Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research Unit

Title: Testing the utility of matK and ITS DNA regions for discrimination of Allium species

Authors
item Ipek, Meryem -
item Ipek, Ahmet -
item Simon, Philipp

Submitted to: Turkish Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 27, 2013
Publication Date: February 14, 2014
Repository URL: http://handle.nal.usda.gov/10113/58552
Citation: Ipek, M., Ipek, A., Simon, P.W. 2014. Testing the utility of matK and ITS DNA regions for discrimination of Allium species. Turkish Journal of Botany. 38(2):203-212.

Interpretive Summary: Garlic, onion, leek, and chives are crop plant species that are classified by plant taxonomists into the genus Allium. This plant genus includes over 300 plant species, and molecular “fingerprinting” techniques referred to as “barcodes” have been designed to help identify species accurately. The most commonly used barcode is referred to as MatK, but other barcodes such as ITS and rbcL have also been proposed. In this study, the ability to discriminate among closely related Allium species was compared using the MatK and ITS barcodes. Both barcode systems were found to work equally well, although both were unable to discriminate among some species on their own, leading to the suggestion that both be used. This research is of interest to plant taxonomists, curators of botanical collections, and evolutionary scientists.

Technical Abstract: Molecular phylogenetic analysis of the genus Allium L. has been mainly based on the nucleotide sequences of ITS region. In 2009 matK and rbcL were accepted as a two-locus DNA barcode to classify plant species by the Consortium for the Barcode of Life (CBOL) Plant Working Group. MatK region has been chosen as a DNA barcode because of its effective species discrimination power, high quality sequence recovery and easy experimental procedures. Integration of matK sequences into Allium phylogeny could improve phylogenetic reconstruction of this genus. This study was carried out to test usability of nucleotide sequences of matK for discrimination of Allium species and to compare topology of the phylogenetic trees based on matK and ITS analyses. Phylogenetic relationships among the Allium species based on both ITS and matK analyses were in agreement with the previous studies. In addition, topology of phylogenetic trees based on ITS and matK analyses were very similar. However, neither ITS nor matK analyses discriminated some closely related Allium species. Although the ITS region has been successfully used for phylogenetic analysis of the genus Allium, we can suggest to use matK region as an additional tool for phylogenetic analysis in Allium because characterization of the nucleotide sequences of matK region was easier to recover and more cost effective than those of ITS region.

Last Modified: 11/26/2014
Footer Content Back to Top of Page