Transcriptome analysis of leaf senescence in red clover (Trifolium pratense L.)

Abstract

Red clover ( L.) is an important cool-season legume plant, which is used as forage. Leaf senescence is a critical developmental process that negatively affects plant quality and yield. The regulatory mechanism of leaf senescence has been studied, and genes involved in leaf senescence have been cloned and characterized in many plants. However, those works mainly focused on model plants. Information about regulatory pathways and the genes involved in leaf senescence in red clover is very sparse. In this study, to better understand leaf senescence in red clover, transcriptome analysis of mature and senescent leaves was investigated using RNA-Seq. A total of about 35,067 genes were identified, and 481 genes were differentially expressed in mature and senescent leaves. Some identified differentially expressed genes showed similar expression patterns as those involved in leaf senescence in other species, such as Arabidopsis, and rice. Differentially expressed genes were confirmed by quantitative real-time PCR (qRT-PCR). Genes involved in signal transduction, transportation and metabolism of plant hormones, transcription factors and plant senescence were upregulated, while the downregulated genes were primarily involved in nutrient cycling, lipid/carbohydrate metabolism, hormone response and other processes. There were 64 differentially expressed transcription factor genes identified by RNA-Seq, including ERF, WRKY, bHLH, MYB and NAC. A total of 90 genes involved in biosynthesis, metabolism and transduction of plant hormones, including abscisic acid, jasmonic acid, cyokinin, brassinosteroid, salicylic acid and ethylene, were identified. Furthermore, 207 genes with direct roles in leaf senescence were demonstrated, such as senescence-associated genes. These genes were associated with senescence in other plants. Transcriptome analysis of mature and senescent leaves in red clover provides a large number of differentially expressed genes. Further analysis and identification of senescence-associated genes can provide new insight into the regulatory mechanisms of leaf development and senescence in legume plant and red clover.

Transcriptome Analysis Reveals Biosynthesis of Important Bioactive Constituents and Mechanism of Stem Formation of Dendrobium huoshanense

“…NPR1 can positively regulate defense responses mediated by SA and induce systemic resistance; two homologous NPR1 genes were up-regulated in stems 48 . Four CTK genes, they were down-regulated in stems, suggesting postponed effects of cytokinin-related signaling pathways on senescence 49 . Moreover, several IAA, ABA, ETH, and BR related genes were detected in our study, suggesting that the developmental processes involved in stem formation in D. huoshanense were complicated and controlled by the possible presence of more than one gene.…”

Arabidopsis WRKY53, a Node of Multi-Layer Regulation in the Network of Senescence

“…OsWRKYs Rice Oryza sativa [21] 17 OsWRKYs (including OsWRKY40, OsWRKY53) Rice Oryza sativa [22] 161 ZmWRKYs Maize Zea mays [23] 11 BnWRKYs Oilseed rape Brassica napus [24] 7 TpWRKYs Clover leaf Trifolium pratense [25] 13 TaWRKYs (including TaWRKY7, TaWRKY6, TaWRKY45)…”

Advances in legume research in the genomics era

“…The recent sequencing of its genome (Ištvánek et al 2014;De Vega et al 2015) has provided another forage genome resource for comparative analyses to assist breeding (Annicchiarico et al 2015). Furthermore, transcriptomic studies have enabled advances in seed set (Kovi et al 2017), drought (Yates et al 2014) and leaf senescence (Chao et al 2018a). For example, Chao et al (2018b) used PacBio to sequence and analyse full-length transcripts, enabling the detection of over 30 000 novel isoforms and 5492 alternative splicing events, the majority of which involved intron retention.…”