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Introduction Drought is a major environmental stress for plants and negatively affects growth and reproduction. Drought events cause yield loss in crop systems (Brevedan and Egli 2003; van Asten et [...], Water stress associated with drought-like conditions is a major factor limiting plant growth and impacts productivity of natural plant communities and agricultural crops. Molecular responses of plants to water stress have been studied most extensively in model species and crops, few of which have evolved natural drought tolerance. In the current study, we examined physiological and transcriptomic responses at multiple timepoints during increasing water stress and following initial recovery from stress in a drought-tolerant C3 species, Festuca ovina. Results demonstrated non-linear transcriptomic changes during increasing stress, but largely linear declines in physiological measurements during this same period. Transcription factors represented approximately 12.7% of all differentially expressed genes. In total, 117 F. ovina homologs of previously identified and molecularly characterized drought-responsive plant genes were identified. This information will be valuable for further investigations of the molecular mechanisms involved in drought tolerance in [C.sub.3] plants. Key words: Festuca ovina, RNA-seq, water stress, transcription factor, drought tolerant. Le stress hydrique associe a des conditions de secheresse est un facteur important limitant la croissance des plantes et affectant la productivite au sein de communautes vegetales naturelles et chez les especes cultivees. Les reponses moleculaires des plantes au stress hydrique ont ete etudiees le plus chez des especes modeles et des especes cultivees, dont certaines ont acquis une tolerance naturelle a la secheresse. Dans le present travail, les auteurs examinent les reponses physiologiques et transcriptomiques a differents stades temporels suite a l'imposition d'un stress hydrique croissant et apres retablissement post-stress chez une espece C3 tolerante a la secheresse, Festuca ovina. Les resultats ont montre une evolution non-lineaire des reponses transcriptomiques en reponse a l'accroissement du stress, alors que les declins physiologiques etaient largement lineaires au cours des memes periodes. Les facteurs de transcription constituaient environ 12,7 % des genes montrant une expression differentielle. Chez F. ovina, les auteurs ont identifie 117 homologues de genes precedemment connus au plan moleculaire pour reagir a la secheresse. Cette information sera utile pour des futurs travaux des mecanismes moleculaires impliques dans la tolerance a la secheresse chez les plantes [C.sub.3]. [Traduit par la Redaction] Mots-cles : Festuca ovina, RNA-seq, stress hydrique, facteur de transcription, tolerance a la secheresse.

Identifying the genetic mechanisms that underlie phenotypic responses to natural environments is one of the greatest challenges in modern biological research (NSF 2011; Losos et al. 2013). Organismal responses to [...]

Phenotypic plasticity and genotype-environment interactions (GEI) play a prominent role in plant morphological diversity and in the potential functional capacities of plant life-history traits. The genetic basis of plasticity and GEI, however, is poorly understood in most organisms. In this report, inflorescence development patterns in Arabidopsis thaliana were examined under different, ecologically relevant photoperiod environments for two recombinant inbred mapping populations (Ler X Col and Cvi X Ler) using a combination of quantitative genetics and quantitative trait locus (QTL) mapping. Plasticity and GEI were regularly observed for the majority of 13 inflorescence traits. These observations can be attributable (at least partly) to variable effects of specific QTL. Pooled across traits, 12/44 (27.3%) and 32/62 (51.6%) of QTL exhibited significant QTL X environment interactions in the Ler X Col and Cvi X Ler lines, respectively. These interactions were attributable to changes in magnitude of effect of QTL more often than to changes in rank order (sign) of effect. Multiple QTL X environment interactions (in Cvi X Ler) clustered in two genomic regions on chromosomes 1 and 5, indicating a disproportionate contribution of these regions to the phenotypic patterns observed. High-resolution mapping will be necessary to distinguish between the alternative explanations of pleiotropy and tight linkage among multiple genes.

