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

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.

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


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!!

F1 hybrid between domestic tomato and Solanum pennellii
Flowers of an F1 hybrid between domestic tomato and Solanum pennellii
F2 cross of domestic tomato and Solanum habrochaites

A Teosinte Christmas in Colorado

So, i know I’ve blogged a bit about experimentally growing Teosinte in my post about growing prehistoric corn and also in my post about differences between teosinte species. Both posts have gotten quite a bit of traffic over the years and have brought people to my blog who are interested in Teosinte specifically.

For those of you who don’t know Teosinte is a progenitor to modern Corn (Also known as Maize), which is still able to interbreed with Corn. Some teosinte is annual, while others are perennial (or maybe bi-annual). There are many people who are interested in breeding perennial teosinte with corn to make perennial or bi-annual corn.

The major problem with trying to grow Teosinte in a moderate climate as here in Colorado in the United States is that it is adapted to grow in the climate of mexico and our growing season just isn’t really long enough. Even more so since Teosinte is day-length sensitive and does not even start to tassel, silk, and pollinate until the days get short and the sunlight shifts deeper into the red spectrum. By the time that happens here it is usually around August and often we get snow by September or October. Definitely not enough time for Teosinte or Corn seeds to mature and dry down for saving. …Or is it?!

Well, this year it just happened to turn out just barely long enough. I’m calling it my Christmas miracle! haha. I think it was a combination of it being a La Nina weather year with an unusually warm fall with no snow until here in December. But also with the fact that i dug up my clump of teosinte plants and put them in a pot in the garage. Though they were a bit unhappy in the garage and were touching the ceiling.

Still i was able to keep them in there long enough to hand pollinate them. But to be honest i thought i had again failed to get viable Teosinte seeds. But when the plants were dead i went out and happened to find some! Above is a picture of what i believe to be seeds of ‘Zea mexicana’ teosinte seeds.

If there is one moral of this story that you should take away it is this: Never give up even when everyone else thinks you are crazy or tell you that what you believe is impossible. I learned this in gardening from my friend Joseph Lofthouse of Utah. He has had success with so many of his unusual crops that no one else in his valley of Utah is able to grow. He often starts with many varieties of a plant as possible and grows as many as he can. Often more than 90% of them die or fail to produce seeds. But he only needs a few that do. Once he gets seeds he can start to effort to plant them year after year and adapt them to his climate. If they still fail to thrive he lets them die or culls them off himself. But he has a variety of unusual crops, such as Landrace Watermelon adapted to Utah (and by extension Colorado), Landrace Cantaloupe, Landrace inter-species hybrid squashes, Tomatoes that are self-incompatible and are highly attractive to bees (modern tomatoes are not at all and are highly inbred), and more.


On the left here is a photo of one small cob of a teosinte hybrid (zea diploperennis-corn hybrid from the USDA) pollinated with what i believe to be flour or field corn pollen. On the right is the same teosinte-corn hybrid cob line but i believe this one was self pollinated with its own pollen. It seems to have popcorn heritage as the seeds show popcorn / flint corn characteristics.


Here is another strain of day-length neutral teosinte (decended from Zea mexicana) that a collaborator Joseph Lofthouse of Utah is growing and having success with. I believe he got the seed originally from NativeseedsSEARCH in Arizona. He decided to test if it makes good popcorn.


Here is my Teosinte clump in the summer of 2016.


Here is the same spot with snow on it now in winter.

If you’d like to follow the discussion about growing teosinte in places it is not normally supposed to grow (or other unusual crops) then visit the Alan Bishop Homegrown Goodness plant breeding forum here!

Gardening with Conductive Helical Coils 2016


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.

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.


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.


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.


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:





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.. 😀



‘Wild Pueblo’ Squash Variety (2015)

Wild Pueblo Squash, Loveland Colorado 2012

I feel somewhat bad that i haven’t done much with plant breeding posts or other projects like my homemade Taffy Machine, or chemistry. I had some of those projects listed on my website. Unfortunately my website has been neglected my me and is currently down and redirects here. Perhaps by next year i can work on it again. Until then, i will try my best to diversify my blog and post some of it here.


