Field/Greenhouse Notebook¶
Shantel A. Martinez | Updated 2018.11.16¶
This Field/Greenhouse Notebook contains notes, data, and protocols for field and greenhouse work that are not included in the other specific notebooks. When topics overlap, links to other notebooks were added for reference.
TABLE OF CONTENTS:
General Protocols
Spike wetting test
Cayuga/Caledonia BC1Fx Population
BC1F7 Field Emergence
2018 PHS Field Notes and Files
2019 Planting Prep
Field and Greenhouse Granary Photo Album
Flowering Date Estimate¶
Typically in this program, they use Heading date + 3 days for flowering date. Of course, it varies from line to line, but in general, its a good estimate to add 3 days to HD.
Additional BC to Cayuga and Caledonia¶
James T. made additional backcrosses to both Cayuga and Caledonia. Double check, but he thinks he made the crosses to BC1 lines that had the 'other' parents 2B QTL region. Meaning, Cayuga x 18872, where 18872 has the Caledonia 2B QTL genotypes.
| Female | Male | No Kernels | Cross Date |
|---|---|---|---|
| Cayuga | 278-3 | 4 | 2018.07.25 |
| Caledonia | 1703-4 | 6 | 2018.06.18 |
| Caledonia | 179-4 | 1 | 2018.07.17 |
| Caledonia | 1905-1 | 10 | 2018.06.15 |
| Caledonia | 1325-3 | 11 | 2018.07.25 |
| Caledonia | 1887-2 | 7 | 2018.07.16 |
We will plate them in a petri dish this November (date) to germinate. Vernilize for 8 weeks in the fridge because there is limited space in the Vrn chamber. Leaf tissue will NOT be harvested for DNA extraction since the leaf DNA will be heterozygous.
2019 CC BC1F8 Planting
| Population | Field | Entries | Pl. Date | Plot No. |
|---|---|---|---|---|
| BC1F8 PHS 1 | Caldwell 7 | 433 | 2018.10.26 | 1-433 |
| BC1F8 PHS 2 | McGowen 6 | 433 | 2018.11.08 | 501-933 |
2018.10.16
TO: David and Amy
I've reviewed the planting file called CCBC1_Source_Plot-db, it looks great. It is very clear which lines have GH material and which do not.
It looks like, based on your comment below about the 2-6g being good to plant, that 322 BC1 lines + the 2x6 parents are ready to go. Which leaves the remainder <2g and noGH seed material needing more seed. I have added in column 11 (just for clarification and sorting) the lines that need seed from the 2018 field material. Is that still a go ahead to subsample from that material? Even though it is sprouted, it at least is something... some lines may not even be worth it if its sprouted so bad?
Also, there are 10 lines that are duplicates in 2018 for a reason I am not exactly sure. I believe there was probably a reason at one time, but I will omit them from this years planting, since the GH source is not differentiated between one versus the second rep. So in column 10, I added the info for which lines to omit.
That will leave a total of 431 lines plus the 12 parents for plantings. This is assuming we can get decent seed for that extra 109 BC1 lines. If we cant find any seed, just make a note in the file.
2018.10.01
TO: David and Amy
I left the material I did harvest, thresh, clean, and weighed into envelopes from the greenhouse material for the 2019 planting.
There are two sets:
- one set has the total 6-8 gram amount per entry needed to fill the 2 location headrow trays (3-4g per loc). This is the left stack of 3 boxes.
- the other set is less than 6 grams, so not enough seed to fill up both hr trays. This is because the plants in the gh did not yield enough seed, if any seed at all. This is the right stack of 2 boxes.
Within each set, they are ordered by 'Source' order. However, the <6g unfinished subset needs more seed. The only other seed source I have is from the 2018 field material that got rained on. So as you are filling the hr trays, you can bring the final weight to 8 grams by adding in 'ungerminated' seed (as best as you can, since the PHS was bad) from the field material to that designated entry/source of the already subsetted gh material. Ive added a reference table called CCBC1_Source_Plot with the source number next to the 2018 snyder plot number and the 2018 helfer plot number.
Unfortunately I didnt have time to organize the field hr envelopes by source number, but they are together in 2 harvest boxes in the barn. You can call me if you need direction when I left them in August (oh so long ago haha).
I gave you the source of all of my greenhouse Cayuga and Caledonia parent. Use what is needed to plant and I will keep the remainder.
Also, when you are done with these envelopes, Keep them aside for me, because I am going to record how much GH seed (in grams) was used for the 2019 planting, which also indicates if/how much field material was used.
There were also duplicate families/sources used in the 2018 GH and field material, I left them in the sheet attached, but crossed the out. Lets just plant the one of the two duplicates.
That leaves 434 entries + duplicated parents throughout each location for 2019 hr planting.
PHS Event¶
July 23rd - 24th, 2018 there was a natural rain event at both Helfer and Snyder. This was post PM harvest, however, all of the remaining headrows were still in the field.