Genetic variation for quantitative traits is often greater than that expected to be maintained by mutation in the face of purifying natural selection. One possible explanation for this observed variation is the action of heterogeneous natural selection in the wild. Here we report that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. At one QTL, the allele that enhanced the viability of fall-germinating seedlings in North Carolina reduced the fecundity of spring-germinating seedlings in Rhode Island. Several other QTL experienced strong directional selection, but only in one site and seasonal cohort. Thus, different loci were exposed to selection in different natural environments. Selection on allelic variation also depended upon the genetic background. The allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus. Moreover, alternative alleles at each of these loci caused reversals in the allelic fitness effects of a QTL closely linked to TFL1, a candidate developmental gene displaying nucleotide sequence polymorphism consistent with balancing selection. Thus, both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.

The extent to which genetic background can influence allelic fitness is poorly understood, despite having important evolutionary consequences. Using experimental populations of Arabidopsis thaliana and map-based population genetic data, we examined a multigeneration response to selection in populations with differentiated genetic backgrounds. Replicated experimental populations of A. thaliana with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were subjected to strong viability and fertility selection by growing individuals from each population at high density for three generations in a growth chamber. Patterns of genome-wide selection were evaluated by examining deviations from expected frequencies of mapped molecular markers. Estimates of selection coefficients for individual genomic regions ranged from near 0 to 0.685. Genomic regions demonstrating the strongest response to selection most often were selected similarly in both genetic backgrounds. The selection response of several weakly selected regions, however, appeared to be sensitive to genetic background, but only one region showed evidence of positive selection in one background and negative selection in another. These results are most consistent with models of adaptive evolution in which allelic fitnesses are not strongly influenced by genetic background and only infrequently change in sign due to variation at other loci.

Molecular biologists are rapidly characterizing the genetic basis of flowering in model species such as Arabidopsis thaliana. However, it is not clear how the developmental pathways identified in controlled environments contribute to variation in reproductive timing in natural ecological settings. Here we report the first study of quantitative trait loci (QTL) for date of bolting (the transition from vegetative to reproductive growth) in A. thaliana in natural seasonal field environments and compare the results with those obtained under typical growth-chamber conditions. Two QTL specific to long days in the chamber were expressed only in spring-germinating cohorts in the field, and two loci specific to short days in the chamber were expressed only in fall-germinating cohorts, suggesting differential involvement of the photoperiod pathway in different seasonal environments. However, several other photoperiod-specific QTL with large effects in controlled conditions were undetectable in natural environments, indicating that expression of allelic variation at these loci was overridden by environmental factors specific to the field. Moreover, a substantial number of QTL with major effects on bolting date in one or more field environments were undetectable under controlled environment conditions. These novel loci suggest the involvement of additional genes in the transition to flowering under ecologically relevant conditions.

Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler x Col and Cvi x Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi x Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.

A Primer of Ecological Genetics. Jeffrey K. Conner and Daniel L. Hartl. Sinauer Associates, Sunderland, MA, 2004. 304 pp., illus. $34.95 (ISBN 087893202X paper). The field of ecological genetics became [...]

Abstract Background Long terminal repeat (LTR) retrotransposons are a class of mobile genetic element capable of autonomous transposition via an RNA intermediate. Their large size and proliferative ability make them important contributors to genome size evolution, especially in plants, where they can reach exceptionally high copy numbers and contribute substantially to variation in genome size even among closely related taxa. Using a phylogenetic approach, we characterize dynamics of proliferation events of Ty3/gypsy-like LTR retrotransposons that led to massive genomic expansion in three Helianthus (sunflower) species of ancient hybrid origin. The three hybrid species are independently derived from the same two parental species, offering a unique opportunity to explore patterns of retrotransposon proliferation in light of reticulate evolutionary events in this species group. Results We demonstrate that Ty3/gypsy-like retrotransposons exist as multiple well supported sublineages in both the parental and hybrid derivative species and that the same element sublineage served as the source lineage of proliferation in each hybrid species' genome. This inference is based on patterns of species-specific element numerical abundance within different phylogenetic sublineages as well as through signals of proliferation events present in the distributions of element divergence values. Employing methods to date paralogous sequences within a genome, proliferation events in the hybrid species' genomes are estimated to have occurred approximately 0.5 to 1 million years ago. Conclusion Proliferation of the same retrotransposon major sublineage in each hybrid species indicates that similar dynamics of element derepression and amplification likely occurred in each hybrid taxon during their formation. Temporal estimates of these proliferation events suggest an earlier origin for these hybrid species than previously supposed.

