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    Methylobacterium, a major component of the culturable bacterial endophyte community of wild Brassica seed
    (PeerJ, Inc, 2020-07-10) Roodi D; Millner JP; McGill C; Johnson RD; Jauregui R; Card SD; Souza V
    BACKGROUND: Plants are commonly colonized by a wide diversity of microbial species and the relationships created can range from mutualistic through to parasitic. Microorganisms that typically form symptomless associations with internal plant tissues are termed endophytes. Endophytes associate with most plant species found in natural and managed ecosystems. They are extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Plant domestication has reduced endophyte diversity and therefore the wild relatives of many crop species remain untapped reservoirs of beneficial microbes. Brassica species display immense diversity and consequently provide the greatest assortment of products used by humans from a single plant genus important for agriculture, horticulture, bioremediation, medicine, soil conditioners, composting crops, and in the production of edible and industrial oils. Many endophytes are horizontally transmitted, but some can colonize the plant's reproductive tissues, and this gives these symbionts an efficient mechanism of propagation via plant seed (termed vertical transmission). METHODS: This study surveyed 83 wild and landrace Brassica accessions composed of 14 different species with a worldwide distribution for seed-originating bacterial endophytes. Seed was stringently disinfected, sown within sterile tissue culture pots within a sterile environment and incubated. After approximately 1-month, direct isolation techniques were used to recover bacterial endophytes from roots and shoots of symptomless plants. Bacteria were identified based on the PCR amplification of partial 16S rDNA gene sequences and annotated using the BLASTn program against the NCBI rRNA database. A diversity index was used as a quantitative measure to reflect how many different bacterial species there were in the seed-originating microbial community of the Brassica accessions sampled. RESULTS: Bacterial endophytes were recovered from the majority of the Brassica accessions screened. 16S rDNA gene sequencing identified 19 different bacterial species belonging to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria with the most frequently isolated species being Methylobacterium fujisawaense, Stenotrophomonas rhizophila and Pseudomonas lactis. Methylobacterium was the dominant genus composing 56% of the culturable isolated bacterial community and was common in 77% of accessions possessing culturable bacterial endophytes. Two selected isolates of Methylobacterium significantly promoted plant growth when inoculated into a cultivar of oilseed rape and inhibited the growth of the pathogen Leptosphaeria maculans in dual culture. This is the first report that investigates the seed-originating endophytic microorganisms of wild Brassica species and highlights the Brassica microbiome as a resource for plant growth promoting bacteria and biological control agents.
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    Comparative Transcriptomics of Multi-Stress Responses in Pachycladon cheesemanii and Arabidopsis thaliana.
    (MDPI (Basel, Switzerland), 2023-07-11) Dong Y; Gupta S; Wargent JJ; Putterill J; Macknight RC; Gechev TS; Mueller-Roeber B; Dijkwel PP; You FM
    The environment is seldom optimal for plant growth and changes in abiotic and biotic signals, including temperature, water availability, radiation and pests, induce plant responses to optimise survival. The New Zealand native plant species and close relative to Arabidopsis thaliana, Pachycladon cheesemanii, grows under environmental conditions that are unsustainable for many plant species. Here, we compare the responses of both species to different stressors (low temperature, salt and UV-B radiation) to help understand how P. cheesemanii can grow in such harsh environments. The stress transcriptomes were determined and comparative transcriptome and network analyses discovered similar and unique responses within species, and between the two plant species. A number of widely studied plant stress processes were highly conserved in A. thaliana and P. cheesemanii. However, in response to cold stress, Gene Ontology terms related to glycosinolate metabolism were only enriched in P. cheesemanii. Salt stress was associated with alteration of the cuticle and proline biosynthesis in A. thaliana and P. cheesemanii, respectively. Anthocyanin production may be a more important strategy to contribute to the UV-B radiation tolerance in P. cheesemanii. These results allowed us to define broad stress response pathways in A. thaliana and P. cheesemanii and suggested that regulation of glycosinolate, proline and anthocyanin metabolism are strategies that help mitigate environmental stress.
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    The molecular genetic basis of natural variation in trichome density in Arabidopsis thaliana : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
    (Massey University, 2013) Bloomer, Rebecca
    Understanding the genetic basis of natural variation in phenotypes is a central, yet often elusive, goal in evolutionary biology. Trichome density, an herbivory defence trait in Arabidopsis thaliana, is a powerful model for investigating natural phenotypic variation, combining a genetically well characterised developmental pathway with a quantitatively and qualitatively variable phenotype of selective importance. Here, Quantitative Trait Locus (QTL) mapping and candidate gene analyses were undertaken to explore the genetic basis of variation in trichome density in natural accessions of A. thaliana, under an overarching hypothesis that allelic variation in the epidermal development pathway plays a significant role. QTL mapping for constitutive and wounding-induced trichome density and for plasticity of density was undertaken in two newly developed mapping populations, broadening the range of allelic variation sampled in trichome density studies. This study is the first to address the genetic architecture of induced density and plasticity, finding a genetic basis to plasticity and a surprising negative response to wounding among some members of the populations used. Some QTL mapped are unique, while others appear common to both constitutive and induced density phenotypes or to overlap across mapping populations, suggesting particular loci may be key to generating variation for trichome phenotypes. Epistatic interactions and candidate genes for QTL within, up- and downstream of the epidermal development pathway are identified. Candidate gene analyses focussed on genes within the epidermal development pathway: the trichome-specific MYB GL1 and the pleiotropic WD-repeat TTG1. In both GL1 and TTG1, a pattern of high frequency polymorphism correlates with variation in trichome density. In GL1, variation has both qualitative and quantitative effects, with both protein-coding and regulatory changes proposed as underlying bases. The TTG1 coding region is subject to strong purifying selection, and the observed quantitative effect on density appears to be based on variation in regulatory sequence. Both QTL mapping and candidate gene approaches support the hypothesis of a key role for the epidermal development pathway in generating variation in trichome density in A. thaliana, and more generally a role for variation in regulatory genes contributing to natural phenotypic variation.