Genetic and maternal contributions to offspring viability under different environmental conditions in various salmonids

Summary : Due to anthropogenic impacts and natural fluctuations, fish usually have to cope with constantly changing and often hostile environments. Whereas adult fish have various possibilities to counteract unfavourable environmental conditions, embryos have much fewer options. Besides by their developing immune system, they are protected by the egg envelopes and several immune substances provided by their mothers. In addition to this, they may also adjust their hatching timing in reaction to various risks. However, individuals may vary in their defensive potential. This variation may be either based on their genetics and/or on differential maternal investments and may be dependent on the experienced stress. Nevertheless, in fish, the impact of such parental contributions on embryo and/or juvenile viability is still poorly investigated. The main objective of this thesis was to investigate the importance of paternal (i.e. genetic) and maternal (i.e. genetic + egg investment) contributions to offspring viability under different environmental conditions and at different life stages. In order to investigate this, we used gametes of various salmonids for in vitro fertilisation experiments based on full-factorial breeding designs. The individual studies are summarised in the following chapters: In the first chapter, we tested the effectiveness of the embryonic immune system in Lake whitefish (Coregonus palaea). Namely, we investigated paternal and maternal contributions to the embryos' tolerance to different kinds of pathogen exposure. Additionally, we tested whether an early sub-léthal exposure has a positive or a negative effect on an embryo's susceptibility to later pathogen exposures with the same pathogen. We found that pre-challenged embryos were more susceptible to future challenges. Moreover, pathogen susceptibility was dependent on maternal investments and/or the embryos' own genetics, depending on the challenge level. Chapter 2 summarises a similar study with brown trout (Salmo trutta). In addition to the previously described investigations, we analysed if genetic effects on offspring viability are mediated either by parental MHC genotypes or relatedness based on neutral microsatellite markers, and we tested if males signal their genetic quality either by their body size or their melanin-based skin colouration. We found that embryo survival was lower at higher stress levels and dependent on the embryos' genetics. Addirionally, parents with similar and/or, very common MHC genotypes had higher offspring viabilities. Finally, darker males produced more viable offspring. In the first two chapters we investigated the embryos' defensive potential based on their immune system, i.e. their pathogen tolerance. In chapter 3 we investigate whether hatching timing of Lake whitefìsh (C. palaea) is dependent on parental contributions and/or on pathogen pressure, and whether there are parental-environmental interactions. We found that whitefish embryos hatch earlier under increasing pathogen pressure. Moreover, hatching timing was affected by embryo genetics and/or maternally provided resources, but the magnitude of the effect was dependent on the pathogen. pressure. We also found a significant paternal-environmental interaction, indicating that the hatching efficiency of a certain sib group is dependent on the pathogen environment. Chapter 4 describes an analogous study with brown trout (S. trutta), with similar findings. In the former chapters, we only looked at offspring performance during the embryonic period, and only under semi-natural conditions. In chapter 5 we now test the performance and viability of embryonic and juvenile brown trout (S. trutta) under natural conditions. To measure embryo viability, we put them in brood boxes, buried them in the gravel of a natural river, and analysed survival after several months. To investigate juvenile survival and performance, wé reared embryos under different stress levels in the laboratory and subsequently released the resulting hatchlings in to a closed river section. Juvenile size and survival was then determined one year later. Additionally, we investigated if sires differ in their genetic quality, determined by embryo and juvenile survival as well as juvenile size, and if they signal their quality by either body size or melanin-based body darkness. We found hat juvenile size was dependent on genetic effects and on maternal investment, whereas this was neither the case for embryo nor for juvenile survival. Additionally, we found that offspring of darker males grew larger, and larger juveniles had also an increased survival. Finally, we found acarry-over effect of the early non-lethal challenge: exposing embryos to higher stress levels resulted in smaller juveniles. To evaluate the long-term performance of differently treated groups, mark-recapture studies are inevitable. For this purpose, effective mass-marking techniques are essential. In chapter 6 we tested the suitability of the fluorescent pigment spray marking method for the mass marking of European graylings (Thymallus thymallus), with very promising results. Our in vitro fertilisation studies on whitefish may reveal new insights on potential genetic benefits of mate choice, but the mating system of whitefish under natural conditions is still poorly investigated. In order to study this, we installed underwater cameras at the spawning place of a Coregonus suidteri population, recorded the whole mating period and subsequently analysed the recordings. Confirmations of previous findings as well as exciting new observations are listed and discussed in chapter 7. Dus aux impacts anthropogéniques et aux fluctuations naturelles, les poissons doivent faire face à des environnements en perpétuel changement. Ces changements font que les poissons doivent s'adapter à de nouvelles situations, souvent hostiles pour eux. Les adultes ont différentes