A bar-coded pyrosequencing approach targeting the V3 region of the bacterial small-subunit rRNA gene was used to address the factors that structure communities along the thermal gradients of two alkaline hot springs in the Lower Geyser Basin of Yellowstone National Park. The community resemblance was found to decay exponentially with increasing differences in temperature between samples but was only weakly correlated with physical distance and the community diversity decreased with increasing temperature at the same rate along both gradients but was uncorrelated with other measured environmental variables.

Three genera of onocleoid ferns have traditionally been recognized (Matteuccia, Onocleopsis, and Onoclea), but some recent studies subsume Onocleopsis into Matteuccia and transfer Asiatic species of Matteuccia to Onoclea. Although the 1995 analysis of fern phylogeny based on rbcL sequences showed that Matteuccia struthiopteris and Onoclea sensibilis constitute one clade of a polyphyletic Dryopteridaceae and that this clade is sister to Blechnaceae, it did not resolve conflicting views of generic circumscription within onocleoids. Sequences of rbcL from all five onocleoid species, including both varieties of Onoclea sensibilis, and from five outgroup species of Blechnaceae were analyzed cladistically under the optimality criteria of maximum parsimony and maximum likelihood. Maximum parsimony yielded a single most parsimonious tree with the three accessions of Onoclea sensibilis var. sensibilis left as an unresolved trichotomy. Maximum likelihood yielded a single set of three optimal trees whose only topological variation was in the trivial positioning of these same three accessions of var. sensibilis relative to each other. Matteuccia orientalis and M. intermedia formed the basalmost ingroup clade strongly separated from the remaining taxa and sister to them, suggesting that they should be recognized in their own genus Pentarhizidium. Onoclea sensibilis is strongly separated from its sister clade of Matteuccia struthiopteris plus Onocleopsis hintonii, and the two varieties of Onoclea sensibilis are well differentiated from each other, warranting varietal or possibly specific recognition. Molecular and other data bearing on the generic status of Matteuccia struthiopteris and Onocleopsis hintonii (which form the least strongly supported clade) are equivocal but perhaps most concordant with their continued recognition as monotypic genera.

Simulation studies of homoploid hybrid speciation suggest that this mode is 'punctuated': long periods of hybrid zone stasis are followed by the rapid establishment and growth of the new hybrid lineage. However, this prediction has not been verified in nature. Here, we evaluate this hypothesis with respect to Helianthus anomalus, a diploid species derived via hybridization between H. annuus and H. petiolaris. Crossing experiments between the parental species revealed that fertile, stable hybrid lineages could be generated after just five generations of hybridization. Moreover, genetic mapping experiments indicated that the genomes of the synthetic hybrid lineages were recognizably similar to that found in H. anomalus, implying a similar rapid pathway to speciation under natural conditions. Analysis of the sizes of parental chromosomal fragments in H. anomalus provides more direct evidence for a rapid tempo of hybrid speciation. Due to recombination, parental fragment sizes should decline in a predictable manner over time, making it feasible to estimate the number of generations of hybridization required to stabilize a hybrid species genome. In the case of H. anomalus, parental chromosomal fragments are large, suggesting that its genome may have been stabilized in as few as 20 generations. However, until greater genetic resolution is achieved and variation in recombination rates is better understood, this estimate must viewed as preliminary.