Development of a coupling-phase SCAR marker linked to the Ur-7 rust resistance gene and its occurrence in diverse common bean lines

Bean rust, caused by Uromyces appendiculatus (Pers.: Pers.) Unger, is an important disease of common bean (Phaseolus vulgaris L.). A coupling-phase random amplified polymorphic DNA (RAPD) marker OAD12.550 previously was identified to be linked (no recombination) to Ur-7 of Middle American (MA) origin for specific rust resistance in the common bean cross of Great Northern (GN) 1140 x GN Nebr. #1. However, a sequence characterized amplified region (SCAR) marker for Ur-7 present in GN1140 has not been reported. Our objectives were to convert the RAPD marker OAD12.550 most tightly linked to Ur-7 to a SCAR marker SOAD12.537 for use as a marker-assisted selection tool, and survey the presence or absence of the SCAR marker SOAD12.537 in 90 MA and Andean bean genotypes for determining the genetic relationship of Ur-7 with Ur-6. The coupling-phase SCAR marker SOAD12.537 based on a specific forward (5'-AAGAGGGCGTGAGATCGTCGT) and reverse (5'-AAGAGGGCGTCTTGAAGGTT-3') primer pair showed no recombination with Ur-7 in an F-2 population of the GN1140 x Nebr. #1 cross. The SCAR marker was also present in pinto US-5 from which the rust resistance of GN1140 was derived and in the closely related pinto US-14. The cosegregating SCAR marker identified MA pinto bean cultivars/lines Olathe, Bill Z, Apache, Montrose, BelDak-RR-1 and-2, and CO 12783 that have rust resistance gene Ur-6 and also have Ur-7, identified in earlier literature as Ur(c), due to presence of the marker. Other cultivars/lines with Ur-6 such as Weihing, Burke, Kodiak, Topaz, Golden Gate Wax, BelMiNeb 1-13, BelDakMi 1-23, and other Colorado breeding lines lack Ur-7 because of absence of the SCAR marker for the MA gene. This SCAR marker linked to Ur-7 on linkage group 11 of the core P. vulgaris linkage map can identify a phenotypically hidden resistance gene, and along with markers for other rust resistance genes, can be utilized to pyramid multiple genes for more durable rust resistance.