Three filter sets (Leica) were used for fluorescent marker detection: TxRed for DsRed (ex: 560/40; em: 610 LP), CFP for AmCyan (ex: 436/20; em: 480/40), and YFP for EGFP (ex: 500/20; em: 535/30).
Based on the analyzed expression profiles an initial list of 172 transcription factors and 204 kinases was derived and the sequences used for SNP detection, marker development and anchoring on the barley linkage map.
Ideally, to avoid bias, this set of markers should be uncorrelated with the set of markers used for PC detection, and not associated with the disease risk.
Additional file 3: List of SNP markers used for deletion detection.
Prostate-specific antigen (PSA) is the most common marker used for prostate cancer detection and follow-up, and until recently, PSA was considered the most reliable marker to predict prostate cancer [ 4].
The transcriptome data generated in the current study, being derived from distinct genotypes, may potentially be also used for the detection of SNP markers in field pea and faba bean, to further enrich the available genomic resources for these two species.
We further computed an adjusted Type I error rate at the chromosome level (αchr) using an Type I error rate at whole genome level of 0.05 and the formula: αchr = 1 – {1 – [1 – (1 – αg)1/ M } m, where M is the total number of markers used for the QTL detection on each map and m the number of markers in the linkage group carrying the QTL [ 71].
Automatic cofactor selection (backward elimination, P < 0.02) was used for the detection of significantly associated markers as cofactors.
This finding confirmed that these markers could be used for the detection of early-stage as well as later-stage tumors.
After checking that meat quality traits differed between the two lines, an F2 population was produced and used for QTL detection, with 108 microsatellite markers.
