Changing concepts in plant hormone action

Summary: A plant hormone is not, in the classic animal sense, a chemical synthesized in one organ, transported to a second organ to exert a chemical action to control a physiological event. Any phytohormone can be synthesized everywhere and can influence different growth and development processes at different places. The concept of physiological activity under hormonal control cannot be dissociated from changes in concentrations at the site of action, from spatial differences and changes in the tissue's sensitivity to the compound, from its transport and its metabolism, from balances and interactions with the other phytohormones, or in their metabolic relationships, and in their signaling pathways as well. Secondary messengers are also involved. Hormonal involvement in physiological processes can appear through several distinct manifestations (as environmental sensors, homeostatic regulators and spatio-temporal synchronizers, resource allocators, biotime adjusters, etc.), dependent on or integrated with the primary biochemical pathways. The time has also passed for the hypothesized ‘specific' developmental hormones, rhizocaline, canlocaline, and florigen: root, stem, and flower formation result from a sequential control of specific events at the right places through a coordinated control by electrical signals, the known phytohormones and nonspecific molecules of primary and secondary metabolism, and involve both cytoplasmic and apoplastic compartments. These contemporary views are examined in this revie

A saturated consensus linkage map of Picea abies including AFLP, SSR, STS, 5S rDNA and morphological markers

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Does maternal environmental condition during reproductive development induce genotypic selection in Picea abies ?

In forest trees, environmental conditions during reproduction can greatly influence progeny performance. This phenomenon probably results from adaptive phenotypic plasticity but also may be associated with genotypic selection. In order to determine whether selective effects during the reproduction are environment specific, single pair-crosses of Norway spruce were studied in two contrasted maternal environments (warm and cold conditions). One family expressed large and the other small phenotypic differences between these crossing environments. The inheritance of genetic polymorphism was analysed at the seed stage. Four parental genetic maps covering 66 to 78% of the genome were constructed using 190 to 200 loci. After correcting for multiple testing, there is no evidence of locus under strong and repeatable selection. The maternal environment could thus only induce limited genotypic-selection effects during reproductive steps, and performance of progenies may be mainly affected by a long-lasting epigenetic memory regulated by temperature and photoperiod prevailing during seed productio

Do maternal environmental conditions during reproductive development induce genotypic selection in Picea abies?

In forest trees, environmental conditions during reproduction can greatly influence progeny performance. This phenomenon probably results from adaptive phenotypic plasticity but also may be associated with genotypic selection. In order to determine whether selective effects during the reproduction are environment specific, single pair-crosses of Norway spruce were studied in two contrasted maternal environments (warm and cold conditions). One family expressed large and the other small phenotypic differences between these crossing environments. The inheritance of genetic polymorphism was analysed at the seed stage. Four parental genetic maps covering 66 to 78% of the genome were constructed using 190 to 200 loci. After correcting for multiple testing, there is no evidence of locus under strong and repeatable selection. The maternal environment could thus only induce limited genotypic-selection effects during reproductive steps, and performance of progenies may be mainly affected by a long-lasting epigenetic memory regulated by temperature and photoperiod prevailing during seed production.L'environnement maternel induit-il une sélection génotypique durant les différents stades de reproduction chez Picea abies ?. Chez les arbres forestiers, les conditions environnementales durant la reproduction peuvent influencer les performances des descendants. Ce phénomène reflète probablement la plasticité phénotypique, mais également il pourrait être associé à une sélection génotypique. Afin de déterminer si des effets sélectifs durant la reproduction sont spécifiques d'un environnement donné, deux familles d'épicéa commun non apparentées ont été obtenues par croisements dirigés dans deux environnements maternels contrastés (conditions chaude et froide). La première famille exprimait de larges différences phénotypiques entre les deux environnements tandis que la seconde ne montrait pas de différence significative. La transmission des polymorphismes génétiques a été étudiée au stade de la graine. Quatre cartes génétiques parentales couvrant 66 à 78 % du génome ont été construites. Aucun effet de sélection n'a été mis en évidence aux différents locus étudiés. L'environnement maternel n'induirait donc que des effets de sélection génotypique relativement faibles durant les stades de la reproduction. Les performances des descendants seraient principalement affectées par une mémoire épigénétique durable régulée par la température et la photopériode régnant durant la production des graines

Characterization of the poplar pan-genome by genome-wide identification of structural variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2?Mb and 62.9?Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome

Génomique comparative entre Muscadinia rotundifolia et Vitis vinifera pour faciliter l'identification de gènes de résistance

Muscadinia rotundifolia est une espèce de la famille des Vitaceae. C est un sous-genre du genre Vitis, le deuxième sous-genre étant celui des Euvitis qui comprend l espèce cultivée Vitis vinifera (2n=38). M. rotundifolia (2n=40) est une source de résistance aux maladies très importante pour l amélioration de la vigne. Son génome commence seulement à être décrit avec deux cartes génétiques récemment publiées. Ma thèse a consisté à utiliser des ressources génomiques chez M. rotundifolia cv Regale (banque BAC, collection de séquence d extrémités de BAC ou BES et séquences de BACs) pour caractériser le génome de cette espèce en comparaison avec celui de V. vinifera. Les résultats obtenus ne montrent pas de différence importante entre les génomes des deux espèces en termes de composition du génome en bases (GC%), en séquences codantes ou en éléments répétés. De même, à une échelle globale, la famille de gènes NBS-LRR semble être similaire en termes de nombre et de balance entre les sous-familles. A une échelle plus fine cependant (carte physique et séquences de BAC), des remaniements relativement importants sont observés dans des régions portant cette famille de gènes, aboutissant parfois à des contenus différents en gènes, de région normalement homologues: duplication différentielles de gènes, présence/absence de gènes.Muscadinia Rotundifolia is a species of the Vitaceae family. It is a sub-genus of the Vitis genus along with the Euvitis sub-genus, which the cultivated species Vitis vinifera belongs to. M. rotundifolia (2n=40) is a very important source of resistance to diseases in grapevine breeding programs. Its genome is only starting to be described with the recent publication of two genetic maps. The present study aimed at using M. rotundifolia cv Regale genomic resources (BAC library, BAC end sequences or BES, BAC sequences) in order to characterize the genome of this species in comparison with the genome of V. vinifera. The results showed that there is no striking difference between the two species in term of base composition (GC %), repeats frequency and gene space. The NBS LRR gene family also seems to be globally quite similar between the two species in terms of numbers and balance between subfamilies. At a finer scale (physical map and BAC sequence), frequent rearrangements are observed in genomic regions carrying the NBS-LRR gene family sometimes clearly associated with a different gene content between the two species in homologous regions: differential gene duplication, presence/absence of genes.EVRY-Bib. électronique (912289901) / SudocSudocFranceF

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2\u2009Mb and 62.9\u2009Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome

The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis

Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in [i]Populus[/i] is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the [i]Populus[/i] genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in [i]Populus trichocarpa[/i]. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of [i]Populus[/i] genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site–leucine-rich repeat (NBS–LRR) class of disease resistance genes in the entire [i]Populus[/i] genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS–LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female [i]Populus[/i] trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in [i]Populus[/i]