Integrated transcriptomic and proteomic analyses revealed molecular mechanisms underlying nutritional changes during seed development of Chenopodium quinoa

Quinoa (Chenopodium quinoa) is a pseudocereal crop of the Amaranthacea family containing highly nutritious seeds which undergo complex physiological and biochemical changes during their development, resulting in final yield and seed nutritional quality (SN-quality). To obtain new insights into the underlying molecular mechanisms, integrated transcriptomic and proteomic analyses of developing seeds from 7 days after flowering (DAF) to maturation (57 DAF) were conducted. A total of 44,776 genes and 8235 proteins were detected; among them, 4130 genes and 3978 proteins were significantly different in pairwise comparisons of samples at various seed developmental stages. Results showed that genes and proteins associated with pathways of sucrose, fructose, mannose, pentose, glucuronate, starch, amino sugar and nucleotide sugar in carbohydrate metabolism; cyano amino acid, taurine & hypotaurine and storage proteins in amino acid and protein metabolisms; cutin, suberin and wax biosynthesis in lipid metabolism and phenylpropanoid and terpenoid biosynthesis in secondary metabolisms of flavonoids and triterpenoidal saponins play a key role in seed developmental process and SN-quality control. Gene regulatory networks correlated with SN-quality traits identified ABA independent (CqDREB2A, Cyclic dof factor 2 (CqCDF2) and AINTEGUMENTA-like5 (CqAIL5),) as well as dependent (CqABI4 and CqWRKY24) associated transcription factors play dynamic role in quinoa SN-quality control by regulating potential target genes and their encoding proteins related to above-mentioned metabolic pathways. The provided multi-omic data sets presented a dynamic picture regarding the developmental process of quinoa seeds, revealing the temporal specific expression of key candidate genes and proteins and providing the basis for crop improvement.