Comparative transcriptome analysis and phenotypic monitoring of Trifolium pratense (Fabaceae) under land use scenarios (TRATSCH II - Trifolium pratense RNA analysis to screen character heterogeneity)
Plant Genetics and Genomics
Plant Cell and Developmental Biology
Final Report Abstract
In the first funding phase transcriptome analysis revealed major transcriptional changes during regrowth after mowing of red clover. Furthermore, we developed a reduced complexity mRNA-GBS approach to combine population genetics and gene expression studies. In the second funding phase, we proposed to investigate a) the impact of mowing on the phenotypic appearance of the model plant Trifolium pratense L. by analysis of morphological and reproduction related characters; b) the intra-population and intra-specific genetic response variability across different land use scenarios by transcriptome fingerprinting; c) the transcriptomes generated from mown and non mown T. pratense plants to detect differentially expressed genes to functionally analyze them by using transgenic approaches. We identified regulatory genes related to growth response and compared these with transcriptome data sets to find regulatory genes differentially expressed between mown and non mown plants under controlled greenhouse conditions. We identified the orthologs of these 20 genes in Arabidopsis thaliana and selected those for which homozygous mutant lines were available and whose gene descriptions indicated that they were involved in phytohormone signaling, transcriptional regulation, or development, as well as a zinc transporter. Because no potential candidate genes were identified that showed statistically significant differences between mown (rosette leaf removal) and non mown plants, we focused on interpreting the results of the transcriptome analysis and generating data to more accurately describe the mowing response in the field than on conducting a transgenic approach. We developed a low-cost transcriptome analysis technique (mRNA-GBS) with reduced complexity, and analyzed red clover individuals from mown and non mown field samples (6 individuals of 3 sites each) on the Biodiversity Exploratories sites in a comparative approach. We determined that the number of read pairs per individual was too low to match against the T. pratense transcriptome, to perform comparative gene expression studies. However, by pooling individuals from each site we could map the sequences to an already published red clover genome and retrieved SNPs for population genetic analyses. To compare our results with population genetic patterns, we modified our work program and performed GBS on the same samples. GBS and pooled mRNA-GBS analysis revealed similar patterns. However, correlation with environmental effects was not possible because treatment-specific signals (e.g., mowed here) were overlaid by multiple environmental effects and correlations with environmental variables were too multifactorial to detect statistically sound signals (Gemeinholzer et al. submitted). We conducted a common garden approach to analyze phenotypic changes in T. pratense in response to repeated mowing, however, due to two very dry summer many plants did not survive. Consequently, we could not generate high-quality data following the T. pratense plants for three consecutive years in the field. The data of the first year resulted in a publication. The results obtained in this project are not of direct economic use. However, we show which mowing regime allows farmers the highest and most nutritious mowing regime for T. pratense.
Publications
- (2018) Cutting reduces variation in biomass production of forage crops and allows low-performers to catch up: A case study of Trifolium pratense L. (red clover). Plant Biology 20: 465-473
Herbert D, Ekschmitt K, Wissemann V, Becker A
(See online at https://doi.org/10.1111/plb.12695) - (2021) Common garden versus common practice – Phenotypic changes in Trifolium pratense L. in response to repeated mowing. Journal of Applied Botany and Food Quality 94:1-6
Gross T, Müller CM, Becker A, Gemeinholzer B, Wissemann V
(See online at https://doi.org/10.5073/JABFQ.2021.094.001) - (2021) Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). BMC Plant Biology 21:95
Herbert DB, Gross T, Rupp O, Becker A
(See online at https://doi.org/10.1186/s12870-021-02867-0) - GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.). bioRxiv
Gemeinholzer B, Rupp O, Becker A, Strickert M, Müller C-M
(See online at https://doi.org/10.1101/2021.11.30.470612)
