Mining the Wheat Grain Proteome

Bread wheat is the most widely cultivated crop worldwide, used in the production of food products and a feed source for animals. Selection tools that can be applied early in the breeding cycle are needed to accelerate genetic gain for increased wheat production while maintaining or improving grain quality if demand from human population growth is to be fulfilled. Proteomics screening assays of wheat flour can assist breeders to select the best performing breeding lines and discard the worst lines. In this study, we optimised a robust LC–MS shotgun quantitative proteomics method to screen thousands of wheat genotypes. Using 6 cultivars and 4 replicates, we tested 3 resuspension ratios (50, 25, and 17 µL/mg), 2 extraction buffers (with urea or guanidine-hydrochloride), 3 sets of proteases (chymotrypsin, Glu-C, and trypsin/Lys-C), and multiple LC settings. Protein identifications by LC–MS/MS were used to select the best parameters. A total 8738 wheat proteins were identified. The best method was validated on an independent set of 96 cultivars and peptides quantities were normalised using sample weights, an internal standard, and quality controls. Data mining tools found particularly useful to explore the flour proteome are presented (UniProt Retrieve/ID mapping tool, KEGG, AgriGO, REVIGO, and Pathway Tools).

Proteomic Analysis of Grain Protein in the Winter Wheat Jimai44 and Jimai229 Based on Strong Gluten Characteristics

Background：To determine the grain proteome of the strong gluten wheat, TMT technology was used to analyze proteomic differences between the winter wheat varieties Jimai 44 and the strong gluten Jimai 229. Results：Comparisons were also made with the winter wheat Jimai 22 as a control. It was found that there were 120 differentially expressed proteins between Jimai 44 and Jimai 22, while 173 between Jimai 229 and Jimai 22. Among these, 27 proteins were up-regulated and 23 down-regulated in jimai 44 and in jimai 229. Conclusions：GO analysis and KEGG pathway analysis showed that the differentially expressed proteins were mainly enriched in cell functions relating to nutrient reservoir activity, metabolic processes, protein processing in endoplasmic reticulum, phenylpropane biosynthesis and nitrogen metabolism. Amongst the screened proteins, many differences were related to storage proteins. This study provides an important basis for further exploring the key factors of quality improvement and genetic variation of gluten protein expression.

Increased wheat protein content via introgression of a HMW glutenin selectively reshapes the grain proteome

ABSTRACTIntrogression of a high molecular weight glutenin subunit (HMW-GS) gene, 1Ay21*, into commercial wheat cultivars increased overall grain protein content and bread-making quality by unknown mechanisms. As well as increased abundance of 1Ay HMW-GS, 115 differentially expressed proteins (DEPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines (NILs). Functional category analysis showed that the DEPs were predominantly other storage proteins, and proteins involved in protein synthesis, protein folding, protein degradation, stress response and grain development. Nearly half the genes encoding the DEPs showed strong co-expression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between these cis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the 1Ay21* improves grain protein content, but also directs selection of protein candidates for future wheat quality breeding programmes.One sentence summaryIntrogression of the 1Ay21* HMW-GS increases wheat grain protein content and improves bread-making quality in association with a broad reshaping of the grain proteome network.