diff --git a/assays/MiniPam/README.md b/assays/MiniPam/README.md index 46c486c63561179d66f52118890888610d2b4781..ec7b7beea5c71e83726b0e70e491d6be3664480f 100644 --- a/assays/MiniPam/README.md +++ b/assays/MiniPam/README.md @@ -1,4 +1,6 @@ -#### Chlorophyll fluorescence +# Chlorophyll fluorescence + +## Assay Description and Instrumentation Fluorescence data was collected using a MINI-PAM-II fluorometer (Walz Heinz GmbH, Effeltrich, Germany). @@ -8,7 +10,7 @@ Germany). <img src="Quinoaimage4.jpeg" width="40%" /> </p> -**To conduct measurements:** +### Protocol - The leaf clip was attached to a leaf and measurements of photosynthetically active radiation (PAR) and the photosynthetic efficiency of photosystem II (PhiPSII) were @@ -22,8 +24,11 @@ recorded. measured 48 days after sowing between 15:00 and 17:00. All blocks were measured 50 days after sowing between 10:24 and 12:49.** +### Calibration and Quality Control The fluorescence kinetics of saturation pulse analyses for measurements were inspected using WinControl-3 Software (version 3.29-rev.1112) (Walz Heinz GmbH, Effeltrich, Germany). Measurements that did not pass inspection were discarded from subsequent analyses. + +### Data Processing PhiPSII values were clustered according to genotype, treatment and PAR level using custom R scripts. **PAR was divided into four levels:** @@ -34,6 +39,15 @@ PhiPSII values were clustered according to genotype, treatment and PAR level usi Agglomerative hierarchical clustering was applied on the scaled PhiPSII means for all plots using the ‘agnes’ function of the R package ‘cluster’ [1] with a cut-off of five clusters. +### Software and tools + +- WinControl-3 Software (version 3.29-rev.1112) (Walz Heinz GmbH, Effeltrich, Germany) +- R (with package 'cluster') + +### Assay Date + +This assay was performed at the visible inflorescence stage of development (BBCH 59); 46-50 days after sowing + Reference: [1] Maechler, M.; Rousseeuw, P.; Struyf, A.; Hubert, M.; Hornik, K.; Studer, M.; Roudier, P.; Gonzalez, J.; Kozlowski, K.; Schubert, E.; et al. “Finding Groups in Dataâ€: Cluster Analysis Extended Rousseeuw et al. Available online: https://cran.r-project.org/web/packages/cluster/cluster.pdf (accessed on 26 February 2021). \ No newline at end of file