Grain protein content (GPC) is one of the most important criteria to determine the quality of common wheat (Triticum aestivum). One of the major obstacles for bread wheat production is the negative correlation between GPC and grain yield (GY). Previous studies demonstrated that the deviation from this inverse relationship is highly heritable. However, little is known about the genetics controlling these deviations in common wheat. To fill this gap, we performed quantitative trait locus (QTL) analysis for GY, GPC, and four derived GY-GPC indices using an eight-way multiparent advanced generation intercross population comprising 394 lines. Interval mapping was conducted using phenotypic data from up to nine environments and genotypic data from a 20k single-nucleotide polymorphism array. The four indices were highly heritable (0.76–0.88) and showed distinct correlations to GY and GPC. Interval mapping revealed that GY, GPC, and GY-GPC indices were controlled by 6, 12, and 12 unique QTL, of which each explained only a small amount of phenotypic variance (R² ≤ 10%). Ten of the 12 index QTL were independent of loci affecting GY and GPC. QTL regions harboured several candidate genes, including Rht-1, WAPO-A1, TaTEF-7A, and NRT2.6-7A. The study confirmed the usefulness of indices to mitigate the inverse GY-GPC relationship in breeding, though the selection method should reflect their polygenic inheritance.

The wheat flour proteome is a complex mixture of non-gluten and gluten proteins. The large number of repetitive sequences, special amino acid composition and similarity of gluten protein isoforms pose a major challenge in bottom-up proteomics. The standard peptidase used in shotgun proteomics is trypsin, which may not be suitable for all wheat proteins. In this study, flour extracts of nine common wheat genotypes were digested with the peptidases trypsin, chymotrypsin, thermolysin, pepsin and the combination of trypsin and chymotrypsin. The results showed large differences for the number of identified peptides. With 4115 peptides, trypsin resulted in by far the most peptide identifications, followed by thermolysin with 1421 peptides. However, this no longer applied at protein level. Most metabolic protein groups (673) were identified with trypsin. Among the gluten protein groups, however, around 130 were identified with each peptidase. The ω-gliadins were detected with all peptidases except trypsin. A comparison with quantitative RP-UHPLC-UV results showed that there was the greatest overlap after thermolysin digestion. Otherwise, there was no great similarity between the different peptidases, which is why their results cannot be compared with one another. The sequence coverage of gluten proteins was 51 % after thermolysin digestion, 27 % after trypsin digestion and 61 % when all peptidases were evaluated together. The results showed that digestion with various peptidases provides a more detailed picture of the wheat proteome. Some wheat protein groups could only be identified with certain peptidases, which is important if these protein groups are to be studied in more detail.