Chickpea Proteome Analysis Reveals Genotype-Dependent Variations Associated with Seed Traits

Chickpea (Cicer arietinum L.) is the second most widely grown legume crop after soybean. Here, we measured the macronutrients and performed proteome profiling of eight chickpea cultivars using two complementary protein extraction solvents. The total protein, starch, and soluble sugar contents significantly differ between cultivars, and we quantified 2434 and 1809 proteins, respectively, from urea- and water-based extraction solvents using a data-independent acquisition approach. The proteome-level differences can vary from 9-25% for the urea-extracted proteins, and the storage protein abundances significantly differed between the cultivars, where legumin content was detected as the highest, followed by vicilin and albumin. Fifty common allergens were detected from two extraction solvents, primarily overrepresented in chromosomes 3, 4, and 5. Integrated analysis revealed distinct subclusters of proteins and their associated pathways for total protein, lipids, and starch content. Overall, we established chickpea pan-proteome resources and provided insights into the key pathways that define the genotypes.