This year i was able to grow some squash. In particular i was able to grow a few plants of my ‘Wild Pueblo’ Squash. Cucurbita maxima ‘Wild Pueblo’. Wild Pueblo is the name i have given it after both of our native pueblo ancestry. The woman who was kind enough to give me seeds was originally calling it Wild Hopi. But since i do not know if this is specifically a squash grown by the Hopi i decided to rename it. In any case it seems to be an Ancestral Puebloan variety of squash that is very old.

Photo by Bobbi HolyOak, 2011, Moab Utah

In the past i never really cared that much about squash. Probably because i always had the attitude that all squash are the same. But, since I’ve been trying to find my own crops that are personal and thrive in my climate (even resorting to breeding some from scratch), I’ve decided that it would be incomplete without my own squash. In fact i think my squash are becoming my favorite thing to grow. I have a feeling that squash are going to be my favorite crop. There is just something special about seeing a squash plant growing from seed. Almost sacred and special. It’s hard to explain. Corn has a similar effect on me, but even more so with squash.


Wild Pueblo was originally recovered growing in the wild of southeast Utah somewhere around the Monticello area. Close to the famous Newspaper Rock historic site. It was said to be found off the beaten track growing behind an old somewhat hidden pueblo ruin. Next to the ruin was a small stream. Growing next to the stream was a large squash plant with several large ripe squash fruit. I estimate that it is possible that it could have been growing undisturbed in that area for over 150 years! If so, this thing could have some awesome genetics. I’m doing my best to grow out the seed and preserve this variety.

Wild Pueblo Squash, 2012
Wild Pueblo Squash, 2012, Loveland Colorado
Wild Pueblo Squash on the left. Hopi White Squash on the right.

I suspect Wild Pueblo is an older variety of squash which may be related to a landrace which may have been used to breed the variety called “lakota squash”. according to reports…

“The Lakota squash, a mid-1990’s open-pollinated introduction developed at the University of Nebraska by Dr. D. P. Coyne. Dr. Coyne experimented with crosses and selections to assure more uniform pigmentation of this beautiful squash before making it available to the trade.

Lakota squash was developed from seeds obtained by the University from Nebraska’s Fort Robinson, once a prairie Cavalry post, later an agricultural site, now a National Park. The variety it was derived from is no longer in cultivation. It had been grown by Native American peoples along the Missouri Valley for centuries before the arrival of Europeans to the continent. This indigenous squash was also cultivated by the troops stationed at Nebraska’s Forts Atkinson and Robinson, and by early Nebraska settlers.”

Edit: after talking to someone at the University of Nebraska who worked with Dr. Coyne with the original germplasm of the non-hubbard parent landrace of squash i am told the fruits were actually oblong. Still might be worth trying to grow out that accession of seed before it’s no longer viable and available… i will see if i can get some seed…

I have only grown this variety twice, but even so it has some incredible diversity which i find absolutely fascinating. In time i think i can do some great things with it, perhaps even selecting it to grow even better.

Photo by Bobbi HolyOak, 2011, Moab Utah

This year was a very odd year to grow things. Perhaps the El Nino weather was to blame. I don’t know. All i can say is that my squash took all season to grow anything at all. I only got one plant that grew big and produced a large squash, the rest were small, but contained seeds. Next year i will try to plant more and do better.

Like i said before, it has a LOT of diverse genetics!


All i can say for now is that it is good to be home.

Pea Breeding Resources

Pea Breeding is actually really awesome. Especially when you can get really neat colors to recombine into new combinations. Punnet Squares to predict the genetics of pea breeding is also very helpful and fun too. This page contains a multitude of information on pea genetics.

(This page was originally hosted on my test website, but since i am hosting it myself on my own computer it is not exactly a reliable place, and hence i have copied all of the relevant information here to my blog as a permanent place to find it.)

