Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula.

BACKGROUND: Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula, in response to rhizobial signals that trigger the formation of root nodules. RESULTS: We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis-regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. CONCLUSIONS: Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.

An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp.

The transcription factor NODULE INCEPTION (NIN) has been studied extensively for its multiple roles in root nodule symbiosis within plants of the nitrogen-fixing clade (NFC) that associate with soil bacteria, such as rhizobia and Frankia. However, NIN homologs are present in plants outside the NFC, suggesting a role in other developmental processes. Here, we show that the biofuel crop Populus sp., which is not part of the NFC, contains eight copies of NIN with diversified protein sequence and expression patterns. Lipo-chitooligosaccharides (LCOs) are produced by rhizobia and a wide range of fungi, including mycorrhizal ones, and act as symbiotic signals that promote lateral root formation. RNAseq analysis of Populus sp. treated with purified LCO showed induction of the PtNIN2 subfamily. Moreover, the expression of PtNIN2b correlated with the formation of lateral roots and was suppressed by cytokinin treatment. Constitutive expression of PtNIN2b overcame the inhibition of lateral root development by cytokinin under high nitrate conditions. Lateral root induction in response to LCOs likely represents an ancestral function of NIN retained and repurposed in nodulating plants, as we demonstrate that the role of NIN in LCO-induced root branching is conserved in both Populus sp. and legumes. We further established a visual marker of LCO perception in Populus sp. roots, the putative sulfotransferase PtSS1 that can be used to study symbiotic interactions with the bacterial and fungal symbionts of Populus sp.

Global analysis of the MATE gene family of metabolite transporters in tomato.

BACKGROUND: Species in the Solanaceae family are known for producing plethora of specialized metabolites. In addition to biosynthesis pathways, a full comprehension of secondary metabolism must also take into account the transport and subcellular compartmentalization of substances. Here, we examined the MATE (Multidrug and Toxic Compound Extrusion, or Multi-Antimicrobial Extrusion) gene family in the tomato (Solanum lycopersicum) genome with the objective of better understanding the transport of secondary metabolites in this model species. MATE membrane effluxers encompass an ancient gene family of secondary transporters present in all kingdoms of life, but with a remarkable expansion in plants. They mediate the transport of primary and secondary metabolites using the proton motive force through several membrane systems of the cell. RESULTS: We identified 67 genes coding for MATE transporters in the tomato genome, 33 of which are expressed constitutively whereas 34 are expressed in specific cell types or environmental conditions. Synteny analyses revealed bona fide paralogs and Arabidopsis orthologs. Co-expression analysis between MATE and regulatory genes revealed 78 positive and 8 negative strong associations (ρ≥|0.8|). We found no evidence of MATE transporters belonging to known metabolic gene clusters in tomato. CONCLUSIONS: Altogether, our expression data, phylogenetic analyses, and synteny study provide strong evidence of functional homologies between MATE genes of tomato and Arabidopsis thaliana. Our co-expression study revealed potential transcriptional regulators of MATE genes that warrant further investigation. This work sets the stage for genome-wide functional analyses of MATE transporters in tomato and other Solanaceae species of economic relevance.

Variabilidade genética associada à germinação e vigor de sementes de linhagens de feijoeiro comum / Genetic variability associated with germination and seed vigor of common bean lines

Objetivou-se, com este trabalho estimar a variabilidade genética para os caracteres relacionados com a velocidade de germinação e a capacidade das plantas em cobrir rapidamente o solo. Foram utilizadas sementes de 94 linhagens do banco de germoplasma de feijão (Phaseolus vulgaris L.) da Universidade Federal de Lavras, que diferiam em vários caracteres, tais como, cor, tamanho e formato das sementes. Foram realizados dois experimentos para avaliação das linhagens. O primeiro foi aos 120 dias e o segundo aos 360 dias após o início do armazenamento (em temperatura e umidade ambientes e sob baixa luminosidade). Foram obtidos as porcentagens de germinação ( por centoG), o índice de velocidade de emergência (IVE) e a matéria seca (MS). As variáveis foram padronizadas e obtido o somatório do IVE + MS. Foram obtidas as correlações fenotípica, genética e ambiental entre todos os caracteres e estimaram-se o ganho esperado com a seleção e a resposta correlacionada. Tanto a por centoG, quanto o IVE tiveram seus valores reduzidos na avaliação aos 360 dias após o armazenamento das sementes, em comparação com a avaliação realizada aos 120 dias. Foi possível obter ganho com a seleção, para maiores por centoG, IVE e MS. O maior ganho foi obtido no primeiro experimento. Entre as linhagens avaliadas há variabilidade suficiente para se proceder à seleção com relação à germinação e emergência. As linhagens JALO EEP 558, PI-103 e CVII 39-24 foram identificadas como as melhores em relação à germinação e emergência e as linhagens RP-2, BP-34 e ESAL 569 foram as que apresentaram menor vigor.

The objective of this study was to estimate the genetic variability for characters related with the germination rate and the capacity of the plants to occupy the ground quickly. Ninety four lines from the common bean (Phaseolus vulgaris L.) germoplasm from the Universidade Federal de Lavras, differing in several characters as color, size and shape of the seeds were used. Two experiments were carried out to evaluate the bean lines. The first was conducted at 120 days and the second 360 days after the beginning of storage (room temperature and humidity and under low light). Percentage of germination ( percentG), emergency speed rate (ESR) and dry matter (DM) were obtained. The variables were standardized and obtained the sum of the ESR + DM. Phenotypic, genetic and environmental correlations between all the characters were obtained and the expected gain was estimated with the selection and correlated response. Both the G percent and ESR presented reduced levels in the evaluation at 360 days after seed storage in comparison with the evaluation at 120 days. It was possible to obtain the gain with the selection, for higher percentG, ESR and DM. The higher gain was obtained in the first experiment. Among the lines evaluated, there are genetic sufficient variability to proceed the selection for germination and emergence. The lines JALO EEP 558, PI-103 and CVII 39-24 were identified as the best for germination and emergence and the lines RP-2, BP-34 and ESAL 569 were those with smaller vigor.