possibilités d'échapper à un environnement peu favorable, ce n'est par contre pas le cas des embryons. Les embryons sont protégés d'une part par leur système immunitaire en développement, d'autre part, par la coquille de l'eeuf et différentes substances immunitaires fournies par leur mère. De plus, ils sont capables d'influencer leur propre date d'éclosion en réponse à différents facteurs de stress. Malgré tout, les individus varient dans leur capacité à se défendre. Cette variation peut être basé sur des facteurs génétiques et/ou sur des facteurs maternels, et est dépendante du stress subi. Néanmoins, chez les poissons, l'impact de telles contributions parentales sur la survie d'embryons et/ou juvéniles est peu étudié. L'objectif principal de cette thèse a été d'approfondir les connaissances sur l'importance de la contribution paternelle (c.a.d. génétique) et maternelle (c.a.d. génétique + investissement dans l'oeuf) sur la survie des jeunes dans différentes conditions expérimentales et stades de vie. Pour faire ces analyses, nous avons utilisé des gamètes de divers salmonidés issus de croisements 'full-factorial'. Les différentes expériences sont résumées dans les chapitres suivants: Dans le premier chapitre, nous avons testé l'efficacité du système immunitaire des embryons chez les corégones (Coregonus palea). Plus précisément nous avons étudié la contribution paternelle et maternelle à la tolérance des embryons à différents niveaux de stress pathogène. Nous avons aussi testé, si une première exposition non létale à un pathogène avait un effet positif ou négatif sur la susceptibilité d'un embryon a une deuxième exposition au même pathogène. Nous avons trouvé que des embryons qui avaient été exposés une première fois étaient plus sensibles au pathogène par la suite. Mais aussi que la sensibilité au pathogène était dépendante de l'investissement de la mère et/ou des gènes de l'embryon, dépendamment du niveau de stress. Le deuxième chapitre résume une étude similaire avec des truites (Salmo truffa). Nous avons examiné, si la survie des jeunes variait sous différentes intensités de stress, et si la variance observée était due aux gènes des parents. Nous avons aussi analysé si les effets génétiques sur la survie des juvéniles étaient dus au MHC (Major Histocompatibility Complex) ou au degré de parenté des parents. De plus, nous avons analysé si les mâles signalaient leur qualité génétique par la taille du corps ou par leur coloration noire, due à la mélanine. On a trouvé que la survie des embryons était plus basse quand le niveau de stress était plus haut mais que la variation restait dépendante de la génétique des embryons. De plus, les parents avec des MHC similaires et/ou communs avaient des embryons avec une meilleure survie. Par contre, des parents avec un degré de parenté plus haut produisent des embryons avec une survie plus mauvaise. Finalement nous avons montré que les mâles plus foncés ont des embryons qui survivent mieux, mais que la taille des mâles n'a pas d'influence sur la survie de ces mêmes embryons. Dans les deux premiers chapitres, nous avons étudié le potentiel de défense des embryons basé sur leur système immunitaire, c.a.d. leur tolérance aux pathogènes. Dans le troisième chapitre, nous nous intéressons à la date d'éclosion des corégones (C. palea), pour voir si elle est influencée par les parents ou par la pression des pathogènes, et si il y a une interaction entre ces deux facteurs. Nous avons trouvé que les jeunes naissent plus rapidement lorsque la pression en pathogènes augmente. La date d'éclosion est influencée par la génétique des embryons et/ou l'investissement des parents, mais c'est la magnitude des effets qui est dépendante de la pression du pathogène. Nous avons aussi trouvé une interaction entre l'effet paternel et l'environnement, ce qui indique que la rapidité d'éclosion de certains croisements est dépendante des pathogènes dans l'environnement. Le chapitre 4 décrit une étude analogue avec de truites (S. truffa), avec des résultats sitzimilaires. Dans les précédents chapitres nous nous sommes uniquement concentrés sur les performances des jeunes durant leur stade embryonnaire, et seulement dans des conditions semi naturelles. Dans le chapitre 5 nous testons la performance et la viabilité des embryons et de juvéniles de truites (S. truffa) dans des conditions naturelles. Nous avons trouvé que la taille des juvéniles était dépendante d'effets génétiques et de l'investissement maternel, mais ceci n'était ni les cas pour les survie des embryons et des juvéniles. De plus, nous avons trouvé que les jeunes des mâles plus foncés devenaient plus grands et que les grands ont un meilleur taux de survie. Finalement nous avons trouvé un 'carry-over effect' d'une première exposition non létale à un pathogène: exposer des embryons à des plus hauts niveaux de stress donnait des juvéniles plus petits. Pour évaluer la performance à long terme de groupes traités dé manières différentes, une méthode de marquage-recapture est inévitable. Pour cette raison, des techniques de marquage en masse sont nécessaires. Dans le chapitre 6, nous avons testé l'efficacité de la technique `fluorescent pigment spray marking' pour le marquage en masse de l'Ombre commun (Thymallus thymallus), avec des résultats très prometteurs. Les études de fertilisations in vitro avec les corégones nous donnent une idée du potentiel bénéfice génétique que représente la sélection d'un bon partenaire, même si le système d'accouplement des corégones en milieu naturel reste peu connu. Pour combler cette lacune, nous avons installé des caméras sous-marines autour de la frayère d'une population de corégones (C. suidteri), nous avons enregistré toute la période de reproduction et nous avons analysé les données par la suite. Ainsi, nous avons été capables de confirmer bien des résultats trouvés précédemment, mais aussi de faire de nouvelles observations. Ces résultats sont reportés dans le septième chapitre, où elles sont comparées avec des observations antérieures.