Unfortunately, both location populations sprouted very badly, with Helfer being the worst, since it matured earlier. The headrows are harvested anyways as a 'worst-case-scenerio' seed source. However, many lines were sowing coleoptiles and seed protruding out of the glooms.
Harvest¶
2018.07.27
The CC BC1 lines from both Helfer and Snyder were harvested by hand and the intact spikes were bundled using tags. They were put in drying racks for 3 days.
First 2 weeks of Aug
The CC BC1 lines were belt threshed in order to store in smaller envelopes. They were stored in the Barn at ambient temperature.
FHB Notes on CC BC1 Population¶
Caledonia is susceptible to Fusarium Head Blight. The Cay/Cal BC1F7 populations at Helfer and Snyder were not protected this year with fungicide (by accident). I noticed on 07/04/2018 that there were symptoms on some lines at Helfer.
Notes were not taken, but make sure I keep this information in mind when I analyze the data.
Heading Dates 2018¶
CC BC1F7-18_SM.xlsx data file | Julian Date Calendar Reference
| Date | Helfer | Syder | Parents |
|---|---|---|---|
| Julian | Freq. | Freq. | 6 rep avg |
| 154 | 2 | 0 | |
| 155 | 5 | 0 | |
| 156 | 14 | 2 | |
| 157 | 42 | 6 | Cal-Sny/Hel |
| 158 | 49 | 16 | |
| 159 | 52 | 35 | Cay-Hel |
| 160 | 40 | 38 | |
| 161 | 49 | 33 | |
| 162 | 54 | 37 | Cay-Sny |
| 163 | 36 | 24 | |
| 164 | 27 | 38 | |
| 165 | 24 | 46 | |
| 166 | 15 | 38 | |
| 167 | 9 | 17 | |
| 168 | 4 | 21 | |
| 169 | 3 | 14 | |
| 170 | 1 | 27 | |
| 171 | 0 | 3 | |
| 172 | 0 | 8 | |
| 173 | 0 | 2 | |
| n | 426 | 405 |
Understanding the CC BC1F7 Entries¶
The 2018 Entry file for the CC BC1F7:8 population has included the
| Entry Name | 2018 source | 11Sny | 11Ket | Entry | 2009Plot | 18Helf | 18 Sny |
|---|---|---|---|---|---|---|---|
| 028-5 | 344 | 2056 | 4119 | BC1F5-574(NR-cay) | 574 | 3080 | 2023 |
| 035-1 | 167 | 2195 | 4263 | BC1F5-243(NR-cal) | 243 | 3362 | 2188 |
| 035-3 | 94 | 2359 | 4392 | BC1F5-139(NR-cal) | 139 | 3147 | 2144 |
| ....etc |
So it appears the the Entry: BC1F5-574 is a number derived from the 2009 plot:574
We know year by year Entry is not consistent for the line.
I found in the BC1F5 genotype file that the Entry Name: 028-5 stands for Family 028 Plant 5 resulting in the SOURCE: 028-5
This file contains the Somyong 2014 genotype data: SSR + TNAC9025
Labels for PHS¶
CC BC1F7-18_SM.xls data file
Sample only the headrows of the BC1F7 CC population that have 5 or more plants in the headrow. We want a good selection to be able to tag 5 good spikes for PHS testing that mature on the same day.
In addition, I want 5 more spikes for dormancy assays. So I will only harvest lines that have 10 or more plants in a headrow. Just from one location in Helfer. Note, this will increase work, so I can focus on the extra spikes myself if the crew needs to do other things.
Send David and Amy both lists to print off labels and I (or the crew) will label the wired tags. PHS Sampling column 'SproutLabel' with x indicates the lines I want to harvest at both locations. Dormancy sampling column 'DorLabel' with x indicates the lines I want to harvest at Helfer.
Printed 2018.06.18
When about 10% in the nursery are at PM, then we sample every 2-3 days.
| Assay | Location | Number Lines | total |
|---|---|---|---|
| PHS | Snyder | 276 | 287 |
| PHS | Helfer | 363 | 375 |
| Dor | Helfer | 312 | 323 |
CC BC1F7 Seed in Field and GH Summary¶
Between Helfer5, Snyder5, and the greenhouse set1 and set2:
In Good Shape
- 6 BC1F7 lines in the GH but only 2 plants in the field
- 2 BC1F7 lines in the GH but only 1 plant in the field
- 352 BC1F7 lines in the GH and emerged well in the field
- For a total of 360 BC1F7 Lines
Did Poorly
- 10 BC1F7 lines have no plants that grew at all:
| Lines lost | . | . | . | . |
|---|---|---|---|---|
| BC1F5-164(NR-cay) | BC1F5-186(HR) | BC1F5-196(NR-cal) | BC1F5-211(HR) | BC1F5-243(NR-cal) |
| BC1F5-282(HR) | BC1F5-392(HR) | BC1F5-424(HR) | BC1F5-464(HR) | BC1F5-500(HR) |
- 7 BC1F7 lines had only one plant that emerge in the field, no GH material
- 13 BC1F7 lines had only two plants that emerge in the field, no GH material
- 51 BC1F7 lines with no DNA extracted from the GH or grown out but plants emerged well in the field
- For a total of 81 BC1F7 Lines
71 line that did not grow in the GH/DNA was not harvested: DNA was harvested from the Field on 2018.05.14 | Plate # 5
- 3 leaves from 3 different plants, unless there were only 1-2 plants availble
- All were harvested from Helfer, except entries: 1839-1 and 068-4 which were harvested from Synder
Cayuga/Caledonia BC1F7 2018 Greenhouse ¶
Purpose: The BC1F7 seeds were planted for DNA extraction and grown out for seed increase and physiological testing
The DNA was extracted by J. Tanaka on 2018.04.26 | Some of the DNA will be sent to Japan for axiome sequencing
The remainder of the DNA will be used for fine mapping of the QPhs.cnl-2B.1. Markers of the QTL region still need to be created.
