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

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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

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]

Quantification of endogenous levels of IAA, IAAsp and IBA in micro-propagated shoots of hybrid chestnut pre-treated with IBA

Endogenous levels of indole-3-acetic acid (IAA), indole-3-acetylaspartic acid (IAAsp) and indole-3-butyric acid (IBA) were measured during the first 8 d of in vitro rooting of rootstock from the chestnut ‘M3’ hybrid by high performance liquid chromatography (HPLC). Rooting was induced either by dipping the basal ends of the shoots into a 4.92-mM IBA solution for 1 min or by sub-culturing the shoots on solid rooting medium supplemented with 14.8- μM IBA for 5 d. For root development, the induced shoots were transferred to auxin-free solid medium. Auxins were measured in the apical and basal parts of the shoots by means of HPLC. Endogenous levels of IAA and IAAsp were found to be greater in IBA-treated shoots than in control shoots. In extracts of the basal parts of the shoots, the concentration of free IAA showed a significant peak 2 d after either root inductive method and a subsequent gradual decrease for the remainder of the time course. The concentration of IAAsp peaked at day 6 in extracts of the basal parts of shoots induced with 14.8-μM IBA for 5 d, whereas shoots induced by dipping showed an initial increase until day 2 and then remained stable. In extracts from basal shoot portions induced by dipping, IBA concentration showed a transient peak at day 1 and a plateau between day 2 and 4, in contrast to the profile of shoots induced on auxin-containing medium, which showed a significant reduction between 4 and 6 d after transferred to auxin-free medium. All quantified auxins remained at a relatively low level, virtually constant, in extracts from apical shoot portions, as well as in extracts from control non-rooting shoots. In conclusion, the natural auxin IAA is the signal responsible for root induction, although it is driven by exogenous IBA independently of the adding conditions

A Genome-Wide Survey of Switchgrass Genome Structure and Organization

The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications