introns collect more changes as intron changes mostly do not have any effect so remain in the organism. Exon changes are often bad news so are quickly bred out and disappear so you should find more changes in the introns and intragenic sequence than in the exons in terms of changes /length analysed. Clearly analysing both exon and intron will generate more useful information than just analysing either one of them only

Yes, absolutely agree with Paul's answer. You may want to check first whether your target CHS gene is actually contain introns. If it is not, then you may want to also PCR the 3' non coding region of the mRNA (the gene sequence corresponding to the 3' NCR of the mRNA) since this part may also be more informative than the exon part of your target gene.

Good luck in your research...

In addition, make sure that when you design your primer, it should be in an area where there aren't any reported SNPs because if there are it will cause you trouble down the line.

Paul Rutland ,S. Sudarsono and Yara Odeh thank you so much