DNA fingerprinting in botany: past, present, future

Abstract

Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67–73 and Nature 1985, 316:76–79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined “Fingerprint News” was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on “DNA fingerprinting: approaches and applications”. Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting (“the past”) was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as “DNA fingerprinting in the present”, and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of “genotyping-by-sequencing”. Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as “DNA fingerprinting in the future”.

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

“…Several molecular tools, based on DNA polymorphisms, are available to assess plant genetic diversity (Weising et al 2005;Nybom et al 2014). Simple Sequence Repeat (SSR) markers are widely used due to their high reproducibility, multi-allelic nature and co-dominant inheritance (Tautz 1989).…”

Micropropagation of Viola uliginosa (Violaceae) for endangered species conservation and for somaclonal variation-enhanced cyclotide biosynthesis

“…Somaclonal variation induced by culture conditions limits the use of in vitro micropropagation, as it leads to changes in nuclear and cytoplasmic genomes and causes genetic differentiation of regenerated plants (D'Amato 1991; Larkin and Scowcroft 1981; Lee and Phillips 1988;Neelakandan and Wang 2012;Rodriguez-Enriquez et al 2011;Vazquez 2001;Wang and Wang 2012). Confirmation of the genetic identity with maternal material, and the genome size and reproductive normality of regenerated plants, is required before reintroduction (Nybom et al 2014;Ochatt et al 2011;Singh et al 2013;Thiem et al 2013;Thiem and Sliwinska 2003). Molecular markers are valuable tools for detecting the sequence variation of closely related genomes such as those between source plants and somaclones regenerated through tissue culture.…”

“…Molecular markers are valuable tools for detecting the sequence variation of closely related genomes such as those between source plants and somaclones regenerated through tissue culture. Molecular marker systems-random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), simple sequence repeat (SSR), amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP)-each having its advantages and limitations, are used to estimate somaclonal variation in tissue culture (Bairu et al 2011;Nybom et al 2014;Rewers et al 2012;Singh et al 2013). Flow cytometry for somaclone genome size assessment can be used to complement molecular marker analyses (Bairu et al 2011;Ochatt et al 2011;Rewers et al 2012).…”

Population Structure and Genetic Relationships of Melia Taxa in China Assayed with Sequence-Related Amplified Polymorphism (SRAP) Markers

“…This extent of population differentiation in the genus Melia was much greater than that in most conifers (F st = 0.008-0.063) [41] and some broad-leaved tree species (F st = 0.041-0.206) [42,43]. Population differentiation was also greater in Melia than in other outcrossing (F st = 0.22), perennial (F st = 0.19), and wind-pollinated (F st = 0.13) plants [44,45]. These differences may arise primarily from their distinct dispersal properties and reproductive ecology.…”