Saving seeds for next year

F4 Photo updates

Only a genetics nerd...

... would do a Bayesian on this...

From my 28D3 F4s, (red cherries) none have the gf phenotype.  What are the odds that any are gf/+ and thus might have some gf/gf progeny next year?  Bayesian analysis to the rescue...

The F1 plant was gf/+.  F2 plant 28D was not gf phenotype; therefore it's prior probability of being gf/+ was 2/3.    Four F3 plants were grown last year; none had gf phenotype either.  28D3 was one of these.  What are the odds that 28D3 still could be a gf/+ carrier?

Hypothesis	Assume F3 = carrier	Assume F3 = non-carrier
Prior	4/9	5/9
Conditional (prob that all 3 F4s are non-carriers)	27/64	1
joint	0.141	5/9
posterior	(0.141)/(0.141)+(5/9)=0.202

Therefore the posterior probability that the F3 plant,  28D3, was a gf/+ carrier is 0.202.

Given this, the probability that any particular one of the 28D3 F4 plants is also a gf/+ carrier is = 0.202 x 2/3, or ~ 0.135 = 13.5%.    

Notes on F4 plants, etc. 7/24/18.

Passing the peak phase.   While the F4 plants at the farm pretty much accomplished my goals, it was interesting that those plants really struggled to grow large this season. None of the “beefsteak” F4s there – these were 8A, 46A, 55A, 10B - grew taller then about hip height; many of them are sort of dying off, and no so much catastrophically wilting but simply failing to grow while the rest of the plant kinda dies naturally; the growth was really limited.   I think it's mainly due to the late start.  Weather has been hot, but not overly dry.   Nevertheless, I got fruit, and saved F4 seeds from several 55A and 10B subline plants. In contrast, the 28D3’s (cherry size fruit) grew into very vigorous plants with lots of fruit.  Also saved seeds.

So.  Sublines 8A turned out to have no purple, so I am not pursuing these any more.

Sublines 55A has pretty strong purple, mostly, and good size, so I am saving several of these plants.

Subline 46A2 has similar phenotype to the F3.  Have two at home in containers, both of which had nice fruit set and I have saved seeds from the first one with ripe fruit.

Line 10B1 was interesting for a few reasons.  This F3 was not gf, but was large and purple so I saved it.  Turns out it was definitely gf/+, as one of the three F4’s is gf/gf, and so this one will compete with the 55A sublines as having gf/gf ; purple ; large size.    One F4 was large and ripe but had no mature seeds (!); later fruit from same plant had some, but few, seeds despite a nice beefsteak.  And one F4s turned out to be y/y as well as purple    So I have saved these too.

The two 46A2 plants in containers at home did MUCH better than at farm and are still going.  The 55A7 in a hay bale died of wilt, but grew to about 6 ft first and had good fruit set, though most fruit did not ripen before the whole plant died.   

The 28D3 F4 plants were interesting for their slight differences. All three were red cherries like the F3 parent.  However, #2 had more cracking and diseased fruit than #1 and 3, which were pretty much crack-free.  #1 and 2 avg. about 10 g, while #3 is ~12g.  #1 and 2 have no visible purple but #3 has just a tiny bit.  So 28D3.3 is the one to pursue.

Other notes:

The container plants are much better in terms of health and disease protection than hay bales or in-ground.  But the fruit was prone to end-rot.  Flamme and Green Zebra were most prone to this problem. Fruit set on KB and CG was poor.   

GDZ really seems just like RT to me.   GDZ is advertised as having fruit that mature more consistently than RT, but I’m not really convinced.

"Pink" fruit, epidermis pigmentation - the y gene

I've not really tracked the pink epidermis gene in my crosses, but I've realized that I should.  Here is a link to the outstanding Frogsleap Farm web page that explains it in detail.

"Pink" tomatoes are homozygous recessive for mutations in the y gene, which is necessary for yellow pigment accumulation in the fruit's outer epidermis.  Classic "tomato" colored tomatoes are wild type.  "Pink" varieties are slightly pinker than the standard red ripe tomato, which is a little orange-red.  It's pretty useless to really compare online images of pink and regular red tomatoes unless they are together side-by-side in the same photograph.

