I guess both methods serve different purpose, so comparing them is not so logical.

However, this question is not something you ask people about what to do, one has to design such studies based on what one want to see/analyse.

Abhijeet Singh , Thanks for the response. But, I mentioned the trait, earliness. And considering the cost + timeline in getting the candidate genes identified for further use in MAS, which method is advisable?

Rajesh S Patil

Yes you mentioned the trait, however, as no information was provided regarding what studies has been done before regarding markers, i.e. do you already have candidates or this would be first trial for marker selection.

As I am not well aware of the recent advancements in cotton breeding, I was not sure from which stage you should continue.

However, most common techniques in MAS (which I have seen) are genome based, for example: SSR, TILLING etc. So I was wondering what was your rational for transcriptomics studies. Since transcriptome is the expression of genes which happens at certain age of plant, how would that be used as MAS at earlier stage. Sure, that can be used for the identification of genes etc.

Moreover, transcriptomics needs several replicates and careful experimental design. The cost not only depends on the sequencing but data processing and analysis as well. Of course, transcriptomics data analysis is more complicated as compared to genomics data, thus this will also be a big factor for the selection of appropriate technique.

Conclusion:

Based on the current literature, techniques in trend, your purpose, your data processing capabilities, computational resources etc. you can choose a technique which suits your goals the best.