Locus-specific microsatellite markers in common bean (Phaseolus vulgaris L.): isolation and characterization

Abstract

This study aimed at the development of microsatellite markers for Phaseolus vulgaris L. by two techniques: hybridization-based detection, and transfer of microsatellite markers developed for chickpea to the common bean. Small-insert genomic libraries of common bean were screened for simple sequence repeat (SSR)-containing fragments with a set of microsatellite-specific oligonucleotide probes. Twenty-five (GA)10 positive clones detected by a dinucleotide repeat probe were selected for sequencing. Sixteen of 18 primer pairs, complementary to the SSR-flanking regions and tested in eight P. vulgaris L. accessions, are polymorphic at an intra-specific level. Mendelian inheritance of the sequence-tagged microsatellite site (STMS) markers was demonstrated using a set of recombinant inbred lines (RILs) and their parents. A total of 46 chickpea STMS markers of 447 different primer combinations amplified loci in the genome of common bean. Sequencing of amplified products from Phaseolus with these primer combinations demonstrated that the sequence of microsatellite marker TA 176s proved to be significantly similar to transcription factor SCOF1 of soy bean, controlling the response to cold stress, and also to transcription factor zinc finger protein (a Kruppel-like zinc finger protein, or TFIIIA), coordinating the reaction to osmotic stress in Medicago truncatula. Sequence analysis of this site in the two common bean parental lines BAT 477 and DOR 364 revealed that the sequence of BAT 477 was 5 bp longer than the corresponding sequence of DOR 364. Amplification of this fragment in six RILs of common bean detected the existence of sequence polymorphisms between the different lines.