2018 Cayuga/Caledonia BC1F7 entry file and DNA map:\Cayuga Cloning Project\Genotyping\BC1F7 GH 2018 Set 1 layout.xlsx
Initially, the seeds from the 2011? field source did not germinate well for planting in the GH.
Therefore Set 1 was the first round on planting and Set 2 was the second round of planting, only of the BC1F7 lines that did not germinate in Set 1.
| Nursery | Room | NurseryPlanted | DNA Harvest | Vrn In | Transplant | Estimated Harvest |
|---|---|---|---|---|---|---|
| CCBC1 Set1 | 150A | Feb 28, 2018? | Mar 14, 2018? | Mar 14, 2018 | May 10, 2018 | July 26 - Aug 19 |
| CCBC1 Set2 | 150A | Mar 26, 2018? | Apr 13, 2018? | Apr 13, 2018? | Jun 8, 2018 | Aug 8 - Sept 5 |
| CCBC1 Set3 | 157H? | May 21, 2018 | May 28, 2018 | May 29, 2018 | Aug 1, 2018 | Oct 1 - Oct 15 |
Notes about the greenhouse harvest:
BC1 plant 103-1 did not grow after removed from vernalization and died.
- Overhead-water: There are many cracks in the greenhouse ceiling, therefore when it rains, many places throughout a bench gets dripped on. Too many to isolate plants around.
- Drought stress: Once the plants start to turn yellow, the GH staff slows down on watering the plants. I noticed multiple times that some plants ended up showing drought stress symptoms because the plants were still in grain filling stages and were being watered enough. Next time growing in the GH, watch the pots for dryness daily and water myself if need be
- Disease: There was too many mold diseases I havent seen before that were on the heads.
| A | B |
|---|---|
 |
 |
Figure 1: Unknown (to me) greenhouse diseases.
Overall, if germination assays are attempted, it will have to be for a last reasort reason, since I do not trust genetic differences since there was so much plant to plant variation as to whether it had disease, over-head watering, or drought stress.
However, we need non-sprouted seed to plant for 2019 field trials, so using this as a source is a better idea. Uncertian though whether or not the mold on the heads are going to cause an issue in the field
BC1F7 Emergence Data | 2018 ¶
Snyder (taken 2018.05.02):
- 36 BC1F7 lines have no plants emerged (8.2%)
- 38 BC1F7 lines had only one plant that emerge (8.6%)
- 35 BC1F7 lines had only two plants that emerge (8%)
- 165 BC1F7 lines had less than four plants that emerge (37.4%)
Helfer (taken 2018.04.30):
- 13 BC1F7 lines have no plants emerged (3%)
- 16 BC1F7 lines had only one plant that emerge (3.6%)
- 20 BC1F7 lines had only two plants that emerge (4.5%)
- 77 BC1F7 lines had less than four plants that emerge (17.5%)
Between both the Snyder and Helfer locations:
- 10 BC1F7 lines have no plants emerged at either location (2.3%)
- 9 BC1F7 lines had only one plant that emerged between locations (2%)
- 19 BC1F7 lines had only two plants that emerged between locations (4.3%)
2018 PHS Field Notes and Files ¶
2018 Field Maps: \Dropbox\Cornell Small Grains Breeding\2018\Winter Grains18\winter 18 maps
2018 PHS Note folder: \Dropbox\Cornell Small Grains Breeding\2018\Winter Grains18\PHS
2018 Cayuga/Caledonia BC1F7 entry file: \Dropbox\Cornell Small Grains Breeding\2018\Winter Grains18\PHS\CC BC1F7-18
Snyder 5¶
Headrows | Planted 2018.10.19
441 BC1F7 lines planted | 6 Cayuga | 6 Caledonia
Helfer 5¶
Headrows | Planted 2018.10.19
440 BC1F7 lines planted | 6 Cayuga | 6 Caledonia
MISSING source:268-3 2018source:388 entry:BC1F5-751(HR)