Comparative proteomic based analysis of grain nutrients in two hulless barley cultivars

Hullessbarley (Hordeum vulgare L.) is a barley cultivar, serving as one of the major food crops worldwide. The main nutrients in hulless barley are starch, protein, and beta-glucan, the contents of which vary considerably among different cultivars. However, the potential molecular mechanisms that underlie these variations in nutrient are still insufficiently clear. In this study, the nutrient content of two hulless barley cultivars ('Zangqing 2000' and 'C2') was analyzed, and quantitative tandem mass tag-LC-MS/MS proteomics and bioinformatics analysis were used to verify the differentially expressed proteins (DEPs) between the two cultivars. Parallel reaction monitoring (PRM) analysis was used to verify the expression change of candidate DEPs. The content of starch and amylose in C2 was lower than that in Zangqing 2000, and beta-glucan, protein content, and amylopectin showed a higher concentration in C2 hulless barley cultivar. A total of 326 DEPs were identified, with 108 induced proteins and 218 reduced proteins in C2 compared with Zangqing 2000. Further functional and pathways analysis of DEPs revealed that C2 hulless barley cultivar has relatively more biological activities, and DEPs in C2 hulless barley cultivar were mainly associated with the biological processes of multiple important metabolic pathways. Moreover, PRM analysis showed the accuracy level of quantitative proteomic data. Overall, this was the first study that undertook the proteomic analysis in Zangqing 2000 and C2 and the results revealed the molecular mechanisms of seed nutrient biosynthesis and accumulation, which provide key insights about the development of hulless barley quality.