Details of Mendel’s Pea Breeding

Here is a copy of Mendel’s original paper, for those who are interested.

biologyThe Results of Mendel's crosses for seven characters in pea plants

The following pea breeding illustrations were obtained from the Eighth Edition of Biology by Neil A. Campbell. I’ve scanned the relevant illustrations about pea breeding. If you would like to view the genetics section in PDF form instead, then here you go: You can read the whole genetics chapter in a virtual pdf online.

crossing pea plantsF1 Hybrid Pea Plants

Pea Alleles, Locuspeas F2 generation

random combination of the gametes results in the 3:1 ration that Mendel observed in the F2 generationMendel Pea TestcrossMendel Independent Assortment


Rebsie Fairholm's Red-Podded Pea
Rebsie Fairholm’s Red-Podded Pea

If your still interested in pea breeding, then you might be interested in Rebsie Fairholm’s breeding projects involving peas. Not only is she breeding a very neat yellow sugar snap pea called Luna Trick, but she is also breeding an awesome red-podded pea as well! She not only shares photos and info about her crosses on her blog, but she has also provided 2 excellent tutorials for crossing peas with photos! Many of us amateur plant breeders are attempting and making progress on recreating Rebsie’s red-podded pea success here.

Trying to figure out the gentics for this rare red-podded pea is facinationg! Here are my attemopts to figure it all out with punnett squares below.

Parent Generation (P)
F1 generation if purple-pod parent is homozygous for the purple gene

F1 yp yp
purple pea
purple pea
purple pea
purple pea
F1 generation if purple-pod parent is heterozygous for the purple gene
F1 yp yp
purple pea
purple pea
Gp Gypp
green pea
green pea

But as it turns out, Rebsie’s results actually had mostly green pods. And upon doing some research about the genes responsible for the purple-podded trait, we actually find that there may instead be 3 genes needed for the anthocyanins to be present. One gene commonly called “A” is a master swich gene and is epistatic to the other genes coding for anthocyanins. The other two genes are also both required for the pod to have purple-pod’s. If this is correct than that means the punnit squares i completed above are no where close to being accurate. Here is the F1 hypothesis again, and this one as far as i know is correct this time. I have used the letter “A” to represent the on/off gene, along with “P” and “U” to represent the two purple-pod genes. I have left out the yellow podded gene because all offspring will be hetozygous for a base pod color of yellow/green.

Here is the corrected F1 generation hypothesis using the three genes for purple anthocyanin colors. We are ignoring the gene for green/yellow pods for the moment since all offspring in the F1 generation are heterozygous for dominant green and recessive yellow.


That gives us a ratio of 28 Purple : 36 Green.

So I guess Rebsie was right; in the F1 generation mostly green pods appear.

Here is the F2 Generation Hypothesis using the rule of independent assortment. Now this table is not entirely correct, but represents the “average” offspring collected from the purple-podded plants in the F1 generation. I say the average because in the best case scenario you can get purple-podded plants that be homozygous for ALL of the purple genes. On the other hand, the worst case scenario is that the purple-podded plants in the F1 will be heterozygous for ALL of the purple genes. In most cases though i think that the average purple-podded plant in the F1 will have two homozygous genes and the third gene will be heterozygous. In that case you would only need to worry about two sets of genes in the F2, nameley 1 set for anthocyanin and 1 set for yellow pods underneath.
Which in this “average” scenario results in the typical 9:3:3:1 Phenotypic Ratio.
And in this case the red-podded peas are the recombinant offspring that we are loking for.
If we take that a little furthur, that means that if you plant 50 F2 generation seeds, you should get a ratio of about 43 non-red pods : 7 red-pods.

