Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean

Variation in common bean (Phaseolus vulgaris L.) was investigated by sequencing intron 1 of the dihydroflavonol 4-reductase (DFR) gene for 92 genotypes that represent both landraces and cultivars. We were also interested in determining if introns provide sufficient variation for genetic diversity studies and if the sequence data could be used to develop allele-specific primers that could differentiate genotypes using a standard PCR assay. Sixty-nine polymorphic sites were observed. Nucleotide variation (pi/bp) was 0.0481, a value higher than that reported for introns from other plant species. Tests for significant deviation from the mutation drift model were positive for the population as a whole, the cultivar and landrace subsets, and the Middle American landrace set. Significant linkage disequilibrium extended about 300 nucleotides. Twenty haplotypes were detected among the cultivated genotypes. Seven recombination events were detected for the whole population, and six events for the landraces. Recombination was not observed among the landraces within either the Middle American or Andean gene pools. Evidence for hybridization between the two gene pools was discovered. Five allele-specific primers were developed that could distinguish 56 additional genotypes. The allele-specific primers were used to map duplicate DFR genes on linkage group B8.