I have the SNP data within a 500kb region ~for 400 rice genotyeps. Some genotypes may have recombination events at this region, representing as successive SNP alteration. For example, the DNA sequence for most genotypes is AAAATTTT or CCCCGGGG. The sequence for the potential recominated genotypes is AAAAGGGG. The presence of this genotype should be resulted from recombination. My question is that how can I confirm this recombination scientifically and statistically. It should be better to provide me some references. Thanks
Scientifically, you would show the recombination by sequencing the DNA from individual plants. Just find other papers on sequencing plant strains and you'll get a good start on your references. Rice is a classic study plant so there are thousands of good recent publications.
Good luck!
If you have SNP data, it means that you have performed some sort of sequence alignment to determine these variants.
I suggest you use the multi-sequence alignment file as an input into a program that identifies and pinpoints recombination events.
To give an example on bacterial genome sequences that i work with, i align the genome sequences to find SNPs in core genes ( with Snippy https://github.com/tseemann/snippy ) .
Then i use the sequence alignment fasta file as input into Gubbins ( https://github.com/sanger-pathogens/gubbins ) which determines recombinations and is really nice to visualize with Phandango
( http://jameshadfield.github.io/phandango/#/ )
I suggest you use the multiple sequence alignment file as input into Gubbins and then visualize the stacked alignment with recombination loci shown according to the positions in the sequences. Not sure if Gubbins optimized for short sequences of rice genomes, but it's worth a shot.
Hope this helps,
contact me to brainstorm this further
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