Dear Yustina

In the drought grain yield QTL identification as well as introgression programme in rice, SSR markers were widely used for their easy PCR amplification and electrophoresis, the abundance of these markers across the genome that allows elaborate coverage, and their co-dominance nature that allows the detection of heterozygotes, making them suitable for genotyping all kinds of mapping populations.

Flakning SSR markers will be best for this purpose

Yustina,

The methods you listed are very different in time of first application, cost, labor, and equipment demands. They are different in information value provided. If you like to test previously found markers in your plant population, you can apply RFLP, SSR, SNP methods. If you like to generate new data or study new plant - RFLP, AFLP, QAPD. But, if you plan long-term research and will use genomic data - please, concentrate your efforts on SNP.

Alex

Thank you so much for your answer Mr Seied Mehdi Miri , Mr Saheb Pal , and Mr Alex Ignatov.

Thanks also for your explanation about this... Okay I think I know what to do next..

Thanks a lot

First you must differentiate between strategy and tools. In the case of MAS strategies include: Gene pyramiding and marker-assisted backcross (MABC) and tools include any marker system such as SSR, RFLP, SNP etc. In both strategies it can be used a special marker system or combined marker systems that mainly depends on genome size and complexity, population size etc. First strategy is usually used for adding several genes controlling the given trait via selection of progeny carrying the desire allele, and 2nd strategy is used for transferring genomic region(s) containing the desirable gene(s) to a recipient parent via repeated backcrosses.

For more details plz find relevant papers.