Transcriptome profiling identifies transcription factors and key homologs involved in seed dormancy and germination regulation of Chenopodium quinoa

Abstract Chenopodium quinoa, a halophytic crop belonging to the Amaranthaceae, has remarkable resistance to harsh growth conditions and produces seed with excellent nutritional value. This makes it a suitable crop for marginal soils. However, to date most of the commercial cultivars are susceptible to preharvest sprouting (PHS). Meanwhile, understanding of the PHS regulatory mechanisms is still limited. Abscisic acid (ABA) has been demonstrated to be tightly associated with seed dormancy and germination regulation in many crops. Whether ABA metabolism pathway could be manipulated to prevent PHS in quinoa is worth investigating. In the present study, we tested the inhibitory effects of exogenous ABA on quinoa seed germination. By RNA-seq analysis we investigated the global gene expression changes during seed germination, and obtained 1066 ABA-repressed and 392 ABA-induced genes. Cis-elements enrichment analysis indicated that the promoters of these genes were highly enriched in motifs “AAAAAAAA” and “ACGTGKC (K = G/T)”, the specific binding motifs of ABI3/VP1 and ABI5. Transcription factor annotation showed that 13 genes in bHLH, MADS-box, G2-like and NF-YB, and five genes in B3, bZIP, GATA and LBD families were specifically ABA-repressed and -induced, respectively. Furthermore, expression levels of 53 key homologs involved in seed dormancy and germination regulation were markedly changed. Hence, we speculated that the 18 transcription factors and the homologs were potential candidates involved in ABA-mediated seed dormancy and germination regulation, which could be manipulated for molecular breeding of quinoa elites with PHS tolerance in future.