Hi Babar,

CSSLs are highly valuable genetic stocks for the genetic analysis for characterizing the genetic variants.

From my understanding, you are trying to map genomic regions conferring BPH resistance in a set of CSSLs. For this, you need to locate the genomic region, hence you need to survey whole genome (all the set of chromosomes of rice) for the locus conferring BPH resistance. To do that you need to use more polymorphic markers to achieve high resolution mapping. Hence, it is always better to use more polymorphic markers.

Having said so, resources are the key players. If you need to reduce number of markers, you may have to select the markers in a such way that those markers as much as possible equi-distant (genetic distance (cM/bp) on each chromosome. If you have more than 2 markers at the same physical or linkage position , they many not be informative and hence redundant. So, you can delete those markers. Similarly you can remove redundant markers for all the chromosomes to achieve highly informative marker system with high resolution to achieve efficient mapping to locate BPH resistance locus.

Thank you! all the best

Dear Babar

First, clear your aim of your study and related traits or genes and their location on chromosomes.

Second, select linked markers depended on your interested QTL/gene.

Hope this aticle will help to design the study

Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

https://www.nature.com/articles/s41598-017-06084-4

Thanks to all researchers ! You people are really great.