GBS, coverage and heterozygosity

I’m running some tests on my GBS data to look for population expansion. I know from looking at GBS data from an F1 genetic mapping population that for GBS data heterozygotes can be under called due to variation in amplification and digestions. Also, for my data observed heterozygosity is almost always under expected. Heterozygotes can also be overcalled when duplicated loci are aligned together. The tests I’m going to use explicitly use observed heterozygosity so this is worrying.

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Hydroponics test run

Dylan and I have been working on getting hydroponic testing up and running. The basic set up is a large tub filled with dilute nutrient solution, with aeration provided by an air pump. Floating on top of the water is a large foam sheet with holes. In each hole we put a 2 ml tube packed with rock wool and perlite along with a seedling. Extending below the hole is a large bubble tea straw to make sure the roots don’t tangle together while growing.

Dylan with hydroponics

Dylan holding the foam board

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Drooping flowers cured?

Earlier this year, Kate’s sunflowers in the hort greenhouse were having an issue where the stem right under a maturing flower would darken and wither. The flower would droop down and gradually die. This was particularly annoying when trying to collect seed from crosses.

I’ve been growing H. bolanderi in the hort greenhouse and my plants seemed to have the same issue. When I saw this happening I trimmed off the drooping flowers, which occurred on about 10 of 24 plants. I also noticed that the new leaves were browning at the tip, a symptom of nutrient burn, so I flushed the soil by excessively watering it once.

A week later my plants no longer had any head droop and some flowers that seemed iffy before were fine. The leaf tip browning also reduced. I’m not sure if flushing the soil was the cure or something else happened at the greenhouse or it has only temporarily subsided. This is just something to try if you have the same problem.

One interesting note is that my plants are serpentine adapted and Kate’s are dune plants, which are both fairly nutrient poor soils. Perhaps they are extra susceptible to nutrient burn.

GBS protocol Version 2.0

Hi all,

Here is the long awaited updated GBS protocol.

PROTOCOL ->>>> GBSv2.0

There are three main changes from the previous protocol.

-After digestion and ligation, all the product is kept so more attempts can be made at the PCR.

-The PCR uses Phusion Taq, has longer extension times and one additional cycle with more primers/Taq.

-Size selection is done using AMPure beads instead of gel extraction.

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Seed size in H. exilis

Here is a curiosity I noticed while sorting seeds.

At one of my H. exilis sites (G136) there was a serpentine field beside a raised road. The field had a large population of tiny sunflowers, but there were also a few plants on the gravel embankment beside the road. These plants were much bigger, probably because the soil used in the embankment wasn’t serpentine. I collected seeds from both field and roadside plants.

The roadside seeds are much bigger than the serpentine seeds.

This has several possible explanations:

-Plasticity. The non-serpentine plants are much bigger, being bigger makes their seeds also larger.

-Selection. Bigger seeds are better on the disturbed habitat of the gravel embankment.

-Introgression. Gene flow from H. annuus could be coming in and only persisting on non-serpentine areas, bringing larger seed alleles.

GBS Protocol (GregO)

Kristin and I have been working on GBS for a long time and since it now seems to be working, we wrote up a protocol. It is mostly the same from Greg Baute’s previous protocol, but with a few key changes (More DNA, more PCR). I’ve made it look nice and included a diagram for ease of thought.

Also, the official pronunciation of GBS is ‘jibs’

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Compiled Sunflower QTLs (GregO)

Last year I worked on a project to see if any of the domestication outlier genes were found with previously mapped QTLs. The project ultimately fell flat when new data showed that the outlier I was working on wasn’t an outlier, but I did compile a large table of sunflower QTLs which may be useful. The table has 369 mapped QTLs.

I’ve shared this with a couple of people, but I’m posting it here on a google doc for everyone to use. Here is the link: https://docs.google.com/spreadsheet/ccc?key=0AgfXIvTZMEqPdHdJWTk3UVlVa3dkdGFTak9ySlUtNkE

A couple notes:
-It was compiled about a year ago, so it may be out of date. Also, although I tried to include every applicable study, I may have missed some. If you do find a study that I missed, I encourage you to add it to the table.
-It is only from annuus crosses, and a majority are domestics
-The position values are in cM

Anyway, read and enjoy. Change it if you find errors or new papers!