Horticulture Research is a new Open Access, fully peer-reviewed journal which will publish the best and most interesting research focusing on all major horticultural crops from around the world.

PCR allelic discrimination technologies have broad applications in the detection of single nucleotide polymorphisms (SNPs) in genetics and genomics. The use of fluorescence-tagged probes is the leading method for targeted SNP detection, but assay costs and error rates could be improved to increase genotyping efficiency. A new assay, rhAmp, based on RNase H2-dependent PCR (rhPCR) combined with a universal reporter system attempts to reduce error rates from primer/primer and primer/probe dimers while lowering costs compared to existing technologies. Before rhAmp can be widely adopted, more experimentation is required to validate its effectiveness versus established methods. The aim of this study was to compare the accuracy, sensitivity and costs of TaqMan, KASP, and rhAmp SNP genotyping methods in sugar beet (Beta vulgaris L.). For each approach, assays were designed to genotype 33 SNPs in a set of 96 sugar beet individuals obtained from 12 parental lines. The assay sensitivity was tested using a series of dilutions from 100 to 0.1 ng per PCR reaction. PCR was carried out on the QuantStudio 12K Flex Real-Time PCR System (Thermo Fisher Scientific, USA). The call-rate, defined as the percentage of genotype calls relative to the possible number of calls, was 97.0, 97.6, and 98.1% for TaqMan, KASP, and rhAmp, respectively. For rhAmp SNP, 24 of the 33 SNPs demonstrated 100% concordance with other two technologies. The genotype concordance with either technologies for the other 9 targets was above 99% (99.34–99.89%). The sensitivity test demonstrated that TaqMan and rhAmp were able to successfully determine SNP genotypes using as little as 0.2 ng DNA per reaction, while the KASP was unable to ascertain SNP states below 0.9 ng of DNA per reaction. Comparative cost per reaction was also analyzed with rhAmp SNP offering the lowest cost per reaction. In conclusion, rhAmp produced more calls than either TaqMan or KASP, higher signal to NTC data while offering the lowest cost per reaction.

Soil salinization is a common environmental problem that seriously affects the yield and quality of crops. Sugar beet (Beta vulgaris L.), one of the main sugar crops in the world, shows a strong tolerance to salt stress. To decipher the molecular mechanism of sugar beet under salt stress, we conducted transcriptomic analyses of two contrasting sugar beet genotypes. To the best of our knowledge, this is the first comparison of salt-response transcriptomes in sugar beet with contrasting genotypes. Compared to the salt-sensitive cultivar (S710), the salt-tolerant one (T710MU) showed better growth and exhibited a higher chlorophyll content, higher antioxidant enzyme activity, and increased levels of osmotic adjustment molecules. Based on a high-throughput experimental system, 1714 differentially expressed genes were identified in the leaves of the salt-sensitive genotype, and 2912 in the salt-tolerant one. Many of the differentially expressed genes were involved in stress and defense responses, metabolic processes, signal transduction, transport processes, and cell wall synthesis. Moreover, expression patterns of several genes differed between the two cultivars in response to salt stress, and several key pathways involved in determining the salt tolerance of sugar beet, were identified. Our results revealed the mechanism of salt tolerance in sugar beet and provided potential metabolic pathways and gene markers for growing salt-tolerant cultivars.