Generation and validation of genetic markers for the selection of carioca dry bean genotypes with the slow-darkening seed coat trait

Slow darkening (SD) is a trait that helps to maintain a brighter seed coat appearance in certain market classes of dry beans. The aim of this study was to generate new fluorescence-based markers and validate previously identified microsatellite markers for linkage to the SD trait in lines of the carioca market class. Four segregating populations were generated by Embrapa, the Brazilian Agricultural Research Corporation, from crosses between the SD cultivar BRSMG Madrepérola and the regular-darkening cultivars BRS Estilo, BRS Cometa, BRS Notável and BRS Sublime. These populations were screened with the simple-sequence markers Pvsd-1158 and PVM02TC116 and with a TaqMan™ marker designed for the single-nucleotide polymorphism (SNP) PvbHLHp12804. A KASP marker was also designed for the PvbHLHp12804 marker for testing on advanced carioca lines developed by the University of Saskatchewan. In the carioca lines developed by Embrapa, PVM02TC116 proved unsuitable for marker-assisted selection (MAS). Both the Pvsd-1158 and PvbHLHp12804 markers were found to be tightly linked to the gene responsible for the SD trait, with genetic distances calculated at 2.8 cM for Pvsd-1158 and 2.0 and 3.1 cM for PvbbHLHp12804, respectively. These markers presented more than 97% of selection efficiency. The genotypic scoring using the PvbHLHp12804 KASP marker was perfectly correlated with the phenotype in all lines of the University of Saskatchewan. The results of this study validates the use of Pvsd-1158 as a gel-based marker for SD in carioca beans. The new fluorescence-based SNP PvbHLHp12804 markers exhibited very tight linkage to SD in carioca and pinto bean lines. These markers will be ideal for MAS for the SD trait in these market classes.