Stratigraphy, sedimentology and depositional environments of the Permian to uppermost Cretaceous Batain Group, eastern-Oman

Permian to Late Cretaceous allochthonous sedimentary and volcanic rocks exposed in the Batain area (eastern Oman Margin) have received comparably little attention in the past. They largely were considered as part of the Hamrat Duru Group (Hawasina Complex) of the northern Oman Mountains. Structural, kinematic and biostratigraphic results from our mapping campaign in the Batain area have now revealed, that emplacement of these units occurred in a WNW direction during latest Cretaceous/Early Paleogene time. This clearly contrasts with previous models that postulated a S-ward directed obduction in Campanian times such as recorded from the Hawasina Complex and Semail Ophiolite in the Oman Mountains. We herewith establish the `'Batain Group'' comprising all Permian to Late Cretaceous allochthonous units in the Batain Area. These are: 1.) the Permian Qarari Formation deposited in the toe of a slope setting; 2.) the Late Permian to late Liassic Al Jil Formation comprising periplatform detritus and very coarse breccias; 3.) the Scythian to Norian Matbat Formation formed by slope deposits; 4.) the Early Jurassic to early Oxfordian Guwayza Formation with high energy platform detritus; 5.) the Mid-Jurassic to earliest Cretaceous Ruwaydah Formation seamount; and 6.) the Oxfordian to Santonian Wahrah Formation, mainly radiolarites; and 7.) the Santonian to latest Maastrichtian Fayah Formation built by flysch-type sediments. These sedimentary and volcanic rocks represent deposits of the former ``Batain basin'' off eastern-Oman, destroyed by compressional tectonics at the Cretaceous/Paleogene transition. For tectono-stratigraphic reasons the Batain Group does not form part of the Hawasina Complex.

A pseudo-spectral method for simulating of poro-elastic seismic wave propagation in complex borehole environments

We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in cylindrical coordinates. An important application of this method is the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh consisting of three concentric domains representing the borehole fluid in the center, the borehole casing and the surrounding porous formation. The spatial discretization is based on a Chebyshev expansion in the radial direction, Fourier expansions in the other directions, and a Runge-Kutta integration scheme for the time evolution. A domain decomposition method based on the method of characteristics is used to match the boundary conditions at the fluid/porous-solid and porous-solid/porous-solid interfaces. The viability and accuracy of the proposed method has been tested and verified in 2D polar coordinates through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently benchmarked solution for 2D Cartesian coordinates. The proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is handled adequately.

Middle and late Cenomanian oceanic anoxic events in shallow and deeper shelf environments of western Morocco

The response of shallow-water sequences to oceanic anoxic event 2 and mid-Cenomanian events 1a and 1b was investigated along the west African margin of Morocco north of Agadir (Azazoul) and correlated with the deep-water sequence of the Tarfaya Basin (Mohammed Beach) based on biostratigraphy, mineralogy, phosphorus and stable isotopes. In the deeper Mohammed Beach section results show double peaks in delta 13C(org) for mid-Cenomanian events 1a and 1b (Rotalipora reicheli biozone, lower CC10a biozone), the characteristic oceanic anoxic event 2 delta 13C excursion (Rotalipora cushmani extinction, top of CC10a biozone) and laminated (anoxic) black shale. In the shallow environment north of Agadir, a fluctuating sea-level associated with dysoxic, brackish and mesotrophic conditions prevailed during the middle to late Cenomanian, as indicated by oyster biostromes, nannofossils, planktonic and benthonic foraminiferal assemblages. Anoxic conditions characteristic of oceanic anoxic event 2 (for example, laminated black shales) did not reach into shallow-water environments until the maximum transgression of the early Turonian. Climate conditions decoupled along the western margin of Morocco between mid-Cenomanian event 1b and the Cenomanian-Turonian boundary, as also observed in eastern Tethys. North of Agadir alternating humid and dry seasonal conditions prevailed, whereas in the Tarfaya Basin the climate was dry and seasonal. This climatic decoupling can be attributed to variations in the Intertropical Convergence Zone and in the intensity of the north-east trade winds in tropical areas.

