Methods: Field - wallacelab/lab-wiki GitHub Wiki

The field involves a lot of moving parts, and if we get something wrong we have to wait a whole year to repeat it, so it's worth doing right. Here is the basic timeline we follow each year:

• January - Determine major experiments for the year. Contact farm manager(s)
• February - Determine plots in each experiment and fill out the template for new field experiments.
  • Includes determining which seed packet each plot will come from
• March - Begin pulling and packing seed
• April - Planting
  • Hybrids (=G2F) are usually planted between April 1 and 15
    • Due to issues with getting Statewide to harvest on time, starting in 2025 we delayed G2F planting to early May
  • Inbreds (=Nursery) are usually planted 2-3 weeks later because they don't handle cool temperatures as well.

• May - Weed control. Even with pre-emergent herbicide, the field needs to be weeded until the corn starts to shade them out
• June - July - Phenotyping and pollination
• August - Harvest
  • Hand-harvested plots are usually brought in ~7 weeks after pollination
  • Machine-harvest plots are whenever we can get Statewide Variety on site (usually end of August)

• September - December - Handle seed registration for the nursery

• Always wear gloves when treating with fungicide (or handling seeds that have already been treated), and always wash your hands thoroughly with soap afterward
• Seed treatments legally require a colorant added (pink, blue, green, etc) to make it clear the seed has pesticides on it.

• Generally, commercial seed treatment products recommend 500-800 mL of the solution (made with active ingredients mixed in the right proportion to water) per 100 kg of seeds, which means 5-8 uL/g. However, for much smaller quantities of seeds, we end up using a little more solution - proportionally - since most of the product ends up sticking to the plastic bags where we mix it.
• For experimental plots with 20 seeds, the Falcon tube is actually easier to use than plastic bags. I also use a plastic/transfer pipette, so I just dip its tip in the solution and put a small drop on the sidewall of the Falcon tube before shaking it. This is enough to cover all the seeds without making them stick to each other (which could make planting difficult and compromise germination).
• I keep the envelopes open, and then, on the following day, I staple and shake them well to ensure that none of them have the seeds stuck together

It is VERY IMPORTANT that the correct seeds be put in the correct packet. A mistake at this stage can be almost impossible to detect/correct, so double- and triple-check that see packet numbers and names match before putting seed in.

1. Create a list of packets you will need for all experiments
2. Print out labels and affix them to small coin envelopes
   • The ones we use are 2.5" x 4.5"
   • Sometimes they have a perforation for easy tearing. That's nice, but not required
3. Pull all your seed packets from storage (usually a cold room)
4. Double-check that you have the right seed packet, making sure both the name and packet number match
5. Count out however many seed you need and put them in your envelope
6. Close the envelope.
   • If you're done, it can be sealed with a staple, or left loose so you can treat the seeds with fungicide
7. Put the source packet back where it belongs.
8. Keep a record of how many seeds you pulled from which source packets and make sure that gets given to Jason to update our seed database.

Planting maize in the field is routine but very important. A misplant here--especially one we don't catch--can cause problems with data for years afterward.

The Nursery is hand-planted with jab planters. The planters should be checked that they're clean and adjusted to the correct depth (~1.5-2[?] inches) beforehand, and arrangements made with the farm crew to mark out the field with dry-planting and tire tracks. This can be time-consuming, and so having lots of people helps. (Though no more than there are planters, obviously.)

Genomes to Fields requires uniform planting, so we borrow a tractor-drawn cone planter from the farm. (It might technically belong to Zenglu Li's lab.) The farm crew adjusts it to the normal size (30-inch spacing between the 2 rows) and marks out the alleys beforehand, and we spend several hours getting everything planted. This planting requires 2 people: one to dump the seeds, and one to double-check that they match what's on the map. (Plus the driver, who is one of the farm crew.)

• Historically we have planted 72 plants in 2-row, 19-foot plots with 6-foot alleys. More recently (2024), Iron Horse asked us to increase the alleys to 10 feet to allow a tractor to drive down them.

