Identification of SCAR and RAPD markers linked to Rz1 gene in Holly sugar beet using BSA and two genetic distance estimation methods

  • Seyed Mohammad Amin Feghhi, Peyman Norouzi , Abbas Saidi, Katayoun Zamani and Reza Amiri
Keywords: Sugar beet, Rhizomania disease, RAPD marker, primer pairs, Rz1 gene.


Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), is the most economically important diseases of sugar beet in
Iran. We have identified molecular markers associated with resistance gene(s) to this disease. A F2 population including of 106
individuals developed at the Sugar Beet Seed Institute, Karaj, Iran, was used to identify molecular markers associated with
rhizomania resistance gene from the Holly source. In this study, we used pair combinations of single RAPD primers in bulked
segregant analysis (BSA) of two bulks (resistant and susceptible) and F2 population individuals. Accordingly 397 pair
combinations of single RAPD primers were used. However, nine primer pairs showed polymorphism between DNA bulks. The
polymorphic markers were tested among the individual plants of the two susceptible and resistant bulks and further were used to
analyze the F2 individuals. Finally, the markers distance from the resistance gene was estimated by using both the Map maker
ver.3.0 and the frequency of recombinant plants method. Using frequency of recombinant plants method to tag Rz1 gene, it was
found that R1, R2 and R3 markers were 2.3, 8.3 and 16.6 cM apart in repulsion phase and C3, C4, C1, C2, C5, and C6 markers were
20, 21.4, 27.5, 32.9, 43.7, and 51.9 cM apart in coupling phase, respectively. On the other hand, tagging Rz1 gene by Map
maker ver.3.0 method showed that R1, R2 and R3 markers were 32.4, 44.5 and 60.1 cM apart in repulsion phase and C3, C2, C4
and C1 markers were 25, 34.7, 46.5 and 57.9 cM apart in coupling phase, respectively. After sequencing the products amplified
by MF1 and MF2 (Operon primers number have been replaced by these characters) primer pairs, new PCR primers were used to
generate the SCAR marker R1 (this primer sequence is under patent processing and will be shared once it gets patented) which
can be readily used for marker assisted selection in breeding programmes.
Research Article