Andrew's Gardening and Plant Breeding Projects


#1

Okay, so since there was at least a few people interested in my various projects i figured i’d share in a little more detail some of my previous or ongoing plant breeding or gardening adventures and projects. I will try to track down some really good photos if i can too.

p.s. Just realized there are two growing categories. Not sure which one this belongs in or whether both categories can be merged to help eliminate confusion.

Where to start, where to start. umm. okay why don’t i start of with a list of various things i have grown or tinkered with that might be unique or interesting.

  1. I have grown and bred my own indian corn that had/has high purple foliage, pollen anthers, husks, and tassels. They are unique and attract lots of native black bees that i have yet to positively identify. The black bees are way cooler than bumble bees though. This is what started me on my journey. I even am mentioned briefly in the book Plant Breeding for the Home Gardener: How to Create Unique Vegetables & Flowers by Joseph Tychonievich. The first year i did this i planted an old Indian corn thanksgiving decoration. I got a giant surprise as one corn plant was completely purple with no trace of green while all the others were normal. It was awesome. Sadly the photo was lost, i do have this photo though, it looked like this. I may try to recreate that again someday, who knows maybe this year.

I grew yellow striped corn once. That was fun.

Then i started growing Teosinte. Teosinte is fascinating stuff. The ancestor to modern corn. I’ve grown every variety/species of teosinte. I think modern corn was bred by crossing two teosinte species together, Zea parviglumis and Zea mexicana. Zea diploperrennis and Zea perennis are interesting because in their natural habitat in Mexico are perennial rather than annual like modern corn and most teosinte species. Zea diploperennis is diploid whereas Zea perennis is not. Zea diploperrennis gows very wild and bushy i guess you’d say.

I’ve been working for a number of years trying to slowly adapt teosinte to my Colorado temperate climate to save seeds and breed it with modern corn. After several years of frustration and failure i finally was able to find one accession of Zea mexicana from the USDA GRIN system that is just barely able to produce seed here. Teosinte naturally is adapted to the light patterns in Mexico so when grown here it only starts to tassel and silk in late fall when the sunlight shifts into the red spectrum more. I was curious if teosinte seeds would pop like popcorn so a collaborator of mine tried it in Utah. Apparently they do!

I have put the teosinte stuff on hold as i dont have enough room to grow it right now, nor the energy to fight with the racoons. Raccoons don’t understand that teosinte is different than corn and that there is nothing to eat so they tear down teosinte just like corn looking for a free meal. But i want to return to it someday. I love corn and teosinte. Nothing else quite like it.

For a few years I’ve also been working on adapting and breeding my own watermelon to grow here in Northern Colorado. Watermelons don’t grow in Colorado. Let me put it that way. Trust me, they don’t. At least not without considerable effort to have really lush soil and black plastic, etc. It can be done. But i’m lazy. I want a watermelon i can plant even in marginal soil and expect it to thrive and grow well in my conditions with my soil, my pests, my intense sunlight, my dry air, etc. Hence me starting my own watermelon breeding project. It has taken several years but i have had success. This year was the best one yet. It was originally a collaboration between me and Joseph Lofthouse of Utah. Joseph has started to become a little world famous for his landrace vegetable varieties and other crazy plant breeding projects like restoring onions to produce true seeds, planting other crops from true seeds like potatoes and sweet potatoes, restoring tomatoes to be highly attractive to pollinators and obligate outcrossers rather than inbreeding, etc. He has great success with a Cantaloupe landrace where no other cantaloupes would grow. After having success with that it inspired both of us to try the same technique with watermelons. It works!

This year i have also branched into a separate watermelon breeding project involving crosses between domestic watermelon and the rock-hard but hardy Colorado Red Seeded Citron melon which is just a very old variety of watermelon (or close watermelon species) that produces lots of pectin and bland flavor. It was once used for canning and preserves like a hundred years ago. I may have briefly mentioned it in another thread, but the russians from the soviet union (USSR) experimented with a lot of crazy cross-species plant breeding. They already tried this watermelon-citron hybrid idea and had success breeding winter storage watermelons that were sweet and edible but that stored for months just fine! Crazy cool! So, this new project has potential. These are my current hybrid seeds. They were originally bright red like the citron parent, but now are various seed coat colors and patterns indicating the crosses have been successful. There are several people excited about this project of mine.

and i’m getting a little tired of typing. But two other main projects of mine are currently with wild tomato species and pea breeding.

