Applying DNA barcodes for identification of economically important species in Brassicaceae.

Brassicaceae is a large plant family of special interest; it includes many economically important crops, herbs, and ornamentals, as well as model organisms. The taxonomy of the Brassicaceae has long been controversial because of the poorly delimited generic boundaries and artificially circumscribed tribes. Despite great effort to delimitate species and reconstruct the phylogeny of Brassicaceae, little research has been carried out to investigate the applicability and effectiveness of different DNA regions as barcodes - a recent aid for taxonomic identification - to identify economically important species in Brassicaceae. In this study, we evaluated the feasibility of five intensively recommended regions [rbcL, matK, trnH-psbA, internal transcribed spacer (ITS), ITS2] as candidate DNA barcodes to discriminate economic species of Brassicaceae in China and try to establish a new digital identification method for economic plants of Brassicaceae. All sequences of 58 samples from 27 economic species (Brassicaceae) in China were assessed in the success rates of PCR amplifications, intra- and inter-specific divergence, DNA barcoding gaps, and efficiency of identification. Compared with other markers, ITS showed superiority in species discrimination with an accurate identification of 67.2% at the species level. Consequently, as one of the most popular phylogenetic markers, our study indicated that ITS was a powerful but not perfect barcode for Brassicaceae identification. We further discuss the discrimination power of different loci due to inheritance pattern, polyploidization and hybridization in species-specific evolution. Further screening of other nuclear genes related to species isolation as plant barcode candidates is also proposed.

Isolation and characterization of polymorphic microsatellite loci from aerial yam (Dioscorea bulbifera L.).

Dioscorea bulbifera L. is widely distributed in pantropical regions along the equator. The taxonomic treatment of this species is ambiguous due to its extreme polymorphic morphological characters. In order to provide tools to facilitate the study of genetic diversity, population structure, patterns of gene flow, and the mating system of this species, and to assess intraspecific variability and relationships in D. bulbifera, 14 novel polymorphic microsatellite loci were developed using the dual-suppression PCR technique. The number of alleles per locus ranged from 4 to 17, with an average of 9.93. The mean observed heterozygosities were 0.7327 and 0.7223, and the mean Shannon-Wiener indices were 1.6431 and 1.811 in the Nanjing and Nanchong populations, respectively. All novel microsatellite loci showed high levels of polymorphism, indicating that these markers offer great potential significance and profound influence for future studies of this species.

Isolation and characterization of microsatellite DNA loci for wild Brassica juncea (Brassicaceae).

Wild Brassica juncea is a widespread weed in China with increasingly great impact on the yield of many crops. This study aimed to develop microsatellite markers for assessing the genetic diversity and population genetic structure of B. juncea, and to provide basic information for biological and chemical control of the weed. The compound microsatellite marker technique was used to develop markers for investigating population genetics of wild B. juncea. Twelve loci were obtained, each of which showed high polymorphisms when tested in two populations in Sichuan and Jiangsu Provinces. The number of alleles per locus ranged from 4 to 27, with an average of 15.2 alleles per locus. The newly developed microsatellite loci will be informative for further investigations of the population genetics and evolutionary patterns of wild B. juncea.

Development of polymorphic microsatellite markers for Dioscorea zingiberensis and cross-amplification in other Dioscorea species.

Dioscorea zingiberensis C.H. Wright (Dioscoreaceae) is an endemic species in central and southwestern China. In order to study the genetic diversity and population structure of this species, 19 novel polymorphic microsatellite loci were developed using a dual-suppression PCR technique. The number of alleles per locus ranged from 3 to 21, with an average of 9.53. All the markers showed high transferability in cross-species amplification in other species of sect. Stenophora.