Transcriptomic Analysis of <i>Medicago truncatula</i> under Long-Day Conditions

Abstract

The objective of this research was to understand the expression characteristics and biological functions of Medicago truncatula genes under long-day conditions. The leaves of “R108” tribulus Medicago truncatula at the branch stage (A), bud stage (B), initial flowering stage (C), and full flowering stage (D) were sequenced using RNA-Seq technology. The genome of Medicago truncatula, a related species of Medicago truncatula, was used as the reference genome for sequence comparison. The transcriptomes of three adjacent periods (A vs. B, B vs. C, and C vs. D) were analyzed for differential gene expression and these genes were screened. A total of 6875 differentially expressed genes were detected. GO functional analysis showed that differentially expressed genes were mainly involved in biological processes, cell components, and molecular functions, among which the most differentially expressed genes were involved in the synthesis of cell components. KEGG enrichment analysis showed that the differentially expressed genes were mainly involved in circadian rhythm, photosynthetic antenna protein, ribosome metabolism, and other pathways. The number of single nucleotide variants detected by cSNP analysis was 312,875, and the frequency of A/G and C/T were the highest. The function of eggNOG was divided into 23 categories, with a total of 26,745 genes having similarities, while 9008 genes were classified as having an unknown function, 2669 genes were classified as part of signal transduction mechanisms, and 2194 genes were classified as being involved in transcription. In different developmental stages (A vs. B, B vs. C, and C vs. D), 3463 up-regulated and 3412 down-regulated differentially expressed genes were found. The difference between up-regulated and down-regulated genes was more noteworthy at the bud stage and the initial flowering stage. In addition, a total of 79 flowering genes were found, of which 51 differential genes were identified as participating in the photoperiodic regulation pathway, consisting of 23 differential genes that were up-regulated, and 28 differential genes that were down-regulated. The ratios of gene-LOC11410562(GI), gene-LOC11435974(CO), gene-LOC11422615(TOC1), and gene-LOC11432385(LHY) were higher than those of gene-LOC25500742(PHYA) and gene-LOC11 431402(ELF3); gene-LOC11434778(Col13), gene-LOC25498015(Col6), and gene-LOC11415514(Col9) were pre-expressed. The above differentially expressed genes were significantly expressed in different developmental stages of Medicago truncatula, which lays a foundation for further study of the molecular mechanism of Medicago truncatula.

Keywords

• photoperiod
• gene expression
• transcriptome analysis
• molecular mechanism