Frogsleap farm reports that Cherokee Purple, Green Zebra and Brandywine are y/y.    (A few years ago I grew Pink Ping Pong, but found it unremarkable.)   Since CP is y/y though, this suggests that "pink" was segregating in my IR x CP F2s, but sadly I did not pay attention to it, and I don't know yet if any of my saved F2s were y/y.   I think the answer is no.  However, there's a decent chance that the y allele was still kicking around in the F3s, so some of my F4s might be y/y.

Example below of +/+ and y/y skin:   A 28D3 fruit is clearly +/+, vs "Carbon" which is y/y (just ripe today).

Crossing progress update

As of about July 7, I counted 11 growing fruit from successful cross-pollinations.  3 others had end rot or broke off accidentally.  Total attempts to date: about 71 I think though not all got assigned serial numbers.  So the success rate is about 20%.

Three places for tomatoes

Comparison: week of July 4, 2018.
Patio containers; bales; farm plot. Lush; wilting; and slow but steady.

Harvest season starts. F4 generation fruit.

Finally seeing some ripe F4 fruit.  Still seeing clear phenotypic variation within progeny of individual F3s.

Blossom end rot

Many of my container plants have one or two fruit with BER. This includes a few cross-pollinated fruit; since BER tends to affect early-forming fruit, it's not surprising it is a problem with some of my early cross attempts.   Bummer though.  Historically I have not had enough BER to really be a problem.  Although the conventional wisdom all says it's a calcium transport problem, there is really nothing much to be done about it.   Apparently it's increased by both over- and under-watering, and over- and under-fertilizing.  !  Good luck figuring that one out.   Calcium sprays are widely recommend for use on the foliage, but it's not clear that this really does any good.   Also, supplementing calcium in the soil may not help much because the problem is not necessarily lack of Ca in the soil.  

The problem is supposedly caused by excess transpiration through leaves, which diverts calcium away from the developing fruit.   This may explain why excess nitrogen is bad, because this stimulates foliage development.  Actually my container plants are kicking ass in terms of foliage, but the fruit set is actually not that amazing.  This all seems related to excess fertilizer/nitrogen.  

More wilt

By now, I think every tomato plant in the bales is affected by wilt to a greater or lesser degree.  I have tried to aggressively prune affected branches on plants. This may have stalled it on a few plants, for a few weeks; for some of them, that may make the difference in getting mature fruit before the plant dies.

I think there are two types of wilt going on.  (1) The first is characterized by classic signs of wilt : drooping leaves at top of plant, asymmetrically affecting different sides or stems on the plant, and yellowing of leaves at the bottom of the plant.  The yellow leaves do not wilt right away.  (2) The second kind of wilt has similar top-wilt symptoms but instead of turning yellow, the leaves turn wilted first, droopy/crumpled up and greenish-brown.  It's a "wet" sort of wilting, not dry and crispy.

Seems like various bugs cause similar symptoms because they are all causing problems by clogging up the plant's vascular system.  Fusarium, verticillium, and "bacterial" wilt are all similar.  However the first is a fungus, the second is bacteria, and the third is a different bacteria - Ralstonia solanacearum.   Also, different "races" of Fusarium apparently exist.   

None of the 13 tomato plants in my containers have any signs of wilt.  

There are about a half dozen sporting tomato plants growing in the bales too.  Clearly, the bales got "well inoculated" with my homemade compost, which was teeming with tomato seeds!  These sports are less affected by wilt.  Perhaps this is just because they are younger, having germinated in (probably) early May.   I'll let 'em grow and see what happens.

Here was my initial bale planting setup:

bales = CA+MS ; WB+BC; HC+HC; FL+FL;  SG +  F4 #55A-7

Here's how each is doing as of 6/30/18.

CA:  Has wilt #2. Good fruit set.  Only part of the plant is affected by wilt. Plant still is somewhat healthy.

