Molecular and phenotypic profiling from base to the crown in maritime pine wood-forming tissue

Research• Environmental, developmental and genetic factors affect variation in wood properties at the chemical, anatomical and physical levels. Here, the phenotypic variation observed along the tree stem was explored and the hypothesis tested that this variation could be the result of the differential expression of genes/proteins during wood formation. • Differentiating xylem samples of maritime pine (Pinus pinaster) were collected from the top (crown wood, CW) to the bottom (base wood, BW) of adult trees. These samples were characterized by Fourier transform infrared spectroscopy (FTIR) and analytical pyrolysis. Two main groups of samples, corresponding to CW and BW, could be distinguished from cell wall chemical composition. • A genomic approach, combining large-scale production of expressed sequence tags (ESTs), gene expression profiling and quantitative proteomics analysis, allowed identification of 262 unigenes (out of 3512) and 231 proteins (out of 1372 spots) that were differentially expressed along the stem. • A good relationship was found between functional categories from transcriptomic and proteomic data. A good fit between the molecular mechanisms involved in CW–BW formation and these two types of wood phenotypic differences was also observed. This work provides a list of candidate genes for wood properties that will be tested in forward genetic

Sex, Subdivision, and Domestic Dispersal of Trypanosoma cruzi Lineage I in Southern Ecuador

Trypanosoma cruzi is transmitted by blood sucking insects known as triatomines. This protozoan parasite commonly infects wild and domestic mammals in South and Central America. However, triatomines also transmit the parasite to people, and human infection with T. cruzi is known as Chagas disease, a major public health concern in Latin America. Understanding the complex dynamics of parasite spread between wild and domestic environments is essential to design effective control measures to prevent the spread of Chagas disease. Here we describe T. cruzi genetic diversity and population dynamics in southern Ecuador. Our findings indicate that the parasite circulates in two largely independent cycles: one corresponding to the sylvatic environment and one related to the domestic/peridomestic environment. Furthermore, our data indicate that human activity might promote parasite dispersal among communties. This information is the key for the design of control programmes in Southern Ecuador. Finally, we have encountered evidence of a sexual reproductive mode in the domestic T. cruzi population, which constitutes a new and intriguing finding with regards to the biology of this parasite

On the Origin of Tibetans and Their Genetic Basis in Adapting High-Altitude Environments

Since their arrival in the Tibetan Plateau during the Neolithic Age, Tibetans have been well-adapted to extreme environmental conditions and possess genetic variation that reflect their living environment and migratory history. To investigate the origin of Tibetans and the genetic basis of adaptation in a rigorous environment, we genotyped 30 Tibetan individuals with more than one million SNP markers. Our findings suggested that Tibetans, together with the Yi people, were descendants of Tibeto-Burmans who diverged from ancient settlers of East Asia. The valleys of the Hengduan Mountain range may be a major migration route. We also identified a set of positively-selected genes that belong to functional classes of the embryonic, female gonad, and blood vessel developments, as well as response to hypoxia. Most of these genes were highly correlated with population-specific and beneficial phenotypes, such as high infant survival rate and the absence of chronic mountain sickness

L'adaptation à la sécheresse chez le pin maritime (Pinus pinaster Ait.) (patrons de diversité et différenciation nucléotidiques de gènes candidats et variabilité de caractères phénotypiques)

Les changements climatiques annoncés risquent de constituer des pressions de sélection importantes sur des caractères tels que la résistance à la secheress, notamment pour des espèces forestières comme le pin maritime. Dans ce contexte, une question essentielle est de savoir si ces espèces pourront s'adapter suffisamment rapidement aux nouvelles conditions climatiques. Les objectifs de cette thèse étaient d'évaluer le potentiel adaptatif de populations naturelles de pin maritime pour des caractères liés à la résistance au déficit hydrique, et d'identifier des gènes potentiellement impliqués dans la variation adaptative intra- et inter-populations. Pour y répondre, la variabilité phénotypique pour des caractères de croissance, de biomasse, et d'efficience d'utilisation en eau (EUE) a été évaluée dans un essai de populations naturelles provenant de milieux contrastés sur les plans climatiques et écologiques. Une grande variabilité phénotypique a été mise en évidence entre performances moyennes des populations, et pour les valeurs relatives d'héritabilité et de corrélations entre biomasse et EUE estimées dans chaque population. Ces résultats ont confirmé le rôle de la sélection dans l'adaptation locale du pin maritime, suggérant des stratégies de réponses à un déficit hydrique différentes selon les populations. Les patrons de diversité et différenciation nucléotidiques de gènes candidats à la résistance au stress hydrique ont également été étudiés. Certains gènes s'écartent significativement de patrons d'évolution neutre, avec des signatures cohérentes et complémentaires entre plusieurs méthodes, qui ont été interprétées en termes de scénarios de sélection. L'hétérogénéité de ces signatures entre gènes candidats et entre populations pour certains gènes, serait aussi cohérente avec un rôle de la sélection naturelle plutôt qu'avec celui d'évènements démographiques qui auraient affecté l'ensemble du génome de façon plus homogène. Enfin, quelques associations remarquables ont été mises en évidence entre la variaton de l'EUE entre populations et au sein des populations, et celles de marqueurs SNPs de gènes de déhydrines, de lignification ou de formation de la paroi cellulaire. Ce travail ouvre ainsi des perspectives encourageantes pour la compréhension de l'architecture génétique moléculaire de l'adaptation à la sécheresse chez cette espèce.BORDEAUX1-BU Sciences-Talence (335222101) / SudocSudocFranceF

Data from: Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Q. petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and non-outlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with non-outlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species’ contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized

Nothofagus_assemblies

Nothofagus_assemblie

Complete genotypes (826 samples and 262SNPs - Genalex format)

Complete genotypes (826 samples and 262SNPs - Genalex format