Single-primer PCR correction: a strategy for false-positive exclusion

DDRT-PCR approaches applied for preeminent results in the isolation of DETs from fish brain tissues

Differential Display (DD) is a technique widely used in studies of differential expression. Most of these analyses, especially those involving fish species, are restricted to species from North America and Europe or to commercial species, as salmonids. Studies related to South American fish species are underexplored. Thus, the present work aimed to describe DD technique modifications in order to improve outcomes related to the isolation of DETs (Differentially Expressed Transcripts), using Leporinus macrocephalus, a large commercially exploited South American species, as a fish design. Different DDRT-PCR approaches were applied to brain samples and the products of the reactions were analyzed on 6% polyacrylamide gels stained with 0.17% Silver Nitrate (AgNO3). The use of PCR reactions under high stringency conditions and longer oligonucleotides based on VNTR (Variable Number of Tandem Repeats) core sequences led to better results when compared to low stringency PCR conditions and the use of decamer oligonucleotides. The improved approach led to the isolation of differentially expressed transcripts on adult males and females of L. macrocephalus. This study indicates that some modifications on the DDRT-PCR method can ensure isolation of DETs from different fish tissues and the development of robust data related to this approach.

Removing PCR for the elimination of undesired DNA fragments cycle by cycle

A novel removing polymerase chain reaction (R-PCR) technique was developed, which can eliminate undesired genes, cycle by cycle, with efficiencies of 60.9% (cDNAs), 73.6% (genomic DNAs), and ~ 100% (four DNA fragments were tested). Major components of the R-PCR include drivers, a thermostable restriction enzyme - ApeKI, and a poly(dA) adapter with mismatched restriction enzyme recognition sites. Drivers were generated from the undesired genes. In each cycle of R-PCR, drivers anneal to complementary sequences and allow extension by Taq DNA polymerase. Thus, ApeKI restriction sites in the undesired genes are recovered, and adapters of these undesired DNA fragments are removed. Using R-PCR, we isolated maize upregulated defense-responsive genes and Blumeria graminis specialized genes, including key pathogenesis-related effectors. Our results show that after the R-PCR reaction, most undesired genes, including very abundant genes, became undetectable. The R-PCR is an easy and cost-efficient method to eliminate undesired genes and clone desired genes.

Single- and double-SSR primer combined analyses in rice

Polymerase chain reaction (PCR) is the foundation of SSR molecular marker technology. We used sib rice varieties J518, XD1 and SD23 as experimental materials, selecting 30 pairs of SSR primers, including RM127, RM337 and RM5172, covering the rice genome, and performed single- and double-SSR primer combined analyses. We found that under the same PCR system and conditions, a single primer of the SSR primer pairs could amplify the same fragments as double primers do. The sequencing results demonstrated that some amplified fragments that we previously believed to come from double primers were actually produced by a single primer. The use of this kind of primer, such as the RM127 primer pair, for marker-assisted breeding will therefore be misleading. Additionally, using the same PCR system and conditions, some single primers that are part of SSR primer pairs can amplify many more specific fragments than double-SSR primers. For instance, in the case of the RM5172 primer pair, a single primer P1 amplified approximately three times the number of fragments as the double primer. This information can contribute to research on genetic diversity of species, understanding of genetic relationships and identification of germplasm resources. Accordingly, combined analyses of single- and double-primer amplification products not only can remove single-primer amplification fragments and false-positives from double-primer amplification products in order to improve test accuracy, but also can facilitate research on genetic diversity, exploration of phylogenetic relationships and identification of germplasm resources. We define this method as "single- and double-SSR primer combined analyses".

Problems with and a system to eliminate single-primer PCR product contamination in simple sequence repeat molecular marker-assisted selection in soybean

Polymerase chain reaction (PCR) provides a foundation for simple sequence repeat molecular marker-assisted selection (SSR MAS) in soybean. This PCR system and its various conditions have been optimized by many researchers. However, current research on the optimization of the PCR system focuses on double-primer PCR products. We compared single- and double-SSR primer PCR products from 50 soybean samples and found that the use of single-PCR primers in the reaction system can lead to amplified fragments of portions of the SSR primers in the PCR process, resulting in both false-positives and fragment impurity of double-primer PCR amplification, inconvenient for subsequent analysis. We used "single-primer PCR correction" to eliminate interference caused by single-primer nonspecific PCR amplification and improve PCR quality. Using this method, the precision and success rates of SSR MAS in soybean can be increased.