MS:  Killed by Wilt #1. Pulled it out on 6/23. 
WB:  Plant has grown to about 6 ft height, but fruit set is poor-to-fair (only a few fruit; blossom number low).   Wilt #1 slightly affected.
BC:  The most vigorous bale plant.  8 ft height.  Good fruit set.  Has slight wilt #1 I think.  Probably strong enough to produce a good number of fruit before it gives in.
HC #1: killed by wilt #1. Pulled on 6/20.
HC #2:  Has wilt #1 and going downhill fast now.   Strangely, this one had 2 germinated seeds in the original planting, right next to each other - so I just transplanted them both - but one of them is not HC, it's clearly a beefsteak-y type.  But it's got wilt #1 too.  Not sure if it will make it long enough to ripen fruit.
FL #1: killed by wilt#1, pulled on 6/20
FL #2: good fruit set, still growing, but has wilt #1 to a modest degree.
SG:  Wilt#1 is getting worse.
55A7:  Wilt#2 is getting serious.  This is a bummer because I've got a few cross-pollinated fruit growing and they are not ripe yet.

Farm update

Plants at the farm plot are mostly ok.  It's easier to maintain 24 plants than 100 like last year.  They are not as vigorous as my home bale and container plants, but that's to be expected as they were planted later, and are not coddled.   A few of the heirlooms died (CG, KB, ZPT) , but no big deal .

Seems like the 8A subline is not really purple.  However, 10B is!   Can't tell yet if any 10Bs are homozygous for gf.   Most 55As are clearly very purple, though I can see some variation in intensity.  28D3 is a vigorous cherry, though I can't detect purple on any. :(

Soon I will have to give these plants F4 identifiers. e.g. 55A-7-1, 55A-7-2, etc.

6/23/18

8A7 

46A2

55A1

55A7

10B1

Another one bites the dust

Mr. Stripey quickly succumbed to the wilt, so I put him out of his misery and pulled him up.  So, three out of 10 tomatoes in bales got bacterial wilt: one HC, one FL and now my only MS.  I'll have to wait till next year to see what that guy's fruit is like.   The MS did not even produce open flowers; some trusses were forming but would probably need another 2 weeks to bloom - about a month later than all the other varieties.

So clearly bales are not a panacea to disease. There are a few possible culprits here in order of my suspicion.  First, I put my own compost on the bales and that was dumb.  Easy to avoid next year.  Second, they have been getting sprayed by my ground irrigation system, so that might have been splashing spores around.  I could deactivate that station on my automated irrigation controller. Third, some of them may have put roots through the bottom of the bale, through the degrading cardboard into the ground.   One possible solution would be to put weed control mat under the cardboard too, to make a better barrier to roots & shoots. Fourth, the bales themselves could already have been contaminated when I bought them, which seems unlikely, and impossible to do anything about really.

On the other hand, the other seven plants are growing mostly great. The surviving FL and HC are OK, do not show signs of wilt and are still growing and producing fruit.     Carbon is doing nicely.  White beauty and BC are growing tall enough that I put 8 foot poles into the bales for more support; these reach about 9 feet off the ground!

Sun Gold had some signs of yellow low branches and a little drooping on one or two secondary stems. I aggressively pruned these off.  As of 6/23 the plant seems OK.


CA+MS ; WB+BC; HC+HC; FL+FL;  SG +  F4 #55A-7;

Flamme... has burned out

Mr. Stripey was not happy.  Two days later it looked awful and I ripped it out.

White Beauty and Black Cherry, together between the wood poles.

Carbon

More Crossing progress

As of today (6/20/18) I have attempted about 40 or so individual flower cross-pollinations.  The first week was sort of lousy because most flowers I used were too early in development I think.  As of June 10 I started using serial numbers.  Of these at least a half dozen are growing fruit already, hooray! And I am pretty sure more will be growing now that I have the hang of it.  Takes about a week to confirm the fruit is maturing.

A few wilting plants .... terminated

Two plants in my bales seem to have bacterial wilt:  wilting from the top down, at first seemingly as if they just needed water on a hot day, but nope.  So after a few days of this, today I just pulled 'em, bagged 'em and threw them in the trash.   These were one HC and one FL, which I note were both prone to wilt last year.  In each bale there is another one of the same type still doing OK.  Interestingly the other FL had some wilting and yellowing bottom branches a week or so ago, which I trimmed off, and now that plant seems pretty good.  I hope the bacterial wilt does not spread.   I am kicking myself because one of the points of bales was to avoid these sorts of contamination - and then what did I do?  I "inoculated" the bales with some of my own compost (because I was trying to help cure the bales).  Which is probably a terrible idea in retrospect because there is at least some old tomato plant material in that compost and god knows what else from my yard.   Duh.

