From e77b936213b7d8d1a51dd6ee740b14e3341c70fa Mon Sep 17 00:00:00 2001 From: Gesa Helmsorig <gesa.helmsorig@hhu.de> Date: Wed, 13 Nov 2024 12:54:28 +0100 Subject: [PATCH] edited growth conditions / readme --- studies/MSA_dissection_eam7/README.md | 20 +++++++++++--- studies/biparental_mapping_eam7/README.md | 20 ++++++++++++++ .../README.md | 23 ++++++++++++---- ...iurnal_plant_material_growth_conditions.md | 9 ++++++- .../README.md | 25 +++++++++++++++++ ...iurnal_plant_material_growth_conditions.md | 10 +++++-- studies/phenotyping_eam7_plants/README.md | 27 +++++++++++++++++++ .../plant_material_growth_conditions.md} | 16 +++++------ studies/phenotyping_lwd1_mutants/README.md | 16 +++++++++++ .../plant_material_growth_conditions.md | 22 +++++++++++++++ 10 files changed, 169 insertions(+), 19 deletions(-) rename studies/{gene_expression_eam7_plants_diurnal/protocols/development_plant_material_growth_conditions.md => phenotyping_eam7_plants/protocols/plant_material_growth_conditions.md} (58%) create mode 100644 studies/phenotyping_lwd1_mutants/protocols/plant_material_growth_conditions.md diff --git a/studies/MSA_dissection_eam7/README.md b/studies/MSA_dissection_eam7/README.md index f010f9d..56f9b03 100644 --- a/studies/MSA_dissection_eam7/README.md +++ b/studies/MSA_dissection_eam7/README.md @@ -1,7 +1,21 @@ **dissection of main shoot apices (MSAs) to score the reproductive development of plants** -Scoring of the development according to: +Scoring of the development according to the Waddington Stage (Waddington et al., 1983). -Waddington SR, Cartwright PM, Wall PC. A quantitative scale of spike initial and pistil development in barley and wheat. Ann Bot. 1983:51(1):119–130. https://doi.org/10.1093/oxfordjournals.aob.a086434 -- assay "MSA_dissection" is applied to the plants \ No newline at end of file +**study overview** + +input: BW, BW(Ppd-H1), BW(eam7), BW(Ppd-H1,eam7) grown under SD and LD + + -> assay: MSA_dissection + output: - Waddington Stage by DAE + - spikelet meristem number by W-Stage + - floret number by W-Stage + + +Results can be found in Figure 1C-E, Supplemental Figure S1 and Supplemental Table S1. + + +**References** + +Waddington SR, Cartwright PM, Wall PC. A quantitative scale of spike initial and pistil development in barley and wheat. Ann Bot. 1983:51(1):119–130. https://doi.org/10.1093/oxfordjournals.aob.a086434 \ No newline at end of file diff --git a/studies/biparental_mapping_eam7/README.md b/studies/biparental_mapping_eam7/README.md index e69de29..aa86078 100644 --- a/studies/biparental_mapping_eam7/README.md +++ b/studies/biparental_mapping_eam7/README.md @@ -0,0 +1,20 @@ +**Biparental mapping to identify eam7** + +The F2 generation of a cross between BW(*eam7*) and BW(*Ppd-H1*) was used to identify and reduced the introgression area of *eam7* and to reduce the number of candidate genes to a minimum. CAPS marker were designed based on the 50k Illumina Infinium iSelect SNP Array (Bayer et al. 2017). + +**study overview** + +F2 plants and parents + + -> assay: biparental mapping + output: - CAPS marker results + - flowering time of F2 plants + - reduced introgression area + - target genes for eam7 + + +Results can be found in Figure 4, and Supplemental Tables S2, S3, S5. + +**References** + +Bayer MM, Rapazote-Flores P, Ganal M, Hedley PE, Macaulay M, Plieske J, Ramsay L, Russell J, Shaw PD, Thomas W, et al. Development and evaluation of a barley 50k iSelect SNP array. Front Plant Sci. 2017:8:1792. https://doi.org/10.3389/fpls.2017.01792 \ No newline at end of file diff --git a/studies/gene_expression_eam7_plants_diurnal/README.md b/studies/gene_expression_eam7_plants_diurnal/README.md index 7d0f2f0..2ad943b 100644 --- a/studies/gene_expression_eam7_plants_diurnal/README.md +++ b/studies/gene_expression_eam7_plants_diurnal/README.md @@ -4,10 +4,23 @@ Gene expression of CO1, ELF3, FT1, GI, LHY, LUX1, LWD1, PHYB, PHYC, Ppd-H1, PRR1, PRR59, PRR73, PRR95 and VRN1 were tested. -**The following assays were applied:** -1. leaf_sampling -2. RNA_extraction -3. cDNA_synthesis -4. qRT-PCR + +**study overview** + +input: 2-weeks old BW, BW(Ppd-H1), BW(eam7), BW(Ppd-H1,eam7) grown under SD + + -> assay: leaf_sampling + output: frozen leaf tissue (3 