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ARS Home » Research » Publications at this Location » Publication #148714


item LEE, RIAN
item Miklas, Phillip - Phil

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2004
Publication Date: 4/1/2004
Citation: Mcclean, P.E., Lee, R.L., Miklas, P.N. 2004. Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean. Genome 47:266-280.

Interpretive Summary: A new genomic-based system for studying evolution and genetic diversity in common bean was devised. A gene is composed of exons and introns. Exons are conserved among germplasm accessions within a species and even among species, whereas introns, which are noncoding regions of the gene are less conserved. The sequence difference for an intron of a specific gene was discovered using 92 bean genotypes, and then used as a blueprint to develop DNA markers. The markers were used to differentiate and group common bean germplasm into gene pools of evolutionary significance. The grouping of germplasm into gene pools gives breeders sufficient knowledge of which crosses to make in order to maximize genetic diversity to eventually attain higher yielding cultivars. This is the first report of the use of intron-based sequence diversity for genetic studies in common bean.

Technical Abstract: Variation in common bean (Phaseolus vulgaris L.) was investigated by sequencing intron 1 of the dihydroflavonol reductase (DFR) gene for 92 genotypes that represent both landraces and cultivars. Sixty-nine polymorphic sites were observed. Nucleotide variation 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, but were not significant for the landraces. 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 among 56 additional genotypes. The allele-specific primers were used for mapping experiments that placed the duplicate DFR genes on linkage group B8.