diff --git a/assays/MiniPam/README.md b/assays/MiniPam/README.md index d1f7292062eef79ccf8a53e3d565bfb8a3172223..5b189df2b70bf3920144e6787b3b3b67f4ed0068 100644 --- a/assays/MiniPam/README.md +++ b/assays/MiniPam/README.md @@ -1,13 +1,34 @@ +#### Chlorophyll fluorescence + Fluorescence data was collected using a MINI-PAM-II fluorometer (Walz Heinz GmbH, Effeltrich, -Germany). To conduct measurements, the leaf clip was attached to a leaf and measurements of +Germany). + +**To conduct measurements:** + +- The leaf clip was attached to a leaf and measurements of photosynthetically active radiation (PAR) and the photosynthetic efficiency of photosystem II (PhiPSII) were -recorded. This was repeated ~10 times per plot. Each FI plot was followed by its RI plot counterpart. Plots of -blocks 1 and 4 were measured 49 days after sowing between 14:45 and 15:45. Plots of blocks 2 and 5 were +recorded. + +- This was repeated ~10 times per plot. + +- Each FI plot was followed by its RI plot counterpart. + +>**Plots of blocks 1 and 4 were measured 49 days after sowing between 14:45 and 15:45. Plots of blocks 2 and 5 were 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. The fluorescence kinetics of saturation pulse analyses for measurements wereinspected using WinControl-3 Software (version 3.29-rev.1112) (Walz Heinz GmbH, Effeltrich, Germany). +between 10:24 and 12:49.** + +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. PhiPSII values were clustered according to genotype, treatment and PAR level using custom R scripts. -PAR was divided into four levels: low (<500 μmol photons m -2 s -1 ), mid-low (500-1000 μmol photons m -2 s -1 ), -mid-high (1000-1500 μmol photons m -2 s -1 ) and high (>1500 μmol photons m -2 s -1 ). Agglomerative hierarchical -clustering was applied on the scaled PhiPSII means for all plots using the ‘agnes’ function of the R package -‘cluster’ [100] with a cut-off of five clusters. \ No newline at end of file + +**PAR was divided into four levels:** +- low (<500 μmol photons m -2 s -1 ),\ +- mid-low (500-1000 μmol photons m -2 s -1 ), +- mid-high (1000-1500 μmol photons m -2 s -1 ) and +- high (>1500 μmol photons m -2 s -1 ). + +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. + +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