biol. replicates) + + -> assay: RNA_extraction + output: RNA samples + + -> assay: cDNA_synthesis + output: cDNA samples + + -> assay: qRT-PCR + output: gene expression data (2 techn. replicates) + + Results can be found in Figure 3 and in Supplemental Figure S3E. \ No newline at end of file diff --git a/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md b/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md index 25d595a..6e3d889 100644 --- a/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md +++ b/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md @@ -34,4 +34,11 @@ genotypes: ZT16 ZT18 ZT20 - ZT22 \ No newline at end of file + ZT22 + + +**References** + +Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, et al. Genetic dissection of barley morphology and development. Plant Physiol. 2011:155(2):617–627. https://doi.org/10.1104/pp.110.166249 + +Gol L, Haraldsson EB, von Korff M. Ppd-H1 integrates drought stress signals to control spike development and flowering time in barley. J Exp Bot. 2021:72(1):122–136. https://doi.org/10.1093/jxb/eraa261 \ No newline at end of file diff --git a/studies/gene_expression_lwd1_mutants_diurnal/README.md b/studies/gene_expression_lwd1_mutants_diurnal/README.md index e69de29..f2ef84c 100644 --- a/studies/gene_expression_lwd1_mutants_diurnal/README.md +++ b/studies/gene_expression_lwd1_mutants_diurnal/README.md @@ -0,0 +1,25 @@ +**Test diurnal gene expression of circadian clock and flowering time genes in *lwd1* mutants and WT plants** + +2-week old plants from the genotypes *lwd1-26*, *lwd1-390*, *lwd1-402*, and GP-fast were sampled at Zeitgeber Time (ZT) 0, 4, 8, 12, 16, and 20. + +Gene expression of CO1, ELF3, FT1, LUX1, LWD1, PHYB, PHYC, Ppd-H1, and PRR1 were tested. + +**study overview** + +input: input: 2-weeks old lwd1-26, lwd1-390, lwd1-402 and GP-fast plants grown under SD. + +-> assay: leaf_sampling + output: frozen leaf tissue (3 biol. replicates) + + -> assay: RNA_extraction + output: RNA samples + + -> assay: cDNA_synthesis + output: cDNA samples + + -> assay: qRT-PCR + output: gene expression data (2 techn. replicates) + + + +Results can be found in Figure 5D-L. \ No newline at end of file diff --git a/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md b/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md index 2edaabf..43e9ec0 100644 --- a/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md +++ b/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md @@ -1,4 +1,4 @@ -**eam7 diurnal expression: plant material and growth conditions** +**lwd1 mutants diurnal expression: plant material and growth conditions** **plant material* @@ -29,4 +29,10 @@ genotypes: ZT8 (lights are turned off) ZT12 ZT16 - ZT20 \ No newline at end of file + ZT20 + +**References** + +Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, et al. Genetic dissection of barley morphology and development. Plant Physiol. 2011:155(2):617–627. https://doi.org/10.1104/pp.110.166249 + +Gol L, Haraldsson EB, von Korff M. Ppd-H1 integrates drought stress signals to control spike development and flowering time in barley. J Exp Bot. 2021:72(1):122–136. https://doi.org/10.1093/jxb/eraa261 \ No newline at end of file diff --git a/studies/phenotyping_eam7_plants/README.md b/studies/phenotyping_eam7_plants/README.md index e69de29..1278a5e 100644 --- a/studies/phenotyping_eam7_plants/README.md +++ b/studies/phenotyping_eam7_plants/README.md @@ -0,0 +1,27 @@ +**Phenotype *eam7* plants under SD and LD conditions** + +Grow plants under short-day (SD) and long-day (LD) conditions. Score flowering time and phenotypic traits at flowering and at harvest when plants are fully dry. + +**study overview** + +input: BW, BW(Ppd-H1), BW(eam7), BW(Ppd-H1,eam7) grown under SD and LD + + -> assay: plant_phenotyping + output: + SD plants + - flowering time (in DAE) + - at flowering: plant height, leaf number, tiller number, flag leaf length/width + - at harvest (on main culm): spike length, floret and grain number, spike fertility + LD plants + - flowering time (in DAE) + - at flowering: plant height, leaf number, tiller number + - at harvest (on main culm): spike length, floret and grain number, spike fertility + + + +Results can be found in Figure 