Chloroplast-specific universal primers and their uses in plant studies

Abstract

Universal (consensus) primers are those primers that have the ability to amplify the targeted region of DNA across a broad range of individuals in a certain group of organisms. In plants, such universal primers have been designed to target regions in the nuclear, mitochondrial or chloroplast genome. Among these three genomes, the chloroplast genome is the most suited for the design of consensus primers due to the lower rate of evolution and hence conservation of gene order and sequence of the genome among the different plant species compared to the other two genomes. Several molecular studies in plants have developed and used chloroplast-specific universal primers. In this review, I present some examples of the nuclear DNA-specific universal primers and discuss the features of the chloroplast DNA that make it the most suited for the design of such primers. I then refer to all chloroplast-specific primers developed so far and provide some examples of molecular studies and applications that made use of them.

Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers

“…Genetic diversity is an important prerequisite for species adaptation to environmental change and the development of disease resistance, the levels of which determine the viability and evolutionary potential of populations, and are often used to predict species trends and potential dangers [ 44 ]. The use of molecular markers, such as RAPD, AFLP, and SSR, has been shown to be an accurate and reliable approach for analyzing the genetic diversity of plant populations [ 45 ], among which, SSRs are widely employed owing to their strengths. In this study, we used 33 novel developed EST-SSR primers to examine the genetic diversity of M. savatieri specimens collected from 10 geographically separated wild areas, the results of which indicated a large variation in the number of alleles of each locus, ranging from 3 to 11 with a mean value of 6.303.…”

The effects of pastoral intensification on the feeding interactions of generalist predators in streams

“…We were unable to amplify DNA from the guts of around 20% of predators and suggest this may be because their guts contained only plant material. Future studies could screen in parallel with general plant primers (Haider, ; reviewed in Pompanon et al., ) to determine the level of herbivory.…”

Cytoplasmic diversity of Brassica napus L., Brassica oleracea L. and Brassica rapa L. as determined by chloroplast microsatellite markers

“…Chloroplast specific SSR-markers (cpSSR) have been developed for a number of species including Arabidopsis (Weising and Gardner 1999;Provan 2000;Jakobsson et al 2007;Haider 2011) and oilseed rape (Provan 2000;Flannery et al 2006;Allender et al 2007). Chloroplast cpSSR repeats may be found in both coding and non-coding regions but more variation were reported in the non-coding regions including introns and intergenic spacer of cpDNA (Provan et al 2001;Jakobsson et al 2007).…”