Cross-pollination progress

This year one of my goals was to master tomato cross-pollination.   Having a dozen different healthy plants in containers on my back patio is a big help.

I started emasculating flowers on June 3, but by about June 10 I was wondering if I was focusing on flower buds that were too immature; turns out I was.  Here's a good link to a guide from UC Davis on tomato cross-pollinating that talks about this subject in detail:

https://tgrc.ucdavis.edu/Guidelines_Emasculating_and_Pollinating_Tomatoes.pdf

Starting around June 10, I focused on flowers that are probably at just the right stage, which is about 1 day before they really open.  This seems to be working to some extent.  I also am giving crossed flowers serial numbers.  By June 16, I could tell that at least a couple of these attempted crosses were growing fruit.    Seems like most of the ones I tried before June 10 obviously failed, or no evidence of success, at any rate.   As of June 19 I am beyond serial number 25 in my crosses.

Why do more crosses? Well why not?  It would be interesting to bring the stripe gene into my IRxCP lines, so I am crossing Pink Berkeley Tie Die to 46A2 and 55A7.   Also of interest, would be to cross Flamme or KB to RT, GDZ or even ZPT to make a yellow fruit with interesting shape.

Finally I am crossing RT to GDZ to test if they fail to complement.  This is tricky since if they fail to complement I expect the "lumpy" phenotype to be similar to either parent, which is probably identical to self-fertilization.   Since this could happen by accident I am hoping to get several crossed fruits so I can validate independently generated F1s (i.e., seeds from different individual fruits).  That would be more convincing than following seeds from a single fruit.

Stakes up

This year I have staked each plant in the farm plot.  With fewer than 30 plants, and more T-posts than that left over from last year, it was easier.  
So far most of the plants at the farm plot survived transplant and are on their way.

All in

Got the SCF farm plot all planted on Sunday May 20.   Layout in the 2018 map page link.  It has the F4 plants and some leftover heirlooms.

Rescued seedlings / damping off

A successful experiment.  I didn't have too many seedlings damp off, but I thought about the fact that when damping off occurs it only affects a very small area of the stem right at the soil/air boundary.  There must be something about that boundary that allows the infective growth.   

Now, tomato stems have hairs that can develop into roots if they contact the soil.  So I reasoned that if I took a damping-off seedling that had not yet wilted and (1) pinched off the roots below the damp-off site, and (2) replanted it deeper in fresh soil - with about 1.5 inches or more of the stem buried - and (3) treated with daconil and (4) kept it moist, then the stem would re-root and the plant could recover.    Tried this with two damping-off seedlings: an HC and an F4 46A-2.  Turns out it worked.  About 3 weeks later they both have started growing again - lagging behind the others by about 2 weeks of stalled growth, but now taking off.  

Still need to plant!!

I still have to put tomatoes in the farm lot.   Got about 23 F4 plants and about 16 heirlooms, tho I'll prob still give some of the latter group away.

Turns out I was fortunate to start seedlings late this year.  We apparently had a frost around April 19, which is a few days after the standard April 15 mid-TN "safe transplant" date for sensitive veggies.   Although I hadn't been hardening off my seedlings yet I was recording outdoor and bale temps and definitely had 35 degree temps in the morning around that time.  My backyard elephant ear plants normally survive the winter, but did not this year, so I suspected that April 19 killed them as they were starting; however I checked records and remembered that we had unusually cold low temps in Jan and Feb - below 10 degrees!  and maybe that did 'em in.