Here is a cool purple-seeded pea i bred in 2015 and grew out this F2 segregate this past season.

And here are some red-podded peas i selected.

If anyone wants to know more about the tomatoes and other stuff let me know and i’ll talk about it more in another post. I’m tired. lol. I’ve also tried growing golden kiwi from seed once. That was fun.

-Andrew


#2

Awesome. I’m curious about how you keep track of data from your experiments over time and about what sources you’ve learned from.

Have you ever thought about ways that customized software tools might make your projects easier?

Do you have any reading list recommendations for people who are curious about finding or creating varieties that are adapted to their local climate?


#3

Great questions! I’ll have to ponder on it some more and see if anything else comes to mind. But here is my first response:

Honestly mostly right now i just keep track in my head. It’s terribly inefficient, but it prompts my brain to get better at remembering things in as best detail as possible. So maybe it’s like a brain workout? haha, i have no idea. It sounded cool though, haha.

I was keeping a notebook with tables for the various pea data. But it was tedious and last year i didn’t even do that as i had way too many peas inter-planted. i had over 17+ unique pea varieties i was growing at one time! It was a pain sorting seed from that as many grew on each other. lol.

Yes! Actually. I’ve tried looking for some open source software before, and tried lots of them but never quite found what i wanted. There is one system that is incredibly expensive and proprietary that might be what i want but it is aimed for traditional corporate large-scale plant trials etc, even if i knew it was perfect and could afford it.

What i really want is just a form of pedigree software like what you see the dog breeders and the genealogy people use, but geared toward plants, and designed to be better. Open source and cross platform is a must. Ubuntu or debian based Linux is my main platform but i switch systems all the time. Tablet designed software would be cool. The ability to track pedigrees, genomic data and the ability to easily attach photos would be awesome. Some of the open source genealogy software might be easily modified, but i’m not a coder or a programmer so i can’t do it myself.

I would be interesting in any ideas or things you had in mind when you posted the question. Different people always seem to have different needs / wants, but perhaps a nice software could be designed to handle all possible features / needs. There seem to be quite a few software people on this forum, so that might be to our advantage. Interested to see where this part of the discussion goes and who else responds on this topic.

Sure. Is there anything specific you are particularly interested in? Here are a few off the top of my head.

The Book: Breed Your Own Vegetable Varieties by Carol Deppe is really good. It is a good place to start. The Book: Plant Breeding for the Home Gardener: How to Create Unique Vegetables and Flowers by by Joseph Tychonievich is okay too.

Joseph Lofthouse, Carol Deppe, Rebsie Fairholm, and Alan Kapuler are all heros of mine and i have learned tremendous things about plants and breeding from them.

Alan Kapuler has various videos about him on Youtube and is basically a really smart Microbiologist who worked with viruses and crazy government stuff way back in the 60’s and 70’s and one day decided he did not want to support such a corrupt lifestyle in his view and went all hippie and moved to Oregon to become a plant breeder and start a seed company with his values and his hope for humanity.

Rebsie Fairholm is the one who discovered the red-podded pea in Nottingham England, in the UK, in 2008. She had an awesome blog dedicated to mostly peas and pea breeding and had some awesome ideas, showed how to cross them, and had the coolest photos imaginable. Her blog continued to capture my imagination and her’s is still a resource i go back to sometimes. Her plant breeding has been inactive for a few years. But she has an incredible book about how to breed potatoes! With the coolest color photos of potatoes ever.

http://www.angelfire.com/az/garethknight/dots/index.html

http://www.skylightpress.co.uk/9781908011190.html

Joseph Lofthouse is probably the most influential of the list. He claims to originally been inspired after reading Carol Deppe’s book. But he is in a class all of his own. He takes random ideas, crazy ideas even, and takes them to whole new levels and runs with them. Sometimes they don’t work out, but more often than not they do. He is a subsistence farmer who doesn’t use paypal, no longer wears shoes, and lives in a cold high mountain valley in Utah. He is motivated to breed better varieties because he has no choice. 99% of all commercial varieties of seed fail to grow for him in his climate, with his soil, with his conditions, and his short season. He has to, otherwise he wont eat. He enjoys this way of life though. He knows a ton about genetics, but he is virtually all self taught.

http://garden.lofthouse.com/adaptivar-landrace.phtml

And finally, you need a good forum to generate ideas, feed off of, and a good network of people to share with, read about other projects similar and different, and even share seeds with on occasion. Mine has traditionally been the Alan Bishop Homegrown Goodness [plant breeding] forum. It has had everyone of the people i mentioned as active members at one point and the source of inspiration and seeds for some of my projects and ideas. It has seen better days, but it still is worth checking out if. Even browsing through the old archives produces a lot of knowledge. it’s kinda like an encyclopedia.

