If I want to go for QTL mapping in chickpea ( n=8) and If I take 90 markers then should it be equally be distributed to all 8 chromosomes.
90 markers are too less for mapping, particularly for QTL mapping in Chickpea (Genome is already published out from ICRISAT). Truly speaking to identify a potential QTL for your trait of interest you need more number of markers densely covered/distributed to all 8 chromosomes or to a chromosome of interest if in case you are going for fine mapping.
The equal distribution is necessary also to have a good picture of 8 chromosomes with markers. Also consider if you are selecting 20 markers each for Chr 1, 2 and 3 which adds to 60 and 8 markers each for Chr 4, 5 and 6 which then adds to 84 and take 3 markers each for chromosome 7 and 8 which then add to 90. In this case your linkage group with 3 markers on 7 and 8 will be the weakest to identify closest marker for your QTL of interest in your analysis.
If you are doing this analysis for the first time then you can do this to see how the analysis works. Moreover what markers are you planning to use ? if its SSR or DArT or SNP markers then i would say 90 is very less. There are several mapping works done and several literature are available from Rajeev K Varshney group of ICRISAT.
I think for initial analysis 90 markers are Ok in chickpea. Later on you can narrow down on the identified QTL with more markers as in chickpea population size is most likely will be around 250 or less so chances of recombination are very less in a narrow region,.
Dear Vaishali,
You should consider designs that optimize QTL mapping, such as F2 design, Back Cross, Half-Sib, Full-Sib, etc.
As long as you have a proper design, the number of markers you have is not a problem.
Also, it is indicated to have markers every 20 cM.
In this kind of QTL mapping you won't be getting sharp peaks as in associations studies (but also, not as nearly false positives as well).
Please let me know if you have more questions. Nick
Thank you all for such a wonderful suggestions. I have all 90 SSRs ( polymorphic in parents) and planning for QTL mapping. My population is RIL, a size of 286. I planted in ALPHA lattice design in two seasons. Being a Genetics and plant breeding, I am little bit weak in marker technology. Kindly help me out for planning for my genotyping?
90 SSRs could be ok if they are well distributed, covering all chromosomes. You can consider that as a "frame map" that, if neede, could be saturated later in specific regions. Any case, 90 SSRs x 286 indiv. represent a considerable work. They will be near 300 PCRs of 96 plates. I would suggest you, before to start the genotyping, to take a time to optimize a few multiplex PCR protocols. This could led later to very important savings in money and time.
Dear Jose,
I would like to thank you for your question. I have finished my Ph D in QTL mapping in wheat using 2 mapping population as in my page in reserachgate.
I think the number of both mapping population and DNA markers is ok.
First try construct your map. and then try to analysis your QTL using different QTL anaylsis software and different type of analysis.
Depend on the LOD score if you find some QTLs more than 3 (LOD >3) and repeated in 2 years it will be perfect QTL and markers.
this is a brief summary if you need any further question do not hestate to send me. With best regards
Khaled
Again with my knowledge on mapping, 90 markers are too less for mapping, particularly for QTL mapping in Chickpea. I would really appreciate if this work has been done a decade (10 years) ago but not in approaching 2015. I would really be surprised if you will identify a putative major QTL for your trait (LOD Score > 4) in your study. I am more afraid on publishing your work in an peer -reviewed journals with this 90 markers.
Anyway good luck for your mapping efforts.
what i can answer to you is that defiantly 90 makers are quite less to cover all regions of genome, even though you have relatively enough number of phenotype, your linkage map isn't gonna be precise to detect qtl and find the position of qtl to use more markers afterwards. if these 90 markers want to defined as frame work map firstly they have to cover almost all genome length (more than 1100 CM)in Chickpea and secondary they have to located in 10 CM interval, if your markers have the mentioned condition, do it, otherwise i dont recommend
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