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The Mediterranean basin is drastically affected by intense and frequent droughts, which jeopardize the diversity and survival of its forest, for example

16 Pág., Increasing temperatures along with severe droughts are factors that may jeopardize the survival of the forests in the Mediterranean basin. In this region, Pinus pinaster is a common conifer species, that has been used as a model species in evolutionary studies due to its adaptive response to changing environments. Although its drought tolerance mechanisms are already known, knowledge about the dynamics of its root microbiota is still scarce. We aimed to decipher the structural (bacterial abundance), compositional, functional and associative changes of the P. pinaster rhizosphere bacterial communities in spring and summer, at DNA and RNA level (environmental DNA, live and dead cells, and those synthesizing proteins). A fundamental aspect of root microbiome-based approaches is to guarantee the correct origin of the samples. Thus, we assessed the genotype of host needles and roots from which rhizosphere samples were obtained. For more than 50% of the selected trees, genotype discrepancies were found and in three cases the plant species could not be determined. Rhizosphere bacterial communities were homogeneous with respect to diversity and structural levels regardless of the host genotype in both seasons. Nonetheless, significant changes were seen in the taxonomic profiles depending on the season. Seasonal changes were also evident in the bacterial co-occurrence patterns, both in DNA and RNA libraries. While spring communities switched to more complex networks, summer populations resulted in more compartmentalized networks, suggesting that these communities were facing a disturbance. These results may mirror the future status of bacterial communities in a context of climate change. A keystone hub was ascribed to the genus Phenylobacterium in the functional network calculated for summer. Overall, it is important to validate the origin and identity of plant samples in any plant-microbiota study so that more reliable ecological analyses are performed., This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness [AGL2015-66048-C2-1-R; RTI2018-098015-B-I00], and by the Spanish Ministry of Science and Innovation project SUMHAL [LIFEWATCH-2019-09-CSIC-13, POPE 2014-2020], both co-financed by the (ERDF)European Regional Development Fund

In the current context of climate change, evaluation of intraspecific genetic and phenotypic variability of lentil (Lens culinaris Medik) in response to early droughts is fundamental to gain novel insight on the adaptive potential of lentil to water deficit. Here we studied in the field the variability of functional traits, leaf biochemical composition and yield components of three Spanish lentil cultivars submitted to an atypically dry spring. The genetic variability was also studied using amplified fragment length polymorphisms based on 156 polymorphic bands. The vulnerability of the cultivars to future drier scenarios was assessed and we identified potential traits related with lentil’s tolerance to early water deficit. Inter-cultivar variability was found in the response pattern of stomatal conductance to water availability but also in other functional traits and yield components. The small-seeded commercial cultivar PAR had the highest harvest index, grain yield, maximum stomatal conductance, stomatal density and specific leaf area while the lowest root-to-shoot ratio. PAR also had early flowering and the shortest life cycle as well as high leaf polyphenol and carotenoid contents. Therefore, the drought escape strategy exhibited by PAR could be beneficial under dry springs in Mediterranean environments. In contrast, despite the big-seeded non-commercial traditional cultivar MAN displayed drought tolerant traits and high genetic and phenotypic variability, it had the lowest grain yield, suggesting that MAN is less valuable than PAR as a source of early drought resistance for the genetic improvement of lentils.

International audience; Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world's conifer forests.

