Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.

Germin-like proteins (GLPs) are defined by their sequence homology to germins from barley and are present ubiquitously in plants. Analyses of corresponding genes have revealed diverse functions of GLPs in plant development and biotic and abiotic stresses. This study describes the identification of a family of 14 germin-like genes from Brassica napus (BnGLP) designated BnGLP1–BnGLP14 and investigated potential functions of BnGLPs in plant defense against the necrotrophic fungus Sclerotinia sclerotiorum. Sequence alignment and phylogenetic analyses classify the 14 BnGLPs into four groups, which were clearly distinguished from known germin oxalic acid oxidases. Transcriptional responses of the BnGLP genes to S. sclerotiorum infection was determined by comparing cultivars of susceptible B. napus ‘Falcon’ and partially resistant B. napus ‘Zhongshuang 9’. Of the 14 BnGLP genes tested, BnGLP3 was transcriptionally upregulated in both B. napus cultivars at 6h after S. sclerotiorum infection, while upregulation of BnGLP12 was restricted to resistant B. napus ‘Zhongshuang 9’. Biochemical analysis of five representative BnGLP members identified a H₂O₂-generating superoxide dismutase activity only for higher molecular weight complexes of BnGLP3 and BnGLP12. By analogy, H₂O₂ formation at infected leaf sites increased after 6h, with even higher H₂O₂ production in B. napus ‘Zhongshuang 9’ compared with B. napus ‘Falcon’. Conversely, exogenous application of H₂O₂ significantly reduced the susceptibility of B. napus ‘Falcon’. These data suggest that early induction of BnGLP3 and BnGLP12 participates in an oxidative burst that may play a pivotal role in defence of B. napus against S. sclerotiorum.

Summary: Brassica napusis highly susceptible towardsVerticillium longisporum(Vl43) with no effective genetic resistance. It is believed that the fungus reprogrammes plant physiological processes by up‐regulation of so‐called susceptibility factors to establish a compatible interaction. By transcriptome analysis, we identified genes, which were activated/up‐regulated in rapeseed afterVl43infection. To test whether one of these genes is functionally involved in the infection process and loss of function would lead to decreased susceptibility, we firstly challenged KO lines of corresponding Arabidopsis orthologs withVl43and compared them with wild‐type plants. Here, we report that the KO ofAtCRT1aresults in drastically reduced susceptibility of plants toVl43. To provecrt1amutation also decreases susceptibility inB. napus, we identified 10 mutations in a TILLING population. Three T3 mutants displayed increased resistance as compared to the wild type. To validate the results, we generated CRISPR/Cas‐inducedBnCRT1amutants, challenged T2 plants withVl43and observed an overall reduced susceptibility in 3 out of 4 independent lines. Genotyping by allele‐specific sequencing suggests a major effect of mutations in theCRT1aA‐genome copy, while the C‐genome copy appears to have no significant impact on plant susceptibility when challenged withVl43. As revealed by transcript analysis, the loss of function ofCRT1aresults in activation of the ethylene signalling pathway, which may contribute to reduced susceptibility. Furthermore, this study demonstrates a novel strategy with great potential to improve plant disease resistance.

The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors’ genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs.

Arabidopsis nuclear- and chloroplast-localized WHIRLY1 adjusts SA content in cells via ICS1, PAL1, and BSMT1 to regulate plant senescence in a developmental-dep