Dear all,
We have been working on QTL analysis for plant multi-parental population. As a initial stage we are going to perform bin mapping process for the population. Thus there is a need of defining the recombination blocks in this population. I understand for bi-parental population it is quite straight forward approach. But for multi-parental population I could only get a package called RABBIT. I am unable to employ that at this time point because I don't know Mathematica. Thus I am looking forward to any other solution to this module of work. I would appreciate if anyone can help or comment on this.
Thanks in advance.
Hi Sourav,
Albeit somewhat complicated, one solution is to calculate founder strain haplotype probabilities (i.e. the probability that each SNP was inherited as a part of founder x's haplotype, giving you N-founder probabilities for each marker) across the genome. A sudden change in probability, as you travel across the chromosome, indicates a recombination event. I'm not sure if this applies to plants as much as it does to model organisms, but here is a paper that uses this method for a Diversity Outbred mouse sample: https://www.ncbi.nlm.nih.gov/pubmed/28592499
Hope this helps,
Kristin M.
Hi Kristin,
Theoretically this should solve the issue. Thanks for suggesting the specific solution to the problem. I will try to employ the same.
Thanks again.
Sourav.
The above approach assumes you have marker order but I assume you are doing this as a step towards ordering. Two point linkage mapping can be used to establish bins by collecting sets of markers with zero recombination. This will be complicated by pairs not being fully informative for each parent. If you start with a subset of higher informative markers that would help. Multipoint mapping in each set at the end would check the set has no recombination.
- Badges
- Science topic
- Similar topics
- Microbiology
- Assays