RESUMEN
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation.
Asunto(s)
Adaptación Fisiológica/genética , Proteínas de Arabidopsis/genética , Arabidopsis/genética , ADN (Citosina-5-)-Metiltransferasas/genética , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Islas de CpG , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Metilación de ADN , Elementos Transponibles de ADN , Epigénesis Genética , Perfilación de la Expresión Génica , Variación Genética , Estudio de Asociación del Genoma Completo , Temperatura , Transcripción GenéticaRESUMEN
Food associated indigenous microbial communities exert antagonistic effects on pathogens and may routinely deliver health relevant microorganisms to the GI tract. By using molecular, culture independent methods including PCR-DGGE of 16S rDNA-coding regions and real-time PCR (RT-PCR) as well as BIOLOG metabolic fingerprinting, microbial communities on lettuce were analyzed in samples from fields, from supermarkets and soil. Amplified 16S rRNA gene sequences (57.7%) could be assigned to species previously reported as typical for the phyllosphere including Pantoea agglomerans, Pseudomonas flavescens, Moraxella spp., and Mycobacterium spp. 71.8% of the sequences obtained represented so far undescribed taxa. Principal component analysis of BIOLOG metabolic profiles indicated a seasonal variation in the lettuce phyllosphere microbial community structure. Various lactic acid bacteria were detected including several Lactobacillus and Leuconostoc species in particular on lettuce from organic farming. By RT-PCR lactobacilli were found with a range of abundances from 1x10(4 )to 1x10(5 )copies/g lettuce. Considering the importance of salad in many diets lettuce may contribute to a constant supply with LAB.