assays/Phenology/README.md

+#### Phenology
+
+Over the course of the growing season, plots were regularly inspected and phenology was determined visually according to the extended BBCH scale [1].
+
+
+
+**BBCH table: from Phenological growth stages of quinoa (Chenopodium quinoa Willd.) based on the BBCH scale. DOI: 10.1111/aab.12358**
+| BBCH Code (two digit) | Description |
+| :---: | ------ |
+|Principal growth stage 0: germination 
+| 00 | Dry seed |
+| 01| Initiation of seed imbibition |
+|03 | Seed imbibition completed
+|05 |Radicle emergence from seed| 
+|07 |Emergence of hypocotyl |
+|08 | Hypocotyl with cotyledons growing towards soil surface||09 | Emergence of cotyledons through soil| 
+| Principal growth stage 1: leaf development|
+|10 | Cotyledons fully emerged|
+|11 | First pair of leaves visible|
+|12 | Second pair of leaves visible|
+|1. | Coding continues with the same scheme|
+|19 | Nine pair of leaves visible. If required, coding can continue following the same scheme.|
+|Principal growth stage 2: formation of side shoots|
+|20 | Visible lateral buds or expanded leaves without lateral stems| 
+|21 | One side shoot visible| 
+|22 | Two side shoots visible| 
+|2. | Coding continues with the same scheme|
+|29 | Nine side shoots visible. If required, coding can continue following the same scheme.|
+|Principal growth stage 3: stem elongation (omitted)| |
+|Principal growth stage 4: development of harvestable vegetative parts (omitted)|
+|Principal growth stage 5: inflorescence emergence| |
+|50 | Inflorescence present but still enclosed by leaves|
+|51 | Leaves surrounding inflorescence separated, inflorescence is visible from above|
+|59 | Inflorescence visible, but all the flowers are still closed|
+|Principal growth stage 6: flowering|
+|60 | Beginning of anthesis: main inflorescence flowers with first extruded anthers|
+|67 | Early end of anthesis: main inflorescence flowers with first senesced anthers|
+|69 | Complete anthesis: main inflorescence flowers with senesced anthers|
+|Principal growth stage 7: fruit development|
+|70 | Fruit set: ovary thickening and first visible grains in the main stem|
+|Principal growth stage 8: ripening| | 
+|81 | Milky grain, easily crushed with fingernails, liquid content and green pericarp|
+|85 | Thick grain, easily crushed with fingernails, white pasty content, green, beige, red or black pericarp|
+|89 | Ripe grain, difficult to crush with fingernails, dry content, the grain has a beige, red or black colour on its outside. Ready to harvest.|
+|Principal growth stage 9: senescence| |
+|91 | Only basal leaves are dry|
+|93 | Leaves of the first half portion of the plant, starting from the base, are dead|
+|95 | All leaves are dead; stem colour turns from yellow to brown|
+|97 | Plant dead and dry|
+|99 | Harvested product |
+
+
+
+Reference:
+
+[1] Sosa-Zuniga, V.; Brito, V.; Fuentes, F.; Steinfort, U. Phenological growth stages of quinoa (Chenopodium quinoa) based on the BBCH scale. Ann Appl Biol 2017, 171, 117-124. DOI: 10.1111/aab.12358
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assays/Relative_Water_Content/README.md

+#### Leaf relative water content
+
+
+- An approximately 1 cm 3 section of leaf was sampled from each plot
+and transferred to a pre-weighed Eppendorf tube. 
+
+- The tubes were then reweighed, filled with MilliQ water
+and left at 4 °C overnight. 
+
+- The following morning, the turgid leaf section was removed from the tube, carefully dried with a paper towel and reweighed. 
+
+- Samples were then placed back into the emptied
+Eppendorf tubes and placed in an oven at approximately 70 °C overnight. 
+
+- Once leaf sections were completely
+dry, the tubes containing the leaf samples were reweighed. 
+
+
+- The empty tube weight was subtracted from the
+fresh weight and dried weight measurements and relative water content (RWC, %) was calculated using the
+equation:
+
+$$RWC = \frac{fresh~weight - dry~weight}{turgid~weight - dry~weight} ~x ~100 $$ 
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assays/Weather_Data/README.md

