Greetings of the day. I hope to find you all in the best of health and spirit. I am currently working on detection of Bru1 gene in sugarcane germplasm (S. officinarum, E. arundinaceus and S. spontaneum) for brown rust resistance. I have found an increasing dissociation between results of both markers while working on E. arundinaceus and S. spontaneum as among all entries 32 produced target band at 200 bp using 9O20-F4-PCR-RsaI but among them only 4 entries produced target band of 570bp using R12H16-PCR. Moreover, there were few other entries which produced target band of 570 bp with R12H16-PCR only. For S. officinarum both markers gave exactly the same results.

This dissociation between both markers has been attributed to a very rare event of recombination (Costet, L., L. Le Cunff, S. Royaert, L. M. Raboin, C. Hervouet, L. Toubi, H. Telismart, O. Garsmeur, Y. Rousselle, J. Pauquet, S. Nibouche, J. C. Glaszmann, J. Y. Hoarau, and A. D’Hont, 2012: Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars. Theor. Appl. Genet. 125, 825—836). Same dissociation between both these markers has recently been reported in eight accessions (Neuber, A. C., F. R. C. dos Santos, J. B. da Costa, M. Volpin, M. A. Xavier, D. Perecin, R. C. V. Burbano, M. G. de A. Landell and L. R. Pinto. 2017. Survey of the Bru1 gene for brown rust resistance in Brazilian local and basic sugarcane germplasm. Plant Breeding. 136 (2): 182–187.).

I want to have a better and detailed understanding of this phenomenon as I am new to molecular genetics and don't have much expertise in the subject. Therefore, I request your kind opinion and suggestion on it that how I can understand and explain this phenomenon?

Can anybody help?