Improving the Tomato Genome by breeding with wild tomatoes [2017]

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Solanum peruvianum (wild tomato with desert tolerance)

So i haven’t written a blog post in some time. Sorry about that. It has been very hectic this year. That’s not to say that i’m completely dead. And despite my busyness and absence i am still dabbling a little bit in the garden and plant breeding scene. I didn’t have the time, energy, or space to work on my purple Indian Corn or Teosinte this year. I barely made room for beans, peas, tomatoes, and a row of watermelon.

The beans are my special four corners native beans which include, New Mexico Red Appaloosa (aka. Gila River bean), Anasazi, Zuni Gold, Rio Zape, and maybe a few others. The Peas are a large growout of my 17-23 different varieties of genetically unique and rare pea varieties, some of which are segregating crosses that i did two seasons ago. And tough i don’t have many pictures i will post one below of a purple podded umbellatum-type (aka. crown pea) where all the pods come out in a jumble all at once. To have a purple podded one of these is new and kind of cool. I hope to have a yellow and red-podded umbellatum-type pea someday. The watermelon are the result of mine and Joseph Lofthouse’s Watermelon Landrace project. Joseph Lofthouse seems to be world famous now for his widely successful landrace seed varieties and breeding techniques.

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Purple Podded Umbellatum Crown Pea

Anyway, back to the tomatoes. The Tomatoes are a brand new project and sort of an offshoot of one of Joseph’s new landrace breeding projects as well and a few other fellow collaborators and breeders as well. It all started when Joseph was working on wanting to convert tomatoes to a landrace like many of his other successful crops. But there are a number of problems with that and domestic tomatoes in general.

The first problem is that domestic tomatoes are entirely self pollinating and don’t outcross all that much and have tiny closed-up flowers. Another problem is that domestic tomato flowers are not very attractive to pollinators. And the third major problem is that domestic tomatoes went through several genetic bottleneck selection events when they were domesticated that they have a very narrow genetic base. This narrow genetic base means that 1. Most tomatoes are subject to easily succumbing to disease and 2. that when they do outcross there is not much variation anyway. An average bad-tasting disease susceptible red tomato that crosses with another average bad-tasting disease susceptible red tomato means that in the end all you really get is more of the same.

My interest in all of this starts with the basic fact that in my climate here in Northern Colorado with my soil (mostly a dry clayish sandy soil where mostly desert plants grow), and the high altitude with intense sunlight and UV and the dry wind that wicks moisture out of the ground means that most garden varieties of anything don’t do all that well here unless intensely babied. This applies most especially to tomatoes. Even worse when it comes to Heirloom tomatoes. Sure heirloom tomatoes generally taste better, but to have a tomatoe plant produce like ONE good tomato through a whole season… That’s a MAJOR FAILURE in my book.

There are lots of tomato freaks out there that try to tell me that here in Colorado i can grow ANY tomato variety and be successful. And while that might be true if i replaces all my soil with compost or potting mix and provided massive amounts of water, and started them all early and planted them all out perfectly then yes maybe that would be true. But that’s not what i want to do, not should i have to do that. I should be able to just start a tomato plant and plant it where i want and not have to worry about it all that much and have it produce a decent harvest (whatever that happens to be). And not have to worry about disease, or growing slow, or not being adapted to my soil or the intense UV light or whatever. That’s where all this plant breeding comes in.

The goal(s)

  • To breed a superior tomato variety that does well for me (in dry N. Colorado)
  • To increase the genetic diversity in the tomato genome by using wild tomatoes
  • To create or recreate a tomato that is highly attractive to pollinators
  • To create a population of tomatoes that are highly outcrossing
  • To create a tomato that i actually think tastes good and NOT like cardboard

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wild tomato seeds. photo courtesy of Joseph Lofthouse

This project is still in it’s early stage, but it is progressing nicely. On Joseph’s end he is having huge success by using wild tomatoes bred with domestic tomatoes that have large showy flowers with exerted stigmas and have lots of pollen available that make them attractive to bumblebees. He is using mostly Solanum habrochaites but is starting to branch out to other wild tomatoes as well. Others are working on breeding tomatoes that produce a good harvest in under 100 days from being direct seeded and that have frost tolerance.

