Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress

Abstract

BackgroundMicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and quality of broccoli are decreased by heat stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of miRNAomes during the broccoli head formation under heat stress is limited.MethodsIn this study, molecular characterization of two nearly isogenic lines with contrasting head-forming capacity was investigated. Head-forming capacity was better for heat-tolerant (HT) than heat-sensitive (HS) broccoli under heat stress.ResultsBy deep sequencing and computational analysis, 20 known miRNAs showed significant differential expression between HT and HS genotypes. According to the criteria for annotation of new miRNAs, 24 novel miRNA sequences with differential expression between the two genotypes were identified. To gain insight into functional significance, 213 unique potential targets of these 44 differentially expressed miRNAs were predicted. These targets were implicated in shoot apical development, phase change, response to temperature stimulus, hormone and energy metabolism. The head-forming capacity of the unique HT line was related to autonomous regulation of Bo-FT genes and less expression level of heat shock protein genes as compared to HS. For the genotypic comparison, a set of miRNAs and their targets had consistent expression patterns in various HT genotypes.ConclusionsThis large-scale characterization of broccoli miRNAs and their potential targets is to unravel the regulatory roles of miRNAs underlying heat-tolerant head-forming capacity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2201-1) contains supplementary material, which is available to authorized users.

Integrative analysis of genome‐wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids

“…Seven of the sixty-one lncRNAs were differentially expressed lncRNAs between Brassica allohexaploid and its parents. We checked the sequences of lncRNAs to screen out miRNA precursors and found that only 15 of 3,120 lncRNAs (0.48%) harbored complete precursors for 15 miRNAs (Table S11), which was consistent with the earlier study that only 0.2% of lncRNAs serve as miRNA precursors to regulate biological processes (Chen, Fu et al, 2015;Chen, Quan, & Zhang, 2015). Prediction of the secondary structure for the 15 transcripts using the Vienna RNA package RNAfold program showed that these miRNA precursors had stable hairpin structures ( Figure S4), two of which are shown in Figure 14.…”

“…LncRNAs could act as targets or precursors of miRNAs to regulate gene expression (Chen, Fu et al., ; Chen, Quan, & Zhang, ). Target mimicry is a vital function for lncRNAs to regulate growth and metabolic progress in plants (Zhu & Wang, ).…”

“…To determine cis–regulation relationship pairs, we regarded differentially expressed lncRNA and differentially expressed mRNA as a pair if they were co‐expressed and less than 100 kb apart, in accordance with the reported method (Liao et al., ). The target genes of differentially expressed lncRNAs via trans‐acting were identified by sequence complementarity (Chen, Fu et al., ; Chen, Quan, & Zhang, ). A target gene sequence complementary to the lncRNA was selected by BLAST with E ‐value = 1e‐5 and identity = 95%; then, the targets with E ‐value = −30 was singled out using RNAplex program (Tafer & Hofacker, ).…”

“…We also determined if lncRNAs served as miRNA precursors. The secondary structure of lncRNA transcripts was predicted by the Vienna RNA package RNAfold program, which checked out the stability of hairpin structures (Chen, Fu et al., ; Chen, Quan, & Zhang, ).…”

“…They bring about mRNA degradation (Golden, Gerbasi, & Sontheimer, 2008) or protect mRNAs from miRNA-mediated degradation (Faghihi et al, 2010) by base complementary, and they facilitate mRNA translation (Carrieri et al, 2012) or interdict mRNA translation (Kawano, Aravind, & Storz, 2007) by integrating with the 5′ part of the target mRNA. A few studies suggest that a small number of them could act as miRNA precursors (Jalali, Jayaraj, & Scaria, 2012;Chen, Fu et al, 2015;Chen, Quan, & Zhang, 2015;Chen et al, 2016).…”