 168 pp.
Schmidt R, Boudichevskaia A, Cao H X, He S, Meyer R C, Reif J C:
Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays. Plant Cell Rep. 36 (2017) 1871-1881. https://dx.doi.org/10.1007/s00299-017-2200-6
Tran T D, Šimková H, Schmidt R, Doležel J, Schubert I, Fuchs J:
Intergenomic single nucleotide polymorphisms as a tool for bacterial artificial chromosome contig building of homoeologous Brassica napus regions. BMC Genomics 15 (2014) 560. https://dx.doi.org/10.1186/1471-2164-15-560
Kempe K, Boudichevskaia A, Jerchel R, Pescianschi D, Schmidt R, Kirchhoff M, Schachschneider R, Gils M:
Perspectives on genetics and genomics of the Brassicaceae (Chinese translation from English language edition 2011). In: Schmidt R, Bancroft I (Eds.): Genetics and genomics of the Brassicaceae (Chinese translation from English language edition 2011). (Series: Plant genetics and genomics: crops and models, Vol. 9) New York, NY [u.a.]: Springer (2013) ISBN 978-1-441-97117-3, 617-632.
Schmidt R, Bancroft I (Eds.):
Genetics and genomics of the Brassicaceae (Chinese translation from English language edition 2011). (Series: Plant genetics and genomics: crops and models, Vol. 9) New York, NY [u.a.]: Springer (2013) ISBN 978-1-441-97117-3, 677 pp.
Town C, Schmidt R, Bancroft I:
Comparative genome analysis at the sequence level in the Brassicaceae (Chinese translation from English language edition 2011). In: Schmidt R, Bancroft I (Eds.): Genetics and genomics of the Brassicaceae (Chinese translation from english language edition 2011). (Series: Plant genetics and genomics: crops and models, Vol. 9) New York, NY [u.a.]: Springer (2013) ISBN 978-1-441-97117-3, 171-194.
Meyer R C, Witucka-Wall H, Becher M, Blacha A, Boudichevskaia A, Dörmann P, Fiehn O, Friedel S, von Korff M, Lisec J, Melzer M, Repsilber D, Schmidt R, Scholz M, Selbig J, Willmitzer L, Altmann T:
Perspectives on genetics and genomics of the Brassicaceae. In: Schmidt R, Bancroft I (Eds.): Genetics and genomics of the Brassicaceae. (Series: Plant genetics and genomics: crops and models, Vol. 9) New York, NY [u.a.]: Springer (2011) ISBN 978-1-441-97117-3, 617-632. https://dx.doi.org/10.1007/978-1-4419-7118-0_23
Schmidt R, Bancroft I (Eds.):
Genetics and genomics of the Brassicaceae. (Series: Plant genetics and genomics: crops and models, Vol. 9) New York, NY [u.a.]: Springer (2011) ISBN 978-1-441-97117-3, 677 pp.
Town C, Schmidt R, Bancroft I:
Comparative genome analysis at the sequence level in the Brassicaceae. In: Schmidt R, Bancroft I (Eds.): Genetics and genomics of the Brassicaceae. (Series: Plant genetics and genomics: crops and models, Vol. 9) New York, NY [u.a.]: Springer (2011) ISBN 978-1-441-97117-3, 171-194. https://dx.doi.org/10.1007/978-1-4419-7118-0_6
Fischer U, Kuhlmann M, Pecinka A, Schmidt R, Mette M F:
Ecke W, Lange M, Schmidt R, Bach K, Dietrich E, Snowdon R, Link K, Ouzunova M, Breuer F, Stelling D, Hauska D, Leckband G, Dreyer F, Detering J, Duscherer P, Horn W, Tuvesson S:
GABI-Bridge: Die Brücke von Sequenz zu Ölgehalt und Resistenz: DNA-Unterschiede kontrollieren agronomisch wichtige Merkmale bei Raps. GenomXPress Sonderausgabe März (2007) 32.
Nasrallah J B, Liu P, Sherman-Broyles S, Schmidt R, Nasrallah M E:
Bancroft I, Barnes S, Li J, Meng J, Qiou D, Schmidt R, Trick M, Wilmer J:
Establishment of an integrated marker system for oilseed rape breeding (IMSORB). In: Lim Y P (Ed.): Proceedings of the joint meeting of the XIVth Crucifer Genetics Workshop and IVth ISHS Symposium on Brassicas: Daejeon, Korea, October 24 - 28, 2004. (Series: Acta Horticulturae, Vol. 706) Leuven: ISHS (2006) ISBN 978-90-66054-45-5, 195-202.
Lysak M A, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I:
Qiu D, Morgan C, Shi J, Long Y, Liu J, Li R, Zhuang X, Wang Y, Tan X, Dietrich E, Weihmann T, Everett C, Vanstraelen S, Beckett P, Fraser F, Trick M, Barnes S, Wilmer J, Schmidt R, Li J, Li D, Meng J, Bancroft I:
Comparative structural genome analysis - transfer of data across species. In: Freitag J (Ed.): Plant genomics and bioinformatics expression micro arrays and beyond: a course book (European Training and Networking Activity). Potsdam-Golm: MPI-MPP (2006) 16-29.
Gene-Silencing in transgenen Pflanzen. Tätigkeitsbericht 2006. Max-Planck-Institut für Molekulare Pflanzenphysiologie. Potsdam. Max-Planck-Gesellschaft. In: Jahrbuch. München: MPG (2006)