On my end i am experimenting with as many wild tomatoes that i can. I am evaluating several accessions of wild Galapagos tomatoes which so far are not doing much. The S. habrochaites also are not doing much. The ones i am having excitement from are the Solanum peruvianum which have silvery leaves and desert tolerance (in the roots) and a F1 hybrid between a domestic tomato and Solanum pennellii which has a different form of desert tolerance (in the leaves). I am excited about these genetics since they seem to be growing very well in my garden. The largest of any of my tomatoes is this F1 hybrid of S. pennellii. It is HUGE!!

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F1 hybrid between domestic tomato and Solanum pennellii
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Flowers of an F1 hybrid between domestic tomato and Solanum pennellii
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F2 cross of domestic tomato and Solanum habrochaites
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Gardening with Conductive Helical Coils 2016

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So despite the blog and my internet presence being quite mute as of late i actually have been up to quite a lot. My homemade Lulzbot Mini 3d Printer this summer was a success, amd i have constantly been improving it. At some point i will take some photos of it’s final progress. A few of my pea breeding crosses from last year were successful, including one i’m excited to grow again which is a cross of the Purple Passion dark purple seeded pea (which is a small genetically weak pea variety) with another stronger pea variety. That should produce something really cool in the coming years. And this fall and next spring i’m experimenting with school by going through a Precision Machinist course and am learning how to use milling machines, lathes, and CNC equipment to produce Aerospace quality components. Not sure if that’s something i want to do long term, but they are skills i’m interested in and can use throughout my life. So that’s new.

Anyway though, as a throwback or a revisit to my post in 2010 titled “Do Plants Really Need Sunlight?“, which has actually been one of the most visited posts on my blog over the years, i finally got around to building a few of those coils that sounded so interesting.

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Conductive Helical Coil around the stem of a plant

So the basic premise or idea behind using a coil of wire with electricity is that it produces a small amount of electricity or a magnetic current through the air. This is the same idea Nicola Tesla was after all those years ago when his imagination was captured with the idea that everything could have wireless electricity. And in many cases his dream has come true with an ever increasing amount of technology these days using induction to wirelessly power or heat things. The basic premise of applying this technology to plants comes from an article i read once that talked about how researchers were able to measure a small direct current from trees in a forest by placing nails in them. They then had ideas about placing nails in many trees and hooking them up together to power small electronics like a battery or cell phone charger, or a smoke alarm. Basically all plants (and maybe all living things) produce a bioelectric field of energy. If one can tap this field to harvest electricity, then why cant we tap into it and feed these plants with extra electricity to help them grow.

One question i asked in my old blog post was if plants even need sunlight at all as long as they are getting some form of energy to grow. I still haven’t done an experiment to test that idea, but it’s still an interesting question. Because it makes me wonder if there are ways plants could be grown in complete darkness.

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Regardless, this summer i finally built a prototype plant coil. I built it rather late in the season, so i really wasn’t able to give it a good test. My original plan was to plant 3 or 4 genetically identical tomato plants near each other in the relatively same soil with at least one plant being the control. I was then going to observe over the course of the summer f the tomato plants within the coils had larger and better growth than the control. That was plan anyway, i just didn’t quite get to it.

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You can see here we were trying to use a volt meter and another coil to see if we could detect that our coils were working. We weren’t having much success with the meter in the beginning and i don’t remember if we did later after increasing the power supply a bit. But in theory you should be able to measure with a second coil.

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I placed it on three smallest tomato plant clusters in the very late planted tomato patch. Interestingly enough, the three plants it happens to be on might be the only three blue tomato genetic varieties that survived my haphazard tomato disasters this year. Since placing the coils on these plants i have noticed an improvement in them and they have since catched up to the growth of the other tomato plants in that spot. Although at the same time i did also make a furrow and started watering them more. But even so i’d be willing to go out on a limb and say that the coils did help them go from “runt” status to catching up to the others. I may yet get a few tomatoes from the larger two before winter hits. Thanks to Gilbert for providing the motivation to actually build this project. And a thanks to the Homegrown Goodness plant breeding forum where i get so many of my adventurous gardening and plant breeding ideas. You guy’s are the best and a continual inspiration to me. Read more: http://alanbishop.proboards.com/thread/8623/breeding-tower-potato-ideas-wanted?page=13#ixzz4LoiDtFZE

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So, while my experimentation was a bit haphazard this year i think i still did ok. It was a fun project that went from an interesting patent to a cool project idea in my head and at the back of my mind, to a fully functional project / prototype. Plus i think these coils look cool. haha.