Every experiment should have its own SOPs (standard operating procedures) explaining exactly how to measure its target phenotypes. This page just gives a general overview to get familiar with what we tend to look at.

It is VERY IMPORTANT that things be recorded properly. If something gets mislabeled, it's almost impossible to correct, so make sure it's right.

• Stand Count is just a count of the plants in a plot. Can be done early to check germination efficiency ("germination count"), or late ("stand count") as a covariate for harvest.

• Flowering time is when the plant flowers. For a plot with multiple plants, we usually measure when half the plants have flowered.
  • Anthesis is male flowering for maize. A plant has anthesed when at least half the anthers on the main spike have opened up.
  • Silking is female flowering for maize. A plant has silked when you can see any silks at all poking out of the ear (but make sure they're not bits of leaf).

• Yield means how much we got out at the end of the season (usually of grain, but could be biomass, etc.)
  • Machine-harvested maize plots (e.g., Genomes to Fields) are contracted out to Statewide Variety Testing, and their combine automatically counts total weight, test weight (=weight per standard volume), and % moisture.
  • Hand-harvested plots are usually part of the nursery. We usually take 20-kernel weight and Total weight (both in grams) to get the (approximate) total seed count for the plot.

"Seed Registration" is the process of shelling (=removing kernels from) the ears and recording the information about the seeds we need, often including storing them for long-term access.

1. Rip the plot tag off the end plant and put it into the bag
   • ALWAYS INCLUDE THE PLANT TAG. Without the tag we don't know where the ear came from, and all that effort through the season goes to waste.
2. Remove the pollination bag from each ear, rip away the husks, and check for pollination
   • We usually keep pollinations even if they have a single kernel
3. Rip the ear off the plant and put it in the bag
4. When all ears are harvested, form a loose loop and tie the next of the bag
   • IMPORTANT: Do not tie the little black string. They are very hard to get undone. Loop and tie the bag itself.

TODO - ADD DETAILS

1. Dump all bag contents into a container (ideally a sieve)
2. Check for plant tag and that all the ears look roughly the same (=same genetics).
3. Use the metal corn shellers and/or your hands to remove all kernels from cobs
   • If a kernel jumps out of the pan, leave it. It’s better to lose some than risk contamination
   • Try to avoid moldy kernels or ones that look obviously bad/dead
4. Count out 20 kernels and record their weight (in grams)
5. Record the total weight of all kernels
6. Dump kernels into a bag. Tear off the end of the plot tag and drop inside.
7. Fold the bag down to close. Use a rubber band to keep closed and secure the remaining plant tag to the outside
8. Place in bin and move on to next bag.

Things to record:

• Plot ID
• 20 kernel weight
• Total weight

Weeds are a major problem in Georgia, and if we let them they will completely consume the field. Keeping weeds under control is a major component of the summer field season.

Alleys are the easiest to control. Just fill a backpack sprayer with glyphosate at the recommended dosage and walk the alleys every 1-2 weeks during the season. Keep an eye out for any weeds that appear resistant, and kill them dead with other methods (hoe, hand-pulling, etc.)

In-row weeded is usually done with garden hoes. This is especially important early in the season before the corn canopy closes, when there's still plenty of light reaching the ground. Once the canopy closes this becomes less of an issue, except for tenacious vines like Morning Glory or in experiments where the plants don't close canopy (e.g., some inbred experiments).

Some of the worst weeds we deal with are:

• Johnsongrass - A wild relative of sorghum, it can look like maize when young. Sturdy roots and a thick rhizome that lets it come back year after year. (Ploughing breaks up the rhizome, leading to many plants where before you had one.)
• Morning Glory - A tenacious, choking vine, it climbs up the cornstalks and smothers the plant, pulling it down and choking up equipment. If left unchecked it can completely consume entire plots. Usually gets back in July, and important to regularly check G2F for it after flowering is done.
• Nutsedge - A short relative of grasses that can form thick stands that suck up lots of water and nutrients.
• Pigweed (Palmer Amaranth) - A truly noxious weed capable of making half a million seeds per plant. Also becoming glyphosate-resistant.