title: Biodiversity studies in Phaseolus species by DNA barcoding.
abstract: The potential of DNA barcoding was tested as a system for studying genetic diversity and genetic traceability in bean germplasm. This technique was applied to several pure lines of Phaseolus vulgaris L. belonging to wild, domesticated, and cultivated common beans, along with some accessions of Phaseolus coccineus L., Phaseolus lunatus L., and Vigna unguiculata (L.) Walp. A multilocus approach was exploited using three chloroplast genic regions (rbcL, trnL, and matK), four intergenic spacers (rpoB-trnC, atpBrbcL, trnT-trnL, and psbA-trnH), and nuclear ITS1 and ITS2 rDNA sequences. Our main goals were to identify the markers and SNPs that show the best discriminant power at the variety level in common bean germplasm, to examine two methods (tree based versus character based) for biodiversity analysis and traceability assays, and to evaluate the overall utility of chloroplast DNA barcodes for reconstructing the origins of modern Italian varieties. Our results indicate that the neighbor-joining method is a powerful approach for comparing genetic diversity within plant species, but it is relatively uninformative for the genetic traceability of plant varieties. In contrast, the character-based method was able to identify several distinct haplotypes over all target regions corresponding to Mesoamerican or Andean accessions; Italian accessions originated from both gene pools. On the whole, our findings raise some concerns about the use of DNA barcoding for intraspecific genetic diversity studies in common beans and highlights its limitations for resolving genetic relationships between landraces and varieties.
authors.affiliation: Department of Environmental Agronomy and Crop Science, Università degli Studi di Padova, Via dell'Università 16 - Campus of Agripolis, Legnaro, Padova, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Nicolè
authors.forename: David L
authors.initials: DL
authors.lastname: Erickson
authors.forename: Daria
authors.initials: D
authors.lastname: Ambrosi
authors.forename: Elisa
authors.initials: E
authors.lastname: Bellucci
authors.forename: Margherita
authors.initials: M
authors.lastname: Lucchin
authors.forename: Roberto
authors.initials: R
authors.lastname: Papa
authors.forename: W John
authors.initials: WJ
authors.lastname: Kress
authors.forename: Gianni
authors.initials: G
authors.lastname: Barcaccia
mesh_terms: D044822:Biodiversity; D002467:Cell Nucleus / Q000235:genetics; D016384:Consensus Sequence / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D027805:Phaseolus / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012639:Seeds / Q000033:anatomy & histology
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant