:: E. DODINET, M.A. SELOSSE & B. PUJOL Editorial Editorial Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 195-196. Anglais :: B. PUJOL & J.-P. GALAUD A practical guide to quantifying the effect of genes underlying adaptation in a mixed genomics and evolutionary ecology approach Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 197-204. Anglais Abstract In adaptation studies, approaches in genomics investigate the genetic, cellular and biochemical mechanisms involved in adaptation using model organisms. In study systems such as Arabidopsis, the demand is high to test for the effect of genes which polymorphism is known on the ability of plants to cope with adverse environmental conditions. In evolutionary ecology, understanding how selection and environmental heterogeneity shape the diversity of organisms is crucial. In that regard, tools to decipher how the architecture of standing genetic variation affects the evolutionary potential of plants to adapt are required. Quantitative genetics provide a range of statistical methods that could be used to study those questions but are generally neglected as a consequence of their scary name, as for example for the pedigree based random regression method used in our approach. Here, we provide a practical guide for researchers from multiple domains who would like to use such methods. We begin by providing an overview of some of the challenges in plant sciences, such as understanding the role of regulatory genes in adaptation that could gain from using such approach. We then illustrate the “how to” of the method by applying it to an imaginary example. We also provide a complete tutorial in the supplementary online material under the form of a protocol and data that can be used to train researchers and students by replicating entirely our approach. We conclude by highlighting the advantages and limits of such approach.
:: B. BRACHI, N. FAURE, J. BERGELSON, J. CUGUEN & F. ROUX Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 205-219. Anglais Abstract Often used as a proxy for the transition to reproduction, flowering time (FT) is an integrative trait of two successive biological processes, i.e. bolting time (BT) and the interval (INT) between bolting and flowering time (FT). In this study, we aimed to identify candidate genes associated with these composite traits in Arabidopsis thaliana using a field experiment. Genome-wide association (GWA) mapping was performed on BT, INT and FT based on a sample of 179 worldwide natural accessions genotyped for 216,509 single nucletode polymorphisms. The high resolution conferred by GWA mapping indicates that FT is an integrative trait at the genetic level, with distinct genetics for BT and INT. BT is shaped largely by genes involved in the circadian clock whereas INT is shaped by genes involved in both the hormone pathways and cold acclimation. Finally, the florigen TSF appears to be the main integrator of environmental and internal signals in ecologically realistic conditions. Based on FT scored in a previous field experiment, we also studied the genetics underlying reaction norms across 2 years. Only four genes were common to both years, emphasizing the need to repeat field experiments. The gene regulation model appeared as the main genetic model for genotype year interactions.
:: C. CARRÉ, F. GAMBOA, B. PUJOL & E. MANFREDI Genetic links among individuals: from genealogies to molecular markers Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 221-226. Anglais Abstract Genetic links among individuals are widely used to characterize the diversity of domesticated and natural populations and they also provide complementary information for statistical population summaries. We first discuss the measures used by geneticists based on genealogy and DNA data. The choice of metrics of genetic links should be coherent with the objectives: biodiversity or genotype–phenotype relationships. For the last objective, we evaluate by simulation the interest of genetic distances when the objective is the prediction of individual genetic values and phenotypes using kernel regression. A pseudo-distance based on correlations between marker genotypes of pairs of individual yields better predictions than other classical definition of distances.
:: J. GAUZERE, S. ODDOU-MURATORIO, C. PICHOT, F. LEFÈVRE & E. KLEIN Biases in quantitative genetic analyses using open-pollinated progeny tests from natural tree populations Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 227-238. Anglais Abstract In plant quantitative genetic studies conducted ex situ, the large number of seeds produced per individual has promoted the use of open-pollinated progeny tests. In subsequent analyses, seeds collected on the same mother-plant are assumed to be half-sibs. The consequences of the departure from half-sib assumption in progeny tests have been investigated since the 1960s using simulation approaches and, more recently, using molecular-based experimental approaches. This review aims to synthesize the results and conclusions of these simulation and empirical studies. We focus on tree species, where controlled crosses are difficult to carry out experimentally and departures from half-sib assumptions occur frequently in natural populations. First, the average level of relatedness expected within maternal progeny for many tree populations is higher than that of half-sibs. This is the consequence of non-random mating resulting from the small number of effective pollen donors per female, unequal male reproductive success and/or selfing. As result, estimates of genetic variance and heritability for quantitative traits may be upward biased. Alternatively, inbreeding depression, dominance effects and the heterogeneity of the male gamete pool among females are often neglected, which may lead to underestimation of the heritability of traits. A correction based on the mean genetic relatedness between offspring and the relatedness between parents is often used to compensate those biases. However, such correction cannot accurately adjust the estimates in situations where variable levels of genetic relatedness among families, dominance effects or inbreeding depression exist within the progeny. An alternative and promising approach is the use of the “animal model” approach, which optimizes the use of molecular data and paternal information to estimate heritability more accurately.
:: G. CHOMICKI Analysis of rhizome morphology of the Zingiberales in Payamino (Ecuador) reveals convergent evolution of two distinct architectural strategies Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 239-254. Anglais Abstract Rhizome morphology of 18 Zingiberales species growing in situ in lowland Ecuadorian rainforest (Payamino) covering six of the eight families of the order is presented. Phenetic and morphological analyses reveal two strategies that vary starkly in their mode of construction and geometry. Furthermore, parsimony-based character evolution in a resolved phylogenetic framework identifies convergent evolution of these strategies. The two strategies uncovered by the phenetic and morphological analyses are correlated with branching localization and timing: species showing delayed, non-positional–preferential branching exhibit poorly predictable, non-geometric rhizomes whereas species exhibiting immediate branching occurring at specific internodes display predictable, highly geometric rhizome morphologies. Hence, the control of two simple developmental parameters defines two distinct modes of construction in basitonically branched, rhizomatous plants. Multiple switches in the state of these characters during the evolution of Zingiberales resulted in diversification and convergence of rhizome morphologies in the order.
:: K. S. RAO, K. S. RAJPUT & Y. SOON KIM Secondary growth and occurrence of laticifers in the root of papaya (Carica papaya L.) Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 255-260. Anglais Abstract The pattern of secondary growth and occurrence of laticifers was studied in the tap root of papaya (Carica papaya L., Caricaceae). The vascular cambium was differentiated, producing secondary phloem centrifugally and xylem centripetally. Phloem was composed of sieve tube members, companion cells, fibres and parenchyma, whereas the xylem was mainly thin-walled parenchyma tissue with lignified vessels embedded in it. The root vascular tissue was characterized by the occurrence of isolated, narrow, but thick-walled articulated laticiferous cells. Fusiform cambial cells produced laticiferous cells only in the centripetal direction, whereas ray cambial cells produced these cells both centripetally and centrifugally. Laticifers underwent intrusive tip growth and their maturation was marked by the disappearance of transverse septa. These cells appeared as narrow segmented cells close to the cambial zone whereas in the xylem they were isolated and elongated with sinuous or constricted walls. Radial growth, structure and distribution of laticifers in the root are discussed.
:: E. MATTEUCCI, J. NASCIMBENE, S. E. FAVERO-LONGO & D. ISOCRONO New and noteworthy lichens from the Western Italian Alps Paru dans Acta Botanica Gallica, 2013, 160 (3-4), pp. 261-269. Anglais Abstract Western Italian Alps (namely Piedmont and the Aosta Valley) are among the lichenologically best known regions of Italy with c.1200 species listed. However, despite the long temporal continuity of lichen studies, information is still geographically uneven and data on the occurrence and distribution of many species are missing. An opportunity to fill this gap is currently provided by ecological and applied studies that assess the response of lichen communities to environmental factors in terms of species richness and composition. This study reports species that are new or interesting records for the western Italian Alps or noteworthy mainly because of their conservation status provided by ecological and applied studies in Aosta Valley and Piedmont and by some recent floristic surveys. A list of 51 records referring to 47 species is reported and discussed; 20 species are new to the Aosta Valley, 17 are new to Piedmont and 11 species are reported for the first time in the Western Italian Alps, being new for both regions. More than 25% of the records derive from stonework biodeterioration studies providing noteworthy data due to substrata analysed. About 35% of records derive from both air pollution monitoring studies and research on lichen conservation in relation to forest management. Biomonitoring studies are based on robust sampling design that allows data to be compared across regions and time series, improving the information associated with floristic data. Research on epiphytic lichens in Italian forests, rapidly increasing in Italy in the last years, has contributed significant advances in lichen floristics in Italy and in modelling environmental factors that are relevant for lichen ecology and conservation.