Comprehensive transcriptomic profiling identifies key regulatory genes mediating phytohormone signaling pathways during seed germination in Chenopodium quinoa

BACKGROUND: Pre-harvest sprouting (PHS) significantly reduces the yield and quality of Chenopodium quinoa (quinoa). A key determinant of PHS resistance is the balance between seed dormancy and germination, a process primarily regulated by phytohormones. RESULTS: To elucidate the molecular mechanisms underlying hormone-mediated germination regulation, we performed transcriptome sequencing on Jingli 1 quinoa seeds 6 h after treatment with six phytohormones: abscisic acid (ABA), indole-3-acetic acid (IAA), jasmonic acid (JA), gibberellic acid (GA₃), brassinolide (BR), and 6-benzylaminopurine (6-BA). The results showed that ABA, IAA, and JA significantly inhibited germination, with a maximum inhibition rate of 36.73%. In contrast, optimal concentrations of GA₃ (45 µM), BR (20 µM), and 6-BA (4.44 µM) promoted germination, with a maximum promotion rate of 22.67%. Transcriptome analysis identified 4,738 differentially expressed genes (DEGs), which were significantly enriched in pathways such as plant hormone signal transduction, starch and sucrose metabolism, and terpenoid backbone biosynthesis. Furthermore, we identified 102 coregulated DEGs, revealing intricate hormone signaling networks (such as ABA-GA-JA and JA-IAA-6-BA). Importantly, we pinpointed 20 core regulatory genes (including CqWRKY33, CqAnxD3, CqbHLH18L, CqMYB-V, CqSES, CqHMGCS, CqMVK1/2, CqCKX7-1/-2, CqWAT1-1/-2, CqORR9/10, CqBNM2AL, CqSAUR72L, CqRAV1L, CqABCG31L, Cq2-ODD, and CqBG7Sg2) that showed antagonistic expression patterns in response to promotive versus inhibitory hormones. CONCLUSIONS: This study systematically elucidates the multi-hormone regulatory network underlying quinoa seed germination, thereby enhancing our understanding of phytohormone-mediated regulatory mechanisms in quinoa. It also identifies promising candidate genes for breeding pre-harvest sprouting (PHS)-resistant quinoa varieties.