Dear Sovetgul,

Thanks for your interest. At this stage you can't conclude nothing. To confirm if you find a partial resistance in your case you need to test at least 2 SSR marker (same chromosome or closely) in your F2 BSA population. The best way is to use an homozygotes individual (resistant and susceptible) as marker genotype. The second thing is to determinate the phenotype of your F2 individual. You need to performe Marker-phenotype association test (SMA in QTLIcimapping for example) with your 2 SSR. In case of association you have a partial resistance and you need exactly to order more markers on Chr 8 (near position or better to focus on other chromosome) to identify the position of each QTL associated to your trait.

I hope I anwered to your question.

I saw the bands and becomes unclear about your parents background. So, It would be better to know about which parent is resistance and which one is suceptible at first or either of them are resistance? In the BS1, both bands representing for suceptibility. Similarly, In BS2 also showed as nearly similar as P2.So, It looks like P2 is resistance but, what about P1? please clear first.

I examined your PCR products.The polymorphism result is not too clear . Between P1 and P2, which parent is resistant?. Do you try F1? , how is its resistance ?

I re-check my F2 and Parents as well. SORRY for dis-apart data I rushed with my findings thinking that was successful result. P1-Resistant parent and P2 is susceptible. However, BS1 is susceptible (two bands on picture) and BS2 is resistant (one band). Could it be recessive gene? We check F2 from green house inoculation and the inheritance ratio showed 186 susceptible and 228 resistant plants.

I think the SSR marker is not linked to the R gene. Normally, if P2 is susceptible parent , BS2 should be susceptible then your SSR marker is linked to the R gene. You need to add more markers and perform linkage analysis. Regarding the genetic inheritance of your Rgene you can do chi-square test.How did you proceed to get 186 susceptible plts and 228 resistant plants in F2 pop. Did you refer to the visual assessment of symptom severity based on different scale?(I want to know if there is clear difference between susceptible and resistant plants in F2 pop). On the other hand, you can evaluate phenotypic expression of F1?.

Thank you for your promt reply Amen Adedze,

I also think now it is not linked to R gene, now I design and order more SSR markers and this time i will focus on other (LG) chromosomes. yES, did visual assessments of 400 F2 pop like "0"-no symptoms, "1"-slight wilt of leaves, "3"- wilt and minor blight on leaves, "5"-minor doscoloration in stem, "7"-clear discoloration of stem and wilting and "9"- damoing off and withering. But our assesment based on "0", "1" resistant and "7", "9" as susceptible, because progenies showed clear symptoms . Is it necessary to evaluate expressison of F1? If we still have seeds of F1, we need to check based on your comments...

Ok i fully understand . You have performed short cut for gene tagging analysis. You have pooled two extreme phenotypes (resistance and susceptibility) in this study (see attached file for more explanation) . I have suggested F1 because this will help you to know if the R gene is completely dominant or partially dominant. Howver, this can be ignored . You do well to add more new markers for linkage analysis .

i think that if you are working with BSA than RAPD or ISSR marker should be best than SSR because RAPD and ISSR are single primer marker so it will amplify multiple locus in PCR. you will get definite result of BSA. after finding proper result you should illute that band and sequence it that will definitely perform as a linked marker to your trait of intrest