Long non-coding RNAs (lncRNAs) mediate important epigenetic regulation in various biological processes related to the stress response in plants. However, the systematic analysis of the lncRNAs expressed in Brassica rapa under heat stress has been elusive. In this study, we performed a genome-wide analysis of the lncRNA expression profiles in non-heading Chinese cabbage leaves using strand-specific RNA-sequencing. A total of 4594 putative lncRNAs were identified with a comprehensive landscape of dynamic lncRNA expression networks under heat stress. Co-expression networks of the interactions among the differentially expressed lncRNAs, mRNAs and microRNAs revealed that several phytohormones were associated with heat tolerance, including salicylic acid (SA) and brassinosteroid (BR) pathways. Of particular importance is the discovery of 25 lncRNAs that were highly co-expressed with 10 heat responsive genes. Thirty-nine lncRNAs were predicted as endogenous target mimics (eTMs) for 35 miRNAs, and five of them were validated to be involved in the heat tolerance of Chinese cabbage. Heat responsive lncRNA (TCONS_00048391) is an eTM for bra-miR164a, that could be a sponge for miRNA binding and may be a competing endogenous RNA (ceRNA) for the target gene NAC1 (Bra030820), affecting the expression of bra-miR164a in Chinese cabbage. Thus, these findings provide new insights into the functions of lncRNAs in heat tolerance and highlight a set of candidate lncRNAs for further studies in non-heading Chinese cabbage.

The mating system transition in polyploid Brassica napus (AACC) from out-crossing to selfing is a typical trait to differentiate it from their diploid progenitors. Elucidating the mechanism of mating system transition has profound consequences for understanding the speciation and evolution in B. napus. Functional complementation experiment has shown that the insertion of 3.6 kb into the promoter of self-incompatibility male determining gene, BnSP11-1 leads to its loss of function in B. napus. The inserted fragment was found to be a non-autonomous Helitron transposon. Further analysis showed that the inserted 3.6 kb non-autonomous Helitron transposon was widely distributed in B. napus accessions which contain the S haplotype BnS-1. Through promoter deletion analysis, an enhancer and a putative cis-regulatory element (TTCTA) that were required for spatio-temporal specific expression of BnSP11-1 were identified, and both might be disrupted by the insertion of Helitron transposon. We suggested that the insertion of Helitron transposons in the promoter of BnSP11-1 gene had altered the mating system and might facilitated the speciation of B. napus. Our findings have profound consequences for understanding the self-compatibility in B. napus as well as for the trait variations during evolutionary process of plant polyploidization.

Tribenuron-methyl (TM) is a powerful sulfonylurea herbicide that inhibits branched-chain amino acid (BCAA) biosynthesis by targeting the catalytic subunit (CSR1) of acetolactate synthase (ALS). Selective induction of male sterility by foliar spraying of TM at low doses has been widely used for hybrid seed production in rapeseed (Brassica napus); however, the underlying mechanism remains unknown. Here, we report greater TM accumulation and subsequent stronger ALS inhibition and BCAA starvation in anthers than in leaves and stems after TM application. Constitutive or anther-specific expression of csr1-1D (a CSR1 mutant) eliminated anther-selective ALS inhibition and reversed the TM-induced male sterile phenotype in both rapeseed and Arabidopsis. The results of TM daub-stem experiments, combined with the observations of little TM accumulation in anthers and reversion of TM-induced male sterility by targeted expression of the TM metabolism gene Bel in either the mesophyll or phloem, suggested that foliar-sprayed TM was polar-transported to anthers mainly through the mesophyll and phloem. Microscopy and immunoblotting revealed that autophagy, a bulk degradation process induced during cell death, was elevated in TM-induced male sterile anthers and by anther-specific knockdown of ALS. Moreover, TM-induced pollen abortion was significantly inhibited by the autophagy inhibitor 3-MA. These data suggested that TM was polar-transported to anthers, resulting in BCAA starvation via anther-specific ALS inhibition and, ultimately, autophagic cell death in anthers.

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Brassica species exhibit both compatible and incompatible pollen-stigma interactions, however, the underlying molecular mechanisms remain largely unknown. Here, RNA-seq technology was applied in a comprehensive time-course experiment (2, 5, 10, 20, and 30 min) to explore gene expression during compatible/incompatible pollen-stigma interactions in stigma. Moderate changes of gene expression were observed both in compatible pollination (PC) and incompatible pollination (PI) within 10 min, whereas drastic changes showed up by 30 min, especially in PI. Stage specific DEGs [Differentially Expressed Gene(s)] were identified, and signaling pathways such as stress response, defense response, cell wall modification and others were found to be over-represented. In addition, enriched genes in all samples were analyzed as well, 293 most highly expressed genes were identified and annotated. Gene Ontology and metabolic pathway analysis revealed 10 most highly expressed genes and 37 activated metabolic pathways. According to the data, downstream components were activated in signaling pathways of both compatible and incompatible responses, and incompatible response had more complicated signal transduction networks. This study provides more detailed molecular information at different time points after compatible and incompatible pollination, deepening our knowledge about pollen-stigma interactions.