EDIT: oh, i forgot. The best tips i can give to creating your own crops for your climate are this: 1. first search local and regional sources of seed for varieties that do well in your area or climate. Even branch out to slightly different but close climates and areas as well. 2. Then check foreign places but that still have some similar climate as well. 3. don’t give up. keep at it. if plants die right away that’s okay. The third year is when they start to shine. 4. let them mix up promiscuously. Don’t be afraid to use hybrid seed or save from hybrid seed. Generally those are even the best to start with from a genetic standpoint. Though some crops like carrots are bad to save seed from hybrids because commercially they are all cytoplasmic sterile male carrots. In cases like that go heirloom and mix them up.


#4

I feel like my best shot at making a contribution around here is with organizing information and potentially writing software if the right circumstances came about.

Toward the organizing information goal, I’ve put together a couple posts with links on hydroponics and aeroponics. For software, I made my own data logging system to track a crops of microgreens and aerogarden lettuce. That didn’t attract much interest around here–I guess because people were mostly focused on trying to build their own food computer according to one of the MIT designs. I also made some minor contributions to Howard and Peter’s MVP design–mostly by way of discussion.

In the past year, I’ve done what I can to answer questions about the PFC software stack when opportunities came up, but after studying the PFC designs, I decided not to try building one of my own. As I’ve mentioned, I’m not sold on the premise of crowdsourced climate recipe research. I’d rather help people grow food to eat or sell. I’m also interested in potential opportunities to help people reduce water consumption, reduce carbon emissions, adapt to changing weather patterns, etc.

From what I hear, and from what I’ve seen on small farms I’ve worked on, there’s lots of room to apply open source principles to crop planning, farm logistics, record-keeping, etc. That stuff maybe isn’t as sexy as building robots to grow food, but it is practical and useful.

For me, no. I don’t have any plans to start breeding plants, but I ask because it seems like an important subject that you seem to know a lot about. It looks to me that a lot of the motivations people cite for wanting to do climate recipe research could also be addressed by finding varieties that are suitable for local climate conditions. Again, it’s old school, and not as sexy as fancy robots, but it seems more practical to me. Maybe some of the people who wander by here will want to learn more.

It also seems like matching varieties and local climate conditions has lots of room for applying tech. You’ve mentioned elsewhere trying to use adjustable spectrum lighting with plants that don’t want to grow where you live. Another obvious possibility would be building tools to help expose the kind of information in seed catalogs or the USDA plant hardiness zone map to people who’ve never heard of such things. Also, keeping good records of what works and what doesn’t.


#5

oh, ok.

That makes sense. I still am interested in a hacked or modified version of dog/human genealogy / pedigree software for plants. Perhaps that is different than the kind of software that you write, but if you ever do look into it let me know. I have no coding skills other than rough arduino c-like code and the ability to compile the occasional program. But it’s a handicap of mine otherwise i would have written or cobbled my own together by now.

I am tinkering with a plant database wiki of sorts right now. I don’t really know what it will turn into if anything, but i figured i’d mention it anyway: https://biolumo.com

EDIT: Oh, p.s. you asked about software and tools to track my data on experiments and projects that i have used. One piece of software i have used and REALLY liked was the lab notebook feature on the OpenWetWare wiki site. If something similar to that could be added or copied to the OpenAg wiki i think it could come in handy and lots of people could use it for their projects!

https://openwetware.org/wiki/Lab_Notebook


#6

Woah… your links are really interesting but also a bit over my head due to my unfamiliarity with the terminology. I may look at this more to see if I can figure out what’s going on.

