Regulatory Networks of Flowering Genes in Angelica sinensis during Vernalization

Abstract

Angelica sinensis is a low-temperature and long-day perennial herb that has been widely used for cardio-cerebrovascular diseases in recent years. In commercial cultivation, up to 40% of flowering decreases the officinal yield of roots and accumulation of bioactive compounds. Although the regulatory mechanism of flowering genes during the photoperiod has been revealed, the networks during vernalization have not been mapped. Here, transcriptomics profiles of A. sinensis with uncompleted (T1), completed (T2) and avoided vernalization (T3) were performed using RNA-seq, and genes expression was validated with qRT-PCR. A total of 61,241 isoforms were annotated on KEGG, KOG, Nr and Swiss-Prot databases; 4212 and 5301 differentially expressed genes (DEGs) were observed; and 151 and 155 genes involved in flowering were dug out at T2 vs. T1 and T3 vs. T1, respectively. According to functional annotation, 104 co-expressed genes were classified into six categories: FLC expression (22; e.g., VILs, FCA and FLK), sucrose metabolism (12; e.g., TPSs, SUS3 and SPSs), hormone response (18; e.g., GID1B, RAP2s and IAAs), circadian clock (2; i.e., ELF3 and COR27), downstream floral integrators and meristem identity (15; e.g., SOC1, AGL65 and SPLs) and cold response (35; e.g., PYLs, ERFs and CORs). The expression levels of candidate genes were almost consistent with FPKM values and changes in sugar and hormone contents. Based on their functions, four pathways that regulate flowering during vernalization were mapped, including the vernalization pathway, the autonomic pathway, the age pathway and the GA (hormone) pathway. This transcriptomic analysis provides new insights into the gene-regulatory networks of flowering in A. sinensis.

Integrated transcriptomic and metabolomic analysis reveals the regulation mechanism of early bolting and flowering in two cultivars of Angelica sinensis

“…We integrated the changed genes in five pathways related to the EBF of A. sinensis . Compared with previous studies [ [4] , [5] , [6] , [7] , 10 , 11 ], we found that FT , SOC1 , LFY , and Sucrose were the key factors and common characteristics affecting EBF. And we compared two cultivars with different EBF rates and found that the genes influencing the consistent EBF rate may be CDF1 , HK , treX , bglX , AUX/IAA , PR-1 , ACSL , and CO .…”

“…Plants must undergo vernalization and long-day conditions to bolt and flower. Refraining from exposure to vernalization or long-day conditions can diminish the EBF rate of A. sinensis [ 6 , 7 ]. The EBF can be influenced by various factors, such as germplasm selection, seedling age and weight, geographical coordinates (latitude and longitude), and soil conditions [ 4 ].…”

“…The previous studies on the EBF of A. sinensis have concentrated on its physiology and ecology [ 8 , 9 ]. Some studies have already reported that many genes and pathways can affect the EBF of A. sinensis , for example, COL3 , AS1 , SPL5 , and HDR1 in the photoperiodic pathway, GA2OX8 in the GA pathway, and WIN1 and PAS2 in the VLCFA biosynthesis [ [4] , [5] , [6] , [7] , 10 , 11 ]. How to effectively explore the essential genes from these large numbers of genes remains a scientific issue.…”

Transcriptome Analyses Show Changes in Gene Expression Triggered by a 31-bp InDel within OsSUT3 5′UTR in Rice Panicle

“…Upstream noncoding regions, such as promoter and 5′UTR, contain a number of cis-acting elements responsive to the various expression pattern of gene and the environmental changes [ 12 ]. For the FT gene, which regulates the flowering time in a range of plant families, a staggering number of InDels within the promoter ranging in size from 20 to 6850 bp have been identified in wild and domestic wheats [ 13 , 14 , 15 , 16 ]. Similarly, a 598-bp InDel variation in the promoter region of Bna.SOC1.A05 has a huge impact on mRNA expression and is associated with winter types in rapeseeds [ 17 ].…”