In that condition most of the people utilized SNP and SSR markers ..............
SNP markers have become increasingly important tools for molecular genetic analysis, as single base-pair changes are the most abundant small-scale genetic variation present between related sequences of DNA.
Better start with AFLP as AFLP does not need any prior sequence information. Other markers like SSR and SNP needs genomic sequence informations.
If you can get the genomic sequences of a related species try few SSRs along AFLPs that may give you polymorphism and then you will be able to say something about the chromosomal origin of that marker as well. I have tried few in cereals (but not for QTL analysis) and they given very good results.
if you are willing to sequence two parents of a mapping population, then you could make a SNP panle to screen the population and build a linkage map to map the QTL for your tait(s). However, i agree with the above, AFLP analyses usually give you alot of data to begin constructing a framework map, in the long term these are not as good as SSR or SNPs due to their repeatablty/ transferability between occasions and labs.
If there are SSRs for other members of the ginger family - that have been mapped to chromosomes, then these would be good in combination with the AFLPs to assign chromosomes. You could also try RFLPs. I assume you have a mapping population - thus as long as the marker type works, and is polymorphic for the parents then you can start to collect data to build your map. Good luck.
I you have a population suitable to produce a genetic map (say, a biparental population with enough number of individuals), then you may try genotype-by-sequencing (GBS). It is probably the hottest method, for a good reason. It provides large amounts of markers, and the cost per data point is really cheap, and you do no need prior genome information. But the total cost for a population and thousands of data points can be a problem. But costs are dropping rapidly, and SSRs or other in-house markers are not cheap either. There are a few companies that offer this service already, and you can shop around. The output combines SNPs and presence/absence variation.
Sequence AFLP by high-throughput sequence technology, it's my work under doing. AFLP, SSR, all are tedious task.
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