You mentioned Debian and Ubuntu. Do you ever use emacs? If so, have you ever experimented with org-mode, calendar-mode, picture-mode, etc.? I’m curious about the possibility of making an emacs mode to help you draw charts and take notes in text files. Another thing you might like is graph-viz.

I ask about emacs because I’ve been studying Common Lisp lately, using emacs a lot, and exploring a bit of emacs lisp. I’ve been super-impressed with how some of the emacs modes make it quick and easy to do things that somebody who didn’t know of such magic might spend weeks trying to implement as a web app with a bunch of Python, Rails, Node, or whatever.

The obvious catch with emacs would be that the command line version doesn’t do images inline with the text, but I think you might be able to get org-mode to open images for you with a keyboard shortcut. You might look for an emacs org-mode tutorial and see if it’s anything you could tolerate or perhaps enjoy. Emacs is definitely an acquired taste with a near vertical learning curve, but once you get the concepts and learn your way around, it’s very powerful. I think there may also be ways to render org-mode outlines as html if you wanted to share stuff that way on your website.

For a notebook like thing where you could mix text, images, and charts built from code, a couple other possibilities might be Dr. Racket (see the Scribble documentation tool) and the IPython Jupyter notebook. I’ve heard people like to use IPython notebooks for a lot of scientific computing projects, and I know that python has good support for making different kinds of charts and diagrams.

My impression is that the three main things you need are:

  1. A way to take notes on both individual trials/crops and also on progress over time. Probably plain text would be fine for this.

  2. A way to associate pictures with notes and descriptions (seeds, fruit, different lifecycle stages of the plants, etc.). Ideally it would be easy to view the pictures with the associated text as in a book, pdf, or webpage.

  3. A way to create and display ancestry charts for plants. This seems like the big missing piece that you will have a hard time doing without custom code (unless graph-viz or emacs org-mode would do it for you).


#7

No i’ve never used emacs before. But I’ll take a look at it.


#8

@BioLumo, rather than start a new thread, I figured there was no better place to come than here. I have a question I’ve become obsessed with and since you have an extensive understanding of breeding/genetics and a curious mind I’d love to get your help trying to answer it. Just to give you some context, my deeper curiosity is to design a seed for CEA (architecture, circadian, tolerance, etc.) while engineering its environment.

What would be the best plant to grow in space, or on Mars - more importantly, how are they different?

I know there are a million factors so I’m not looking for a factual answer, just your opinion, and thoughts. If you know nothing about the topic, here’s a good podcast to start: https://www.nasa.gov/mediacast/episode-1-mars

Feel free to rant!


#9

Hi Peter,

Haha, i’ve thought about this already from time to time, though not necessarily in depth, and more about Mars than space, but an interesting question for sure, and one i am always willing to discuss. I will give some of my thoughts as they come.

I’m not sure what the acronym CEA stands for. Cost Effectiveness Analysis? But i think i get what you might be hinting at. Maybe to both design the best environment for a plant but also to help breed the best plant and genetics to suit that environment. If that is what you were getting at then cool i actually think that is a good method to employ for both space and mars habitation. And actually a good strategy for here on Earth as well now that i think about it.

The “best” plant to grow on Mars or in Space?

There are many factors to growing plants well on mars. Mainly I’ve thought about ways one could “terraform” mars by using plants and other means and have them able to survive harsh conditions, but even breeding for self contained “babied” plants is a worth while method too. I think both should try to be employed of possible.

First, mars does have an atmosphere albeit it a very thin and harsh one. It has plenty of Carbon Dioxide that could be used for plants, and has some nitrogen in it’s atmosphere, perhaps enough to use to grow things. Water is obviously of most concern for both plants and humans. One idea i had to try and tackle the water problem would to take advantage of all the Iron Oxide (rust) in the soil. Some have speculated that because mars is rusty that it once must have had lots of water. If one could combine Sulfuric Acid with the Iron Oxide then a natural byproduct would be H2O. Now taking lots of Sulfuric Acid to Mars might not be ideal or practical. I kind of think nuking the volcanoes on Mars might also have the same effect, but who knows. I might be getting off topic.

Okay, so lets say you could grow plants in martian soil fine and had plenty of water, what other issues would you run into and what traits or species of plants would you want or be ideal?

