I do have an offspring of plants. In theory it should be biparental. The plant is a strict outcrossing plant. However, I fear that about 30% are offspring from the selfed mothers plant. (Own quick and dirty analysis using the GBS data of available high quality markers (n ~ 1000))
Is there an already published tool for checking this?
I have the genotypic data for the parents and all offspring plants (GBS data, vcf file).
At he end this might be interesting for quality issues of the input data for a QTL study and eventually for the exclusion of individuals.
See attached: one SNP marker of this offspring with the relative frequency of callings in a diagram. mother is T/C, father is T/T, the last 9 daughter plants are C/C. This is not a mendelian segregation. I want to identify the plants that are inbred using the whole data set (ca 3000 high quality GBS markers).
We have tools for parentage analysis as part of our software for estimating relatedness from GBS data (https://github.com/AgResearch/KGD). The software is a collection of R scripts, and has a perl helper program for converting .vcf to one of the required formats.
Our approach is to account for read depth in the analysis, rather than filter out low depth data. It is still useful to filter variants which don't appear to be Mendelian.
The software needs allele frequencies, taken as the sample allele frequencies by default. For a small, related population this may result in relatedness estimates which don't seem centered correctly (would be better to estimate over a wider population), and so relatedness cut-offs may need adjusted to suit the particular situation. However, it ought to be clear if there are offspring with different parentage. If these are selfed progeny of the mother they would have higher relatedness to the mother (than the other progeny) and would have higher inbreeding.
With 3000 snps you should be able to work out the pairwise kinship of each plant quite readily. You could use Zoological Society of London's Coancestry package (J. Wang) which implements various ways of estimating relatedness including a couple that include inbreeding. The package runs in Windows and is stand alone. The package also includes the facility to simulate specified relationships (e.g. selfs and full-sibs) using the allele frequency of your empirical data to see what sort of bias the various estimates might have. But if you are really only looking to classify the plants into selfs and outcrosses that should be quite easy.
thx. In between, I am fine with the result I got ... cross-pollinations are offspring plants that show an allele that is not present in mothers and fathers genotype.
And selfings are the ones that do not have that allele in a vast amount of markers that the father is homozygous for.
Would be great if there would be a simple prog for that, but checking that by a self written python script is also possible.
Done.
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