Containers 2018

I have twelve* 5-gal buckets on the back patio; holes drilled for drainage.  Tomatoes transplanted into them on 5/9/18.  Bucket mix was as follows:
50 qt bag miracle grow potting mix + about 1/2 of a 25 lb bag of "composted manure" which, since i got it from home depot, was "compost + manure".    I added 1/3 cup of my organic bone compost., which is basically a 7-8-6 fertilizer.   Mixed all this in the wheelbarrow and it was enough for about 4 buckets.
* Got one more bucket = 13 total.
Container tomatoes: PBTD, BZ, GZ, ZPT, RT, CP, BW, GDZ, CG, FL, KB, CA? 46a-2

Hoping to try some crossbreeding on these too.

Straw Bale Experimenting

This year I'm trying to grow tomatoes in six straw bales, as per Craig LeHoullier's book. On 4/1/18 I started his regimen for prepping the bales: basically, watering each day and spiking with granular fertilizer about every other day so they compost inside.  Being the science geek I am, I diligently recorded daily internal temperatures in the bales.  They are "supposed" to warm inside to 120˚ or more, then cool down, over the course of a few weeks.  Well, I never really saw internal bale temperatures over 80 degrees.  However the bale temps were consistently above the ambient air temperature, even on cold days.  And we had kind of a cold April with one or two nights down to 35˚ or so.   Anyway, from what I've read it seems that the increased internal temps, though not spectacular, do indicate microorganism activity was consistently doing its job to break down the bale.     By the first week of May I started seeing some mushrooms popping out of the bales.  They always died within a day.  This is exactly what one is "supposed" to see with conditioned bales!

On 5/2/18 I put 9 transplants in the bales, and 3 more transplants a few days later.  12 total in 6 bales (2 per bale).   Soaker hose in place.   As of 5/13/18 the transplants are thriving.
Transplants: CA+MS ; WB+BC; HC+HC; FL+FL;  SG +  F4 #55A-7;  plus 2 each store-bought basil and cilantro in one bale.

5/16/18 update:   Good growth so far.

Tomato germination 2018

I had to re-sow some of them, around 4/8/18.   More ZPT - these seeds were from 2013 and had 0/4 seeds germinated, so I re-sowed 2 seeds x 6 wells and got at least 6-8 or so up.   Also re-sowed several F4s, and one or two other heirlooms.    By 4/26/18, almost everything has at least some germinated - at mostly pretty good rates - and all have been transplanted.  The only failed germination was Lucky Cross.  Oddly this was a gift from Tomatoville this year, so they should be "fresh" seeds.  However I didn't plan on this variety anyway so no big deal.

Random notes: I sprayed Daconil on the soil tops after sowing.   By 4/25, just a couple of the last few seedlings that I had not transplanted yet had beginnings of damping-off, which is not bad out of about 70 or so seedlings.  However, I sprayed those guys with Daconil, gave 'em more soil, and the next day seemed more stable.  I guess if the infection is controlled and they can develop new roots above the old infection point they might make it.

Sowing heirlooms

4/1/18 I also sowed these:

BC, BZ, BTD, BW, CA, CP, CG, FL, GZ, HC, GDZ, GZ, HC, KB, LC, MS, RT, SG, WB, ZPT.    = 18 varieties!

New abbreviations:
BZ   Black Zebra
PBTD  (Pink) Berkeley Tie Dye
CA  Carbon
GDZ  Godzilla
LC    Lucky Cross
MS   Mr Stripey
WB  White Beauty

Sowing F4s

4/1/18 -  I sowed F4 seeds from these 2017 F3 plants from the IRxCP cross.

8A-6, 8A-7.                         

Gf. Biggest of the 8As. 250-300 g.  Might see an increase in purple color in F4s?

46A-2                                   

Gf, globe, nice purple

55A-1, 55A-5, 55A-7.  

Gf.  Better purple than 8A but might not be quite as big: 150-200 g.

10B-1

Not gf but good size and good purple, so kinda neat.  Gf homozygotes might emerge in F4s. Chance of any one F4 plant being gf/gf is (2/3 x 1/4) = 1/6.  

28D-3            

The purple-tinged cherry.

Not sure how to handle the nomenclature going forward, but I don't see why after this point I'd be inclined to save fruit from more than just my favorite single individual from any one line.  Going forward I can keep the F3 identifier and just append the generation, e.g. 8A6-F4, 46A2-F4, etc.