Inheritance Of The Colors Of Pea Flowers

Mendelian Inheritance Of The Colour OF The Flower In The Culinary Pea

Pea flowers (the edible kind) come in three major colors. They can come in the “wild” form which is a Bicolour Purple, White, or Salmon Pink (pink-and-white). I first encountered this information on Rebsie’s blog, and after doing some research of my own, i found one refrence to the same imformation in a very old book from 1912 (Breeding and the Mendelian discovery by A.D. Darbishire). The purple form is dominant and is a trait mostly common in field peas. The pink form is recessive to the the purple, but is dominant to the white. The white form is recessive to all color, and is commonly associated with modern peas that have been selected for high sugar content. It’s a bit amusing the way the book talks about the purple form in relation to the other two. Apparently if you breed the pink with the white you will get purple in the F1 generation because the pink has the gene that expresses color, but the white is actually hiding the gene for purple flowers. In the book this is talked about as an ancestral trait, a throwback, and the theory of reversion.

In Darwins book, The Origin of Species, Darwin himself encounters something similar with his breeding of pigeons. Darwin bred a pure white pigeon with another white pigeon (with black tail feathers), and was very surprised because in the next generation he got a blue pigeon (which has the same coloring as the wild rock pigeon). But Darwin didn’t know about genetics, so he could only conclude that it was a ancestral throwback phenomenon. We now know that the white one with black stripes had the gene for color (black) and the pure white pidgeon was actually a blue pidgeon but did not have any active color genes. To my knowlwdge the only variety of pea known to have pink flowers is the one called ‘Salmon-flowered’.

Salmon-flowered, pink, pink-and-white pea flower Bicolour Purple pea flower white pea flower

Pea Breeding 2015: The Quest for the Red Podded (snap) Pea

A rough example of how the genetics work in peas to create a red-podded pea.
A rough example of how the genetics work in peas to create a red-podded pea.

Gardening this year has been sparse. Mainly Peas, Watermelon, a few purple-stalked indian corn plants, 2 sunflowers, and some pepper seedlings. However progress is being made on the pea breeding front. Thanks to Joseph Lofthouse i was able to receive a small sample of his F4 cross between an unremarkable and unnamed, but yellow snow pea and Sugar Magnolia a good purple snap pea. This has expedited my own quest for a good red podded pea.

Joseph’s F4 Red Podded (snap) Pea
Contrast between a red podded snap pea and a yellow snow pea
partially red-podded peas
yellow snap pea with red spots
Partially red partially yellow snow peas

For those who are interested roughly in how the genetics works i will give my best simple explanations here. The modified google logo above is a horrible, but extremely basic diagram of how the red podded peas are bred. It requires the combination of yellow podded peas (which are recessive) and purple podded peas which are dominant (however there are three genes involved, which means that if only some are present they are only partially dominant). Purple pods have a green pod underneath, but if you can get a yellow pod as the base color, then you get red pods. The real trick after crossing such peas is to get the recombinant offspring that you desire. You need to get two recessive genes for yellow pods in addition to at least 1 of each of the purple genes. But if you only get some of the purple genes and not two copies for each then you get splotchy pods. You get partially yellow partially red pods. Sometimes this can be fixed by just growing several generations and letting them segregate themselves. This is possible because peas are naturally self pollinating. The problem is sometimes one of the purple genes will segregate out and you will forever have only a partially red pea pod which will never stabilize unless you use it to do another cross.

Here is the predicted results of the F1 generation between a purple podded parent and a yellow podded parent, with the assumption that the purple podded parent is heterozygous for all 3 purple genes. This chart was done after reading about rebsie’s F1 generation having mostly green pods.


Here is an “average” prediction of the F2 generation. This is excluding one of the purple genes, because by this point you should be selecting from only purple pods. green pods will never give you purple pods, which in turn will never give you red pods.

Even Joseph’s F4 generation is still segregating between Snap pods and Snow pods, and red and yellow pea pods. So, I have some of my first red podded peas thanks to Joseph Lofthouse in Utah. And i’ve been doing as many pea crosses as i can myself. Not only for red-podded peas, but umbellatum types, pink pea flowers, large pods, snap pods, dwarf plants, etc. Should be fun. 🙂