Biodiversity studies inPhaseolusspecies 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.

Genetic identity of common buckwheat (Fagopyrum esculentum Moench) landraces locally cultivated in the Alps

“…In particular, the DNA genotyping method applied in this research allowed us to identify the landraces that most likely represent the historical gene pool of common buckwheat cultivated in Valtellina among different local accessions and foreign materials. Other studies reported that different molecular techniques can be used for characterization of the landraces and investigation on their origin, like DNA barcoding (Nicolè et al 2011) and DNA fingerprinting (Gwanama et al 2000;Ferriol et al 2004). In general, these tools are of special interest because they provide basic information useful, if not essential, for the preservation and valorization (even commercial) of abandoned landraces.…”

DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy

“…There are many advantages in the use of DNA barcoding as it is reproducible and testable as long as the link between DNA test sequences and reference specimens is supported, and also verifiable at any time and by any researcher [4]. Moreover, the experimental procedure for extracting genomic DNA and amplifying specific DNA markers is technically easy and usually does not require the destruction of the sample, which sometimes is valuable and therefore needs to be safeguarded [6].…”

“…Of the protein-coding genes present on the animal mitochondrial genome, the use of cytochrome c oxidase subunit 1 (cox1 or COI) was proposed as a standard barcode marker for animal species for two main reasons: universal primers make a 648 bp fragment at the 5 1 end of this gene easy to amplify in a broad spectrum of phyla, and its nucleotide substitution rate allows not only closely related species to be distinguished but, in some taxa, also different populations, biotypes or races of the same species. Other mitochondrial genes were suggested as barcode markers, including cob, which encodes for apocytochrome b; cox2 and cox3, which encode for the cytochrome oxidase subunits 2 and 3, respectively; nad1, which encodes for NADH dehydrogenase subunit 1; and the mitochondrial 16S-rDNA gene ( [4][5][6] and references therein).…”

“…The NCBI accessions of Nostoc comune var. flagelliforme, scoring 99% identity with NCBI accessions are KC350486.1 and KC350471.1 (for protocol details, see Nicolè et al [4]). Several SNPs and In/Dels were found between the aligned mini-barcode sequences recovered from pectin samples and tnrL sequences of Citrus and Malus spp.…”

The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.)

“…The employment of DNA barcoding at the sub-species level, instead, is not a conventional application of the methodology. Consequently, this research aims to assess the applicability of chloroplast DNA barcoding to unambiguously distinguish varietal genotypes of V. vinifera [21]. Since the genetic distance among subgroups within a species is generally too small to allow the definition of a genetic threshold to delimitate different varieties, a character-state DNA sequencing procedure based on single-copy nuclear genes was also developed [22].…”