ARS | Publication request: INTRON-BASED SEQUENCE DIVERSITY STUDIES IN PHASEOLUS

Submitted to: Bean Improvement Cooperative Annual Report
Publication Type: Abstract Only
Publication Acceptance Date: January 7, 2004
Publication Date: March 15, 2004
Citation: Mclcean, P.E., Lee, R.K., Miklas, P.N. 2004. Intron-based sequence diversity studies in phaseolus. Bean Improvement Cooperative Annual Report. 47:85-86.

Technical Abstract: Molecular markers are useful for diversity studies in plants. DNA sequence analysis has an advantage over traditional marker studies because it can uncover rare genomic changes that can facilitate both shallow and deep diversity studies. The target sequence for diversity studies can be either exons or introns. Our standard approach is to select a gene of interest, obtain the corresponding sequence data from Glycine, Medicago, and Arabidopsis, identify conserved nucleotide sequences, align the sequences with the genomic (exon+intron) sequence of the Arabidopsis, and design primers that span the intron space. The primers are used to amplify DNA fragments that are directly sequenced. A recent publication describes variation at intron one of dihydroflavonol reductase among 95 common bean genotypes. It was observed that cultivar and landrace diversity was equal, while Middle America landrace diversity was greater than among Andean landraces. Several test statistics suggest that selection was acting upon the intron in the Middle America gene pool. Further, it was discovered that race Durango and Jalisco genotypes are monomorphic whereas the greatest variability was noted among race Mesoamerica genotypes. Finally, signature recombination events suggest that an ancestral population existed that contained the variability currently observed in the Middle America and Andean gene pools.