Genome-wide identification, in-silico analysis and expression profiling of regulatory genes involved in essential amino acid biosynthesis during different stages of germination in grain amaranth (Amaranthus hypochondriacus)
摘要
Amaranth, abundant in essential amino acids (EAAs), depends on various regulatory genes to control the accumulation of these amino acids within the grain. This study identifies 10 regulatory genes of EAAs biosynthesis pathway, including aspartate kinase (AK), aspartokinase/homoserine dehydrogenase (AK/HD) bifunctional, cysthathionine-y-synthase (CS), threonine dehydratase (TD), anthranilate synthase (AS), dihydrodipicolinate synthase (DHDPS), threonine synthase (TS), acetolactate synthase (ALS), chorismate mutase (CM) and saccharopine dehydrogenase/lysine ketoglutarate reductase (SD/LKR) bifunctional in grain amaranth. Sequence alignment and motif/domain analysis revealed similarities between these genes in amaranth and other plants, with encoded proteins containing domains crucial for substrate synthesis and feedback regulation. Promoter analysis using PlantPAN4 and PLACE databases identified cis-regulatory elements for Dof, AT-Hook, bZIP, and GRAS transcription factors, which influence gene expression during seed germination, amino acid synthesis, and plant development. In-silico expression analysis revealed tissue-specific expression, with key genes exhibiting highest expression in leaves (AK/HD, TS, ALS, CS), roots (TD, CM), seeds (AK, AS), and embryos (CS, CM), highlighting their diverse roles in various physiological contexts. Real-time expression analysis at various stages of germination revealed peak expression of EAA biosynthesis genes 24 h after germination, with AK, AK/HD, CM, and DHDPS increasing over 20-fold, followed by CS and TS (14-fold) and AS and SD/LKR (seven-fold). This increased expression likely enhances EAAs content during seed germination. This study is the first to identify and analyze regulatory genes for EAA biosynthesis in grain amaranth during germination.