Transcriptome Analysis of Lycoris chinensis Bulbs Reveals Flowering in the Age-Mediated Pathway

Abstract

Lycoris is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsible for floral transition in bulbous flowers is lacking, and only a few genes that regulate flowering have been identified with few reports on the floral transition in Lycoris. In this study, we identified many differentially expressed genes (DEGs) and transcription factors (TFs) by RNA-Seq in L. chinensis bulbs of different ages, including one- to four-year-old nonflowering bulbs and four-year-old flowering bulbs. Some DEGs were enriched in Gene Ontology (GO) terms between the three- and four-year-old bulbs, and there most genes were enriched in terms of metabolic process and catalytic activity. In the four-year old bulbs, most of the DEGs that may be involved in flowering were classified under the GO term biological process, which was a totally different result from the vegetative bulbs. Some DEGs between flowering and nonflowering bulbs were enriched in plant hormone signal transduction, including the hormones auxin, cytokinin, abscisic acid, and ethylene, but no DEGs were enriched in the gibberellin pathway. Auxin is the main endogenous phytohormone involved in bulb growth and development, but cytokinin, abscisic acid, and ethylene were shown to increase in flowering bulbs. In addition, energy-metabolism-related genes maintain a high expression level in large bulbs, and some positive regulators (SPL, COL, and AP1) and early flowering genes were also shown to be highly expressed in the meristems of flowering bulbs. It suggested that sugar molecules may be the energy source that regulates the signal transduction of flowering by connecting with phytohormone signaling in Lycoris. A total of 1911 TFs were identified and classified into 89 categories, where the top six families with the largest gene numbers were C2H2, NAC, AP2/ERF-ERF, C3H, MYB-related, and WRKY. Most DEGs were in the AP2/ERF-ERF family, and most of them were downregulated in 4-year-old flowering bulbs. A number of families were reported to be involved in plant flowering, including NAC, AP2/ERF, MYB, WRKY, bZIP, MADS, and NF-Y. These results can act as a genetic resource to aid in the explanation of the genetic mechanism responsible for the flowering of Lycoris and other bulbous flowers.

Phylogeny and expression patterns of ERF genes that are potential reproductive inducers in hybrid larch

“…In the studies related to flowering regulation, ERF genes are mostly involved as flowering repressors [ 34 ]. In addition to the genes mentioned earlier, ERF1 in Arabidopsis acts as a negative regulator of flowering time by directly inhibiting the expression of the flowering locus FT [ 28 ].…”

Establishing a Virus-Induced Gene Silencing System in Lycoris chinensis

“…The gene sequences of LcCLA1 and LcPDS were obtained from transcriptome data of L. chinensis [6]. Raw reads were deposited in the NCBI database (https://www.ncbi.…”

“…In addition, the bulbs contain a large number of alkaloid compounds, which have anti-malarial and anti-tumor effects and are a treatment for senile dementia [3,4], so the plants also have important medicinal value. Due to the great ornamental and medicinal value of Lycoris, more and more transcriptomic data have been provided, and functional genes related to excellent breeding traits have been identified [5][6][7][8]. However, due to the lack of efficient genetic transformation, there has been no report on the gene function of Lycoris thus far.…”

Transcriptome profiles reveal gene regulation of ginger flowering induced by photoperiod and light quality

“…Environmental factors (such as light and temperature) and endogenous factors (such as plant hormones and age) could regulate flowering time in plants. Light quality and photoperiod control photomorphogenesis, which play an important role in flowering of various plants (Zhang et al 2022 ; Sidhu et al 2021 ). Plants could sense photoperiod variation of light with different wavelengths through photoreceptor proteins, such as phytochrome or cryptochrome, which would be signals to initiate flower (Weller and Kendrick 2008 ).…”