But it makes me wonder what other cool patents are out there that i can exploit, reverse engineer and build to experiment with. One of my next projects i think will go the opposite route and will be heavily steeped in Open Source as i think i will try and build a “Food Computer“. Basically it’s a small climate controlled aeroponic grow box. It should allow me to continue my plant breeding efforts even in the winter which is really what i want. Plus it will allow me to learn more about this “urban gardeng”, “vertical gardening”, and “aeroponic” stuff. I can’t wait to get back to pea, bean, and tomato breeding even though the summer and fall are waning fast. I think i’m going to repurpose my 2ft x 2ft t-slot frame that i was intending to turn into a large 3D printer and/or CNC mill. But it’s still going to be a long time before i finish that project, so i figured hey why not actually use it for something useful in the meantime! So.. that’t the plan.. 😀

 

 

Fixing Mesh Issues & Layer Gaps in 3D Printing

So today i had an interesting experience. As i have been lately, i sometimes go to the library to print out parts I’ve designed for my custom 3D printer project. While they print i use the time to crunch out upcoming essays for for school.

But this time instead of the printer happily moving along and producing perfect parts i got a rude awakening. The parts that came out looked like picture #3. Instead of my corner pieces being printed with two triangular pyramids and four “arms” they printed with one triangle, a “tail” and two “spaghetti blobs” on the side in a mess. It looked more like a deformed geometric fish instead.

Looking for info online i found helpful information on the Ultimaker Forum. It seems if i go into Layer view beforehand i can see what it will print out like and see any obvious gaps before hand. X-ray mode is even more helpful in a situation like this because if there are any faces or walls that have problems they get highlighted in bright red.

As you can see on mine, the bad models have several red triangular “internal” walls. The models have internal walls because they were created in Solidworks as assemblies from smaller parts and “digitally glued together”. Normally that shouldn’t cause a problem, but for some reason it did.

Currently i’m using Solidworks 2007 to create my 3D models. I wish i could use a good Open Source CAD program that works in Ubuntu Linux, but sadly none really exist. Not to my liking anyway. FreeCad has potential, but has a long way to go. OpenSCAD looks decent, but is for people who have mathematical minds. Sadly i don’t. And Blender has amazing graphics, but is not a CAD program. If someone could combine the beautiful elegance of Blender while stripping out it’s over-complexity and merging it with FreeCAD, and taking the user friendliness of Solidworks it would be perfect. Oh, and it has to be cross-platform (meaning runs on Ubuntu Linux). So until that day i’m forced to use a proprietary CAD program on a otherwise useless proprietary operating system, either on it’s own machine (or run in a virtual machine like Virtualbox). Far from an elegant solution. -End Of Rant. lol.

For me my problem was some sort of issue with the internal walls. Normally this should not be a problem. Since my version of Solidworks does not export whole assemblies as STL files (instead each separate part is exported into STL), I’ve been using 3dContentCentral to convert my CAD files into single STL files. Apparently the issue i ran into arises when i export my assemblies into single part files before converting them to STL. If i instead upload the entire assembly (and dependencies) and convert those to STL files it seems to work fine. Somehow that makes a difference when fixing whatever was wrong with those internal walls/faces. Whatever. At least i’m happy to find a solution.

I wanted to fix my bad CAD models from the beginning, but for example if i had a bad STL file that was not created by me and i still needed to print it, i could turn to Cura’s expert settings. In Cura’s expert settings there are some tools that attempt to “fix horrible” models that would otherwise fail to print correctly. I could have gone that route to print them anyway, but for me the better solution was to fix the source of the problem which was a bad CAD model.

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So, all in all, check your parts before you print them. Cura’s x-ray mode and layer mode are invaluable tools that can help you avoid problems with your 3D printing endeavors.

This site also gives some good tips on bad edge geometry and bad STL meshes.