Polymerase chain reaction and allele-specific oligonucleotides in paternity testing of the deceased

Polymorphism of floral type gene Cly1 and its association with thermal stress in barley

Cleistogamy refers to a type of sexual breeding system with closed flowers. Cleistogamous flowers shed their pollen before flower opening, which leads to autogamy. Two SNPs in the open reading frame region of the Cly1 gene are associated with floral type. In the present study, we investigated the floral type of 436 barley accessions. Molecular markers were developed to genotype these barley accessions based on the two SNPs in the Cly1 gene region. The molecular markers explained floral type in 90% of the accessions. The Cly1 gene was sequenced in accessions with inconsistent genotype and phenotype. Thirteen SNPs were detected with ten new SNPs in the gene region. We further investigated whether floral type was associated with temperature stress tolerance in four field trials. One site experienced frost stress with a minimum temperature of -3.4°C during flowering. Grain fertility rates as low as 85% were observed at this site but ranged from 92–96% at the other three sites. The relationship between grain fertility rate and floral type under temperature stress was inconclusive. Some lines with higher grain fertility rates were identified under frost stress, and would be useful for frost stress studies in barley.

Fluorotyping of HLA-C: differential detection of amplicons by sequence-specific priming and fluorogenic probing

Conventional PCR-SSP, which is based on an agarose gel-based read-out, has the disadvantages of time-consuming post-PCR steps and low potential for automation. The aim of our study was to sort out these drawbacks by establishing a fluorescence-based PCR-SSP system for HLA-C. The assay relies on the sequence-specific identification of amplicons with individually labeled probes that are cleaved during successful PCR by the 5'-3' exonuclease activity of the Taq-DNA Polymerase. The oligonucleotides are labeled with a unique and spectrally resolvable fluorescent reporter dye at the 5' terminus (FAM or TET) and a common quencher dye at the 3' terminus (TAMRA). In case of amplification, the reporter escapes from the quenching control caused by the physical separation of the dyes, resulting in a significant increase of the reporter fluorescence. This allows simultaneous and differential detection of the specific HLA (FAM) and internal control (TET) product. The HLA-C fluorotyping information is based on the individual reporter fluorescence released by 18 PCR primer mixes. Using this method, we analyzed 145 samples previously typed with conventional PCR-SSP and found a concordance rate of 100%. Furthermore, fluorotyping revealed quantitative results that may indicate the presence of homozygosity by high signal intensities. This provided extra protection not to miss new alleles which are not amplified by the current primer mixes. These features as well as the capability of high sample throughput and the possibility of automation makes fluorotyping an attractive tool for PCR-based HLA typing.