Genetics and Mapping of the Cl Gene for Circumlineated Pattern in Common Bean Using AFLP-based Bulk Segregant Analysis and SNP-based Bidirectional Selective Genotyping

Abstract

Circumlineatus (cl) in common bean (Phaseolus vulgaris L.) is identified by a precipitation line in the seedcoat at the boundary of the white and colored zones. Cl is recessive and is expressed in partly colored seedcoats (t) with restricted patterns such as virgarcus. In this study, amplified fragment length polymorphism (AFLP) and single nucleotide polymorphism (SNP) markers, and the common bean genome sequence were used in combination with bulk segregant analysis and bidirectional selective genotyping to identify the genetic location of Cl. Markers were identified that cosegregated with Cl using Cl/Cl and cl/cl F3 and F5 progeny bulks from the cross t z cl G b v virgarcus BC3 5-593 × t zsel Cl G b v sellatus BC3 5-593. Two bands from an AFLP primer combination, which yielded unambiguous polymorphisms between the bulks, were cloned and sequenced. The two sequences were used to interrogate the common bean whole genome sequence identifying a region also found through cosegregation analysis using bidirectional selective genotyping with SNPs. Thus, the Cl gene was localized on Pv09 using cosegregating AFLP and SNP markers, and the physical location was confirmed with the whole genome sequence.