One issue is nitrogen. This could be accomplished by fertilizer or bacteria that can pull nitrogen out of the air. If using the latter method i can think of three solutions. 1. Legumes. 2. Maize that have aerial roots and can produce sugary slime to feed nitrogen bacteria (a scientific paper was recently released on this topic). 3. Biotechnology (bacteria, engineered bacteria, algae?, etc.)

Another issue is extremely high UV light because of the super thin atmosphere. Living at high altitude here in Colorado i am already familiar with this phenomenon, although not quite as much as would be on Mars. But it is much easier to get a sunburn here that somewhere else, both for humans and plants. Some genetic resilience for this would be of high importance in my mind unless growing under shade cloth or LED lights. If growing from sunlight, plant chemicals like Anthocyanins can and do act as a sort of plant sunscreen. Plants with high or at least some expression of Anthocyanin Purple or Red leaf color would be a good idea. I grow/breed a special type of Indian Corn (Maize) that has dark purple foliage as opposed to green. Something like this or Red Romaine Lettuce, or other plants i think would be moving in the right direction. I have some special varieties of peas (Pisum sativum) that have purple pods and some that have purple and red and black seeds. I think these varieties might be more protected from UV damage to the seed DNA. Anthocyanins are also really healthy apparently as they reduce free radicals and other stuff. Some people claim they might add bitter overtones to taste, but i have not tasted these and generally prefer them in my food.

Another potential issue is heat / cold tolerance. Mars sees massive temperature fluctuations from daylight to nighttime. Plants that can take massive temperature shifts would be more ideal for a harsh climate like mars. Though likely some climate control might be necessary to reduce the swings some, though might not need to be eliminated entirely. A guy i collaborate with in Utah lives in a cold mountain valley where something like 95% of traditional vegetable varieties die for him if he plants them. This is a combination of his soil, his pests, his cold, his short season, his dry air, his high altitude, his high UV, and the fact that most seeds are bred for other climates and for heavy chemical fertilizer application. It means that the odds are already stacked against those seeds even before he ever plants them. By saving and breeding his own varieties he is able to find and create varieties that not only grow in his conditions but thrive! One technique he uses is landrace or evolutionary breeding by using wide genetic diversity so that at least some survive and then he can continue to select what works best over time. It works well.

What would be best for growing in space? A good question.

One thing to consider is size (there is only so much room), so something like Maize might not be the best choice and something like Lettuce might be better. Another is nutrient density (what you’ll get the most out of what you put in), again Maize is not the most nutritious food, so it may not be a good choice. Another would be whether it can thrive under low light conditions or artificial lighting. Houseplants or plants adapted to growing under heavy jungle foliage or in partial or full shade might be good choices. Perhaps Jungle Cacti or Raspberries or something? Raspberries might not be small or space saving for growing in outer space, but they like partial shade and can grow in relatively poor soil. Things that can grow in poor soil or no soil is another topic. Water needs is another. Perhaps plants or crops more adapted to have desert tolerance is another factor to think about.

One thought that popped into my head was rooting ability. For example, in Domestic Tomatoes it is super easy to take a cutting and root them in water. But in wild tomato species it is very hard to nearly impossible for some. Interspecies hybrids have rooting ability somewhere in between, doable but not great. This seems to be a trait selected for in Tomato domestication which may have helped. It might also be a good trait to have in space or on Mars. Cacti also have the easy ability to take cuttings and grow a new plant.

Seed set. It might be important to have plants that can self pollinate or at least lack self compatibility. Pollinators such as Mason Bees (among others) could be taken to Mars, and perhaps should if possible, but many of our plants, even our domesticated ones, either need external pollinators, or set much higher fruit set with them. It might be possible to do this by hand (like with an electric toothbrush or paintbrush), or possible to hook up cell phone motors to periodically shake the plants, or fans to produce wind. But it’s probably something that should be thought about in depth. Peas (Pisum sativum) for example readily self pollinate and need no pollinators at all.

I guess it would be beneficial to come up with a species list of vegetable or fruits, or herbs, or whatever that hit as many of these criteria as possible and come up with a crude ranking system to list which crops might be better suited than others. I would be interested in seeing such a list or trying to help define one myself.

That is all i can think of for now. LOL :slight_smile:

EDIT: speed of growth too. Many Cacti are slow growing among many other plants. A plant that can grow fast would be more ideal perhaps.

-Andrew