Tubulin-based polymorphism (TBP): a new tool, based on functionally relevant sequences, to assess genetic diversity in plant species

Abstract

TBP (tubulin-based polymorphism) is a new molecular marker based tool that relies on the presence of intron-specific DNA polymorphisms of the plant beta-tubulin gene family. The multifunctional and essential role of the tubulin proteins is reflected in the conservation of regions within their primary amino acid sequence. The ubiquitous nature of this gene family can be exploited using primers that amplify the first intron of different beta-tubulin isotypes, revealing specific fingerprints. The method is rapid, simple, and reliable and does not require preliminary sequence information of the plant genome of interest. The ability of TBP to discriminate between accessions and species in oilseed rape, coffee, and lotus is shown. In all cases, TBP was able to detect specific genetic polymorphisms in the context of a simplified and readily appreciable pattern of DNA amplification. The application of TBP for assessing genetic diversity and genome origins in disseminated plant landraces rather than in highly inbred cultivated species is also discussed.

Lotus tenuis x L. corniculatus interspecific hybridization as a means to breed bloat-safe pastures and gain insight into the genetic control of proanthocyanidin biosynthesis in legumes

“…As species complexes with similar taxonomical traits are present, the taxonomy within this genus is far from being clearly resolved [12]. As an example, the origin of tetraploidy (2n = 4 × = 24) in L. corniculatus and L. alpinus have yet to be clarified [35,36]. The wild and PA-rich Lotus population described here is diploid (2n = 2 × = 12) and morphologically resembles the tetraploid L. corniculatus for many taxonomical traits of both vegetative and reproductive structures and organs (Figure 2 and Additional file 1: Table S3 and S4).…”

Advances in plant gene-targeted and functional markers: a review

“…The polymorphism of these regions also provides a good basis for genetic diversity assessment, identification of different plant varieties for breeding purposes, and even the investigation of eukaryotic evolution [89]. Based on these features Bardini et al [59] developed an assay, Tubulin Based Polymorphism (TBP), to reveal length polymorphisms present in the introns (Figure 2). For this rapid technique they designed a single degenerate primer pair annealing to the conserved parts of the β -tubulin exon after the 132 amino acid codons.…”

“…This might be useful for classification at lower taxonomic levels, either alone or in conjunction with other multi-locus or sequence based methods. Conserved DNA markers can help to characterize the diversity of different species and detect inter- and intraspecies variation [58,59]. Their inheritance follows Mendelian rules, making them suitable for population studies.…”

Certifying the feed to guarantee the quality of traditional food: An easy way to trace plant species in complex mixtures

“…Briefly, the TBP method is a PCR-molecular marker-based tool, that relies on the presence of intron-specific DNA polymorphisms in the plant btubulin gene family (Bardini et al, 2004). Almost all of the plant b-tubulin genes characterised so far, share a common genomic organisation: two introns, of variable lengths in the different isotypes, located at fixed positions within the coding region.…”

“…All these assumptions have been preliminarily verified in rice, where the method was originally developed [pending patent PCT/IT99/00415]. Thereafter the TBP1st intron strategy was successfully applied for assessing intraand interspecific relationships and differences in oilseed rape (Brassica napus), coffee and lotus cultivars (Bardini et al, 2004). In the case that the number of generated molecular markers is too low, the TBP -2nd intron approach can be used as an additional source of molecular variation.…”