1A and B, Figure 2, and Supplemental Figure S2. + + +**References** + +Waddington SR, Cartwright PM, Wall PC. A quantitative scale of spike initial and pistil development in barley and wheat. Ann Bot. 1983:51(1):119–130. https://doi.org/10.1093/oxfordjournals.aob.a086434 diff --git a/studies/gene_expression_eam7_plants_diurnal/protocols/development_plant_material_growth_conditions.md b/studies/phenotyping_eam7_plants/protocols/plant_material_growth_conditions.md similarity index 58% rename from studies/gene_expression_eam7_plants_diurnal/protocols/development_plant_material_growth_conditions.md rename to studies/phenotyping_eam7_plants/protocols/plant_material_growth_conditions.md index cfb1c70..26fd61e 100644 --- a/studies/gene_expression_eam7_plants_diurnal/protocols/development_plant_material_growth_conditions.md +++ b/studies/phenotyping_eam7_plants/protocols/plant_material_growth_conditions.md @@ -1,24 +1,24 @@ -**eam7 developmental expression: plant material and growth conditions** +**Plant material and growth conditions** -**plant material* +**plant material** species: Hordeum vulgare -genotypes: +genotypes: - BW: Bowman, spring cultivar - BW(Ppd-H1): Ppd-H1 introgression line BW281 in BW background, Druka et al. (2011) - BW(eam7): eam7 introgression line BW281 in BW background, Druka et al. (2011) - BW(Ppd-H1, eam7): cross of the two introgression lines - **growth condtions** - short day (SD): 8h light / 16h dark, 20/16 °C, 60% humidity, ~ 250 PAR) +- long day: (LD) 16h light / 8h dark, 20/16 °C, 60% humidity, ~ 250 PAR) + - QuickPot E24/10 trays (HerkuPlast Kubern GmbH, pot volume 480 cm^3) - Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) -**sampling** -- always sample youngest, fully elongated leaf -- sample at ZT 9 (1h after lights turned off, as FT1 expression is highest) -- sample genotypes at 19, 26, 33, 40, 47 and 59 DAE \ No newline at end of file +**References** + +Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, et al. Genetic dissection of barley morphology and development. Plant Physiol. 2011:155(2):617–627. https://doi.org/10.1104/pp.110.166249 diff --git a/studies/phenotyping_lwd1_mutants/README.md b/studies/phenotyping_lwd1_mutants/README.md index e69de29..195ea39 100644 --- a/studies/phenotyping_lwd1_mutants/README.md +++ b/studies/phenotyping_lwd1_mutants/README.md @@ -0,0 +1,16 @@ +**Phenotype *lwd1* mutants under SD conditions** + +Grow *lwd* mutants and the wild-type GP-fast under short-day (SD) conditions. Score flowering time and phenotypic traits at flowering and at harvest when plants are fully dry. + +**study overview** + +input: lwd1-26, lwd1-390, lwd1-402, GP-fast (WT) + + -> assay: plant_phenotyping + output: + - flowering time (in DAE) + - at flowering: plant height, leaf number, tiller number + - at harvest (on main culm): spike length, floret and grain number, spike fertility + + +Results can be found in Figure 5A-C and Supplemental Figure S7. \ No newline at end of file diff --git a/studies/phenotyping_lwd1_mutants/protocols/plant_material_growth_conditions.md b/studies/phenotyping_lwd1_mutants/protocols/plant_material_growth_conditions.md new file mode 100644 index 0000000..659381a --- /dev/null +++ b/studies/phenotyping_lwd1_mutants/protocols/plant_material_growth_conditions.md @@ -0,0 +1,22 @@ +**Plant material and growth conditions** + +**plant material* + +species: Hordeum vulgare +genotypes: + +- GP-fast: WT, Ppd-H1 introgression line in Golden Promise background, lwd1 mutant background, Gol et al. (2021) +- lwd1-26: lwd1 mutant in GP-fast background, truncated protein of 26 aa +- lwd1-390: lwd1 mutant in GP-fast background, truncated protein of 390 aa +- lwd1-402: lwd1 mutant in GP-fast background, truncated protein of 402 aa + +**growth condtions** + +- short day (SD): 8h light / 16h dark, 20/16 °C, 60% humidity, ~ 250 PAR) +- QuickPot 96T trays (HerkuPlast Kubern GmbH, pot volume 75 cm^3) +- Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) + + +**References** + +Gol L, Haraldsson EB, von Korff M. Ppd-H1 integrates drought stress signals to control spike development and flowering time in barley. J Exp Bot. 2021:72(1):122–136. https://doi.org/10.1093/jxb/eraa261 \ No newline at end of file -- GitLab