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

Authors: ALVARES, RENATA - Federal University Of Goias; STONEHOUSE, ROBERT - University Of Saskatchewan; SOUZA, THIAGO - Embrapa; MELO, PATRICIA - Federal University Of Goias; Miklas, Phillip - Phil; BETT, KIRSTIN - University Of Saskatchewan; MELO, LEONARDO - Embrapa; RODRIGUES, LUANA - Federal University Of Goias; SOUZA, LORENA - Embrapa; PEREIRA, HELTON - Federal University Of Goias

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2019
Publication Date: 7/16/2019
Citation: Alvares, R., Stonehouse, R., Souza, T., Melo, P., Miklas, P.N., Bett, K., Melo, L., Rodrigues, L., Souza, L., Pereira, H. 2019. Generation and validation of genetic markers for the selection of carioca dry bean genotypes with the slow darkening seed coat trait. Euphytica. 215:141. https://doi.org/10.1007/s10681-019-2461-y.
DOI: https://doi.org/10.1007/s10681-019-2461-y

Interpretive Summary: The slow darkening seed coat is a novel trait conditioned by a single gene that has been used to increase and retain seed coat brightness of pinto beans in the U.S. and Canada. ARS developed genetic markers linked with this trait which have been widely used by breeders in North America to facilitate development of slow darkening pinto beans. This paper describes the utility for these markers to breed for this slow dark trait in Carioca beans in Brazil. Carioca is similar to pinto bean in appearance but smaller in size and is the largest dry bean market class in the world. Utility of these genetic markers for ‘marker-assisted selection’ of seed coat brightness has now been expanded to South America. The establishment of slow darkening cultivars is relatively new; thus, it is too soon to discern how popular they will become compared to the traditional darkening seed coat types.

Technical Abstract: Seed coat appearance of dry edible beans influences consumer appeal. Slow darkening is a trait that helps to maintain a brighter seed coat appearance in certain market classes. The aim of this study was to generate new fluorescent-based markers and validate previously identified microsatellite markers for linkage to the slow darkening trait in breeding populations of the carioca dry bean market class (cream-colored seed coat background with brown streaked or striped pattern). Four segregating populations were generated from crosses between the slow darkening cultivar BRSMG Madrepérola and the regular darkening cultivars BRS Estilo, BRS Cometa, BRS Notável, and BRS Sublime. These populations were screened with the SSR markers Pvsd-1158 and PVM02TC116, and a TaqManTM marker designed for the SNP designated PvbHLHp12804. A KASP marker was also designed for the PvbHLHp12804 SNP for testing on advanced carioca germplasm lines developed by the University of Saskatchewan breeding program. While PVM02TC116 proved unsuitable for marker-assisted selection (MAS), Pvsd-1158 and PvbHLHp12804 markers were both tightly linked to the gene responsible for the slow darkening trait; with genetic distances calculated at 1.4 and 1.5 cM, respectively. The genotypic scoring using the PvbHLHp12804 KASP marker was perfectly correlated with the slow darkening phenotype segregating in all carioca and pinto (cream colored seed coat background with brown mottled pattern) materials screened at the University of Saskatchewan which fits the hypothesis that the SNP is within or very near the candidate gene. This work validates the use of SSR Pvsd-1158 as a gel-based marker for the slow darkening trait in carioca beans. The new fluorescent-based SNP PvbHLHp12804 markers exhibited very tight linkage to the slow darkening trait in all carioca and pinto bean materials tested to date. These markers will be ideal for marker-assisted selection for the slow-darkening trait within and across different dry bean market classes.