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Background: Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus. Results: Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding. Conclusion: A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future. [ABSTRACT FROM AUTHOR]

The brown planthopper, Nilaparvata lugens is a pest of cultivated rice throughout Asia and is controlled using insecticides and/or resistant rice varieties. This species has developed resistance to many classes of insecticide and biotypes have developed that are virulent against formerly resistant rice cultivars. Insects use a suite of detoxification enzymes, including cytochrome P450s, glutathione S-transferases and carboxyl/cholinesterases to defend themselves against plant secondary metabolites and pesticides. Pyrosequencing on the Roche 454-FLX platform was used to produce a substantial expressed sequence tag (EST) dataset to complement the existing Sanger sequenced ESTs in GenBank. A total of 78 959 reads were combined with the 37 392 publically available Sanger ESTs; these assembled into 8 911 contigs and 10 620 singletons. Analysis of the distribution of tentative unique genes (TUGs) with the gene ontology for biological processes and molecular functions suggests that the 454 and Sanger EST assembly is broadly representative of the N. lugens transcriptome. The brown planthopper transcriptome was found to contain 31 TUGs encoding P450s, nine encoding glutathione S-transferases and 26 encoding carboxyl/cholinesterases and many of these are putatively involved in the detoxification of xenobiotics. The Agilent eArray platform was used to construct an oligonucleotide microarray populated with probes for ∼19 000 unigene sequences, including all those known to encode detoxification enzymes. The genomic resources developed in this study will be useful to the community studying this crop pest and will help elucidate the molecular mechanism underlying insecticide resistance and planthopper adaptation to resistant rice cultivars. [ABSTRACT FROM AUTHOR]

• A 2-year field experiments showed that continuous inflorescence removal (CIR) treatment improved the yield and quality of B. chinense DC. • Transcriptome sequencing analysis showed that BR and JA signal transduction were CIR-induced. • Irrigation experiment confirmed that BR could improve root growth. • Irrigation experiment confirmed that JA could improve SS content in root. The root of Bupleurum chinense DC. is the major source of Radix Bupleuri and widely used for the treatment of inflammatory disorders and infectious diseases in Asia. However, the excessive reproductive growth of B. chinense DC. strongly interferes with its root biomass accumulation and secondary metabolite biosynthesis. Although inflorescence removal or disbudding has been used to improve the yield and quality in rhizome crops, the molecular mechanism is unknown. Here, we compared the differences between the control groups and the continuous inflorescence removal (CIR) treatment groups of B. chinense DC. on physiological, chemical and molecular levels. The results of 2-year field experiments showed that the primary root length and biomass accumulation, as well as the saikosaponin a and d (SS-a and SS-d) contents were all increased under CIR treatment. Illumina sequencing of cDNA libraries prepared from the roots of control groups and CIR groups during four flowering stages identified 172, 243, 1974 and 3024 differentially expressed genes (DEGs) respectively. Most DEGs were involved in brassinolide (BR) signal transduction, jasmonic acid (JA) signal tranduction, 2-methyl-d-erythritol-4-phosphate pathway/Mevalonate (MVA/MEP) pathways and SS pathways. There were 295 differentially expressed transcription factors (TFs) including members of the MYB, bHLH, bZIP, and NAC families that also induced by CIR treatment. Irrigation experiments further showed that 0.05 mg/L exogenous BR improved the root fresh weight and the root/shoot ratio of B. chinense DC. mainly through cyclin D3 , BIR1 , BSK1 and ARFs ; the SS-a and SS-d contents in the roots of B. chinense DC. were increased under 100 mM exogenous Me-JA treatment, most genes involved in MVA, MEP and SS pathways were activated. In all, this study not only provides new insights into the fundamental mechanism underlying the poorly studied inflorescence removal process in B. chinense DC. and other rhizome crops, but also represents an important resource for future research on gene functions during CIR treatment or the reproductive stage. [ABSTRACT FROM AUTHOR]