Drought is an important driver of plant survival, growth, and distribution. Water deficit affects different pathways of metabolism, depending on plant organ. While previous studies have mainly focused on the metabolic drought response of a single organ, analysis of metabolic differences between organs is essential to achieve an integrated understanding of the whole plant response. In this work, untargeted metabolic profiling was used to examine the response of roots, stems, adult and juvenile needles from Pinus pinaster Ait. full-sib individuals, subjected to a moderate and long lasting drought period. Cyclitols content showed a significant alteration, in response to drought in all organs examined, but other metabolites increased or decreased differentially depending on the analyzed organ. While a high number of flavonoids were only detected in aerial organs, an induction of the glutathione pathway was mainly detected in roots. This result may reflect different antioxidant mechanisms activated in aerial organs and roots. Metabolic changes were more remarkable in roots than in the other organs, highlighting its prominent role in the response to water stress. Significant changes in flavonoids and ascorbate metabolism were also observed between adult and juvenile needles, consistent with previously proven differential functional responses between the two developmental stages. Genetic polymorphisms in candidate genes coding for a Myb1 transcription factor and a malate dehydrogenase (EC 1.1.1.37) were associated with different concentration of phenylalanine, phenylpropanoids and malate, respectively. The results obtained will support further research on metabolites and genes potentially involved in functional mechanisms related to drought tolerance in trees. © 2016 Elsevier Masson SAS.

Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular "memory". Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change. © 2013 The Authors. Published by Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Conifers separated from angiosperms 300 million years ago and currently dominate many of the temperate and boreal forests. This chapter aims to highlight the singularities of this phylum, characterized by very large genomes (18 to 35 Gb) and showing very different structure and composition when compared with angiosperm genomes. Despite an apparently conserved genome structure, conifers demonstrate some competitive capacity, as very different lineages are adapted to a wide variety of environmental conditions. All the above reasons make conifers a unique system for the study of adaptive evolution in plants.

Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

Mediterranean trees are expected to be exposed to an increased aridity in the near future. The lack of genetic variability of stone pine (Pinus pinea L.) could limit the adaptation potential of the species to more severe droughts. However, information on intra-specific variability in adaptive traits that might confer potential drought tolerance is scant for stone pine. In this study, we explored the adaptation potential of stone pine to water deficit through variability of key functional traits. In particular, inter-clonal variation in whole plant performance in response to water deficit was studied. The role of inter-clonal variation in functional traits and phenotypic plasticity as determinants of whole plant performance under water deficit were also assessed. Relative growth rate (RGR) and key morphological and physiological traits were studied in ramets of 20 different clones of stone pine from a wide range of populations in the Iberian Peninsula. The plants were grown in climatic chamber under controlled environmental conditions and were submitted to an experimental water deficit of 20 days. The results showed significant inter-clonal variation in total dry mass, RGR, biomass partitioning specific leaf area (SLA), leaf area ratio (LAR), net photosynthetic rate (An), stomatal conductance (gs) and intrinsic water use efficiency (WUEi). Significant phenotypic plasticity in response to drought was found for An, gs and WUEi but it did not differ among clones. The clones could be clustered into different groups according to the variability of the studied traits in a principal components analysis. LAR, SLA and net photosynthetic rates explained most of the variation. A combination of traits (high LAR and low WUEi) agreeing with a water spending strategy rather than with a water saving strategy seemed to underlie enhanced RGR under water deficit. Stone pine showed high phenotypic plasticity and significant intra-specific variation in functional traits in response to water deficit. The pattern of variation found in morphological and physiological traits might allow adaptation to short term water deficit in this species. © 2010 Elsevier B.V.

This study was supported by the Spanish Ministerio de Ciencia e Innovación [AGL2009-12139-C02-02, BIO2009-07490], the European Union [PLE2009-0016] and the Junta de Andalucía [CVI-6075 and BIO-114], Fernández-Pozo, N., Canales, J., Guerrero-Fernández, D., Villalobos, D.P., Díaz-Moreno, S.M., Bautista, R., Flores-Monterroso, A., Guevara, M.Á., Perdiguero, P., Collada, C., Cervera, M.T., Soto, T., Ordás, R., Cantón, F.R., Avila, C., Cánovas, F.M., Claros, M.G.

The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher FST values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower FST values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed in relation to the different genes' putative involvement in drought tolerance responses, from published results in transcriptomics and association mapping in P. pinaster and other related species. These genes clearly constitute relevant candidates for future association studies in P. pinaster. © The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.