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An increasing number of microRNAs (miRNAs) and miRNA‐related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well‐watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA‐like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24‐nt novel miRNA stood out, were strongly down‐regulated. Given the putative roles of the miRNA‐targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions. The present work provides a first characterization of the rich and variable isomiRome encoded by a conifer genome. Results highlight a differential distribution of the isomiRome in different vegetative organs and under contrasting water availability, and potentially targeting transcripts controlling key physiological responses to drought. [ABSTRACT FROM AUTHOR]

Adaptation of long‐living forest trees to respond to environmental changes is essential to secure their performance under adverse conditions. Water deficit is one of the most significant stress factors determining tree growth and survival. Maritime pine (Pinus pinaster Ait.), the main source of softwood in southwestern Europe, is subjected to recurrent drought periods which, according to climate change predictions for the years to come, will progressively increase in the Mediterranean region. The mechanisms regulating pine adaptive responses to environment are still largely unknown. The aim of this work was to go a step further in understanding the molecular mechanisms underlying maritime pine response to water stress and drought tolerance at the whole plant level. A global transcriptomic profiling of roots, stems, and needles was conducted to analyze the performance of siblings showing contrasted responses to water deficit from an ad hoc designed full‐sib family. Although P. pinaster is considered a recalcitrant species for vegetative propagation in adult phase, the analysis was conducted using vegetatively propagated trees exposed to two treatments: well‐watered and moderate water stress. The comparative analyses led us to identify organ‐specific genes, constitutively expressed as well as differentially expressed when comparing control versus water stress conditions, in drought‐sensitive and drought‐tolerant genotypes. Different response strategies can point out, with tolerant individuals being pre‐adapted for coping with drought by constitutively expressing stress‐related genes that are detected only in latter stages on sensitive individuals subjected to drought. [ABSTRACT FROM AUTHOR]

Since 2015, Araucaria araucana, an ecologically and economically important conifer native to Argentina and Chile, has suffered an unusual partial death of the crown throughout almost all of the distribution range in Argentina. No primary pathogen or pest was evident, associated with the phenomenon. Isolates of Mortierella, a poorly studied fungal genus in Patagonia, were obtained from the margins of necrotic phloem tissue of symptomatic trees. Five species of Mortierella were isolated from affected tissues. In inoculation tests, Mortierella alpina and M. aff. basiparvispora were pathogenic to A. araucana. These species caused necrosis of phloem, leading to chlorosis, foliar desiccation and eventually death, demonstrating that Mortierellales may play a role in the decline of the tree. [ABSTRACT FROM AUTHOR]

Haploids are a valuable tool for genomic studies in higher plants, especially those with huge genome size and long juvenile periods, such as conifers. In these species, megagametophyte cultures have been widely used to obtain haploid callus and somatic embryogenic lines. One of the main problems associated with tissue culture is the potential genetic instability of the regenerants. Because of this, chromosomal stability of the callus and/or somatic embryos should also be assessed. To this end, chromosome counting, flow cytometry and genotyping using microsatellites have been reported. Here, we present an overview of the work done in conifers, with special emphasis on the production of a haploid cell line in maritime pine (Pinus pinaster L.) and the use of a set of molecular markers, which includes Single Nucleotide Polymorphisms (SNPs) and microsatellites or Single Sequence Repeats (SSRs), to validate chromosomal integrity confirming the presence of all chromosomic arms. [ABSTRACT FROM AUTHOR]

Background Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought. Results High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area. Conclusions The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response. [ABSTRACT FROM AUTHOR]

Phytophthora austrocedri is a pathogen of Austrocedrus chilensis causing "Mal del Ciprés" (cypress sickness) in Patagonia and killing Juniperus communis in Britain, along with other species in the Cupressaceae. The evident association of the pathogen with members of the Cupressaceae makes it necessary to study the susceptibility of other species related to A. chilensis to prevent the emergence of new diseases. The present study tested the pathogenicity of P. austrocedri to three native and endemic conifers in South America: Fitzroya cupressoides, Pilgerodendron uviferum and Araucaria araucana. The results showed that F. cupressoides and P. uviferum were highly susceptible to P. austrocedri. Since these are endangered tree species, the outcome of this study is crucial for governmental agencies, policymakers and stakeholders. [ABSTRACT FROM AUTHOR]