+#### Weather Data
+
+Weather data over the course of the field experiment from 26 September 2019 to 28 February 2020 collected by a meteorological station at the INIA-Huasco experimental center in the southern Atacama Desert (Vallenar, Chile, 28°34′ S, 70°47′ W and 469 m.a.s.l.) 300 m from the field trial and by soil sensors in the field trial;
+
+
+<img src= "Dumschott_et_al_Weather_Data.png" alt="Weather Data" width= "500">
+
+
+ (a) daily maximum and night mean temperature; <br> (b) daily maximum vapor pressure deficit (VPD);<br> (c) daily total radiation;<br> (d) daily mean volumetric soil water content (VSWC). <br>
+ 
+ >**The full irrigation and reduced irrigation treatments started at branching (35 days after sowing), but the sensor data were only available from 40 days after sowing. The colors in the figure represent the respective quinoa developmental stages.**
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studies/ExperimentalSetup/README.md

+# Experimental Setup
+
+**Field Trial Location:** 
+- The trial took place at the INIA-Huasco experimental center located in the southern Atacama Desert (Vallenar, Chile, 28°34′ S, 70°47′ W and 469 m.a.s.l.) during the 2019/2020 growing season (sowing on 26 September 2019, harvest on 21 February 2020).
+- The Atacama desert is one of the driest regions in the world, ensuring that rainfall would not influence the irritation treatment of the experiment.
+
+**Soil Characteristics:** 
+- Sandy loam textural class, composed of sand (75.5%), silt (10.9%) and clay (13.7%), with a low organic matter content (2.0%), an alkaline pH (8.1), slight salinity (2.4 dS m−1), and with a basic content of N-P-K (45-21-311 mg kg−1 respectively)
+
+**Experimental Design:**
+- Nine coastal lowland self-pollinated quinoa lines (CLS-1 to CLS-9) and one commercial cultivar (cv Regalona)
+- Plots here 2 x 4 m and contained four rows of quinoa with an inter-row spacing of 0.5 m
+- Three plots of each line were sown for each treatment.
+- Seeds were sown at a density of 15 kg ha−1 with >85% germination.
+- Two treatments: 
+    - <ins>Full Irrigation (FI):</ins> Considered the reposition of ET<sub>0</sub> and the lack of a crop coefficient (K<sub>c</sub>) for quinoa growing in the region.
+    - <ins>Reduced Irrigation (RI):</ins> Defined a severe reduction of irrigation time (50%) and kept the same schedule as for the full irrigation treatment (every second or third day) by means of pressurized drip lines. RI treatment started at growth stage 20 (branching, extended BBCH).
+- Fertilizer was provided at sowing (75-120-60 N-P-K) and an additional 75 N was provided at growth stage 12 (second pair of leaves visible, extended BBCH).
+- Chlorothalonil (2 L ha−1 BRAVO 720, Syngenta) was applied from growth stage 16 (six pairs of leaves visible, extended BBCH) to manage disease.
+
+
+## Figure: Field trial plot layout
+
+![Quinoaplots](quinoa_trialplots.png)
+
+## Data Collected & Corresponding Assays
+
+#### Data recorded throughout the trial included:
+
+- **Weather data:** Collected via meteorlogical station located at the INIA-Huasco experimental setup, approximately 200 meters from the trial.
+    -  See Assay: [Weather_Data](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Weather_Data?ref_type=heads)    
+
+- **Soil sensors:** Recorded volumetric water content and temperature (located at the yellow stars in the figure above).
+     -  See Assay: [Weather_Data](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Weather_Data?ref_type=heads)
+
+- **Phenology:** Determined visually via regular inspections of the trial using the extended BBCH scale by Sosa-Zúñiga et al. 2017 [1].
+    - See Assay: [Phenology](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Phenology?ref_type=heads) 
+
+#### Data Collected at the visible inflorescence stage of development (BBCH 59); 46-50 days after sowing:
+
+- **Morphological traits:** Collected for all plots of both treatments on day 47 and included measurements such as plant height and stem diameter.
+
+     -  See Assay:
+ - **Leaf relative water content:** Collected for all plots of both treatments on day 47.
+    -  See Assay: [RelativeWaterContent](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/RelativeWaterContent?ref_type=heads)    
+
+
+
+## References
+
+[1] Sosa-Zuniga, V.; Brito, V.; Fuentes, F.; Steinfort, U. Phenological growth stages of quinoa (Chenopodium quinoa) based on the BBCH scale. Ann. Appl. Biol. 2017, 171, 117–124. 
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