Soil organic matter and fertility of anthropogenic dark earths (Terra Preta de Índio) in the Brazilian Amazon basin

Fertility properties, total C (Ctot), and chemical soil organic matter fractions (fulvic acid fraction - FA, humic acid fraction - HA, humin fraction - H) of anthropogenic dark earths (Terra Preta de Índio) of the Amazon basin were compared with those of Ferralsols with no anthropogenic A horizon. Terra Preta soils had a higher fertility (pH: 5.1-5.4; Sum of bases, SB: 8.93-10.33 cmol c kg-1 , CEC: 17.2-17.5 cmol c kg-1 , V: 51-59 %, P: 116-291 mg kg-1) and Ctot (44.6-44.7 g kg-1) than adjacent Ferralsols (pH: 4.4; SB: 2.04 cmol c kg-1, CEC: 9.5 cmol c kg-1, V: 21 %, P 5 mg kg-1, C: 37.9 g kg-1). The C distribution among humic substance fractions (FA, HA, H) in Terra Preta soils was also different, as shown by the ratios HA:FA and EA/H (EA=HA+FA) (2.1-3.0 and 1.06-1.08 for Terra Preta and 1.2 and 0.72 for Ferralsols, respectively). While the cation exchange capacity (CEC), of Ferralsols correlated with FA (r = 0.97), the CEC of Terra Preta correlated with H (r = 0.82). The correlation of the fertility of Terra Preta with the highly stable soil organic matter fraction (H) is highly significant for the development of sustainable soil fertility management models in tropical ecosystems.

Spodosols pedogenesis under barreiras formation and sandbank environments in the south of Bahia

Morphologically differentiated Spodosols usually occur in the Coastal Plain of the South of Bahia and North of Espírito Santo. They are found in profiles known as "muçungas", i.e. sandy soils that accumulate water. In these areas, two kinds of Spodosols, different from those in the Restinga area, can be found: Spodosols with E albic horizon (white muçunungas) and without this horizon (black muçunungas). Eight soil profiles with spodic characteristics were collected and described in order to evaluate differences in the formation process of Barreiras and Restinga Spodosols in the South of Bahia. The soil profiles were also characterized chemically, physically and mineralogically. Additionally, texture and chemical analysis, Fe and Al extraction by sodium dithionite-citrate-bicarbonate (DBC), acid ammonium oxalate and sodium pyrophosphate, ammonium oxalate extract optic density (DOox), sulphuric acid attack, and X ray difractometry of the clay fraction were performed. In the Spodosols of the Barreiras area, fragipan was found the spodic layers. Cemented B spodic horizon were observed in the white muçunungas, and granular structure and dark color from the surface in the black muçunungas. There was no fragipan or hard spodic horizon in the Restinga Spodosol. This soil is acid, dystrophic and alic, with sandy texture and high clay percentages in the spodic horizons. The CEC, based on H + Al, is predominantly represented by the organic matter. The most representative components of the mineral phase of the clay fraction are kaolinite and possibly vermiculite traces with interlayered hydroxy. Chemical, physical, morphological and mineralogical differences were observed between the Barreiras and Restinga environments. The black and white muçunungas differ in morphologic and chemical properties only.

The fossil record and evolution of freshwater plants: A review

Palaeobotany applied to freshwater plants is an emerging field of palaeontology. Hydrophytic plants reveal evolutionary trends of their own, clearly distinct from those of the terrestrial and marine flora. During the Precambrian, two groups stand out in the fossil record of freshwater plants: the Cyanobacteria (stromatolites) in benthic environments and the prasinophytes (leiosphaeridian acritarchs) in transitional planktonic environments. During the Palaeozoic, green algae (Chlorococcales, Zygnematales, charophytes and some extinct groups) radiated and developed the widest range of morphostructural patterns known for these groups. Between the Permian and Early Cretaceous, charophytes dominated macrophytic associations, with the consequence that over tens of millions of years, freshwater flora bypassed the dominance of vascular plants on land. During the Early Cretaceous, global extension of the freshwater environments is associated with diversification of the flora, including new charophyte families and the appearance of aquatic angiosperms and ferns for the first time. Mesozoic planktonic assemblages retained their ancestral composition that was dominated by coenobial Chlorococcales, until the appearance of freshwater dinoflagellates in the Early Cretaceous. In the Late Cretaceous, freshwater angiosperms dominated almost all macrophytic communities worldwide. The Tertiary was characterised by the diversification of additional angiosperm and aquatic fern lineages, which resulted in the first differentiation of aquatic plant biogeoprovinces. Phytoplankton also diversified during the Eocene with the development of freshwater diatoms and chrysophytes. Diatoms, which were exclusively marine during tens of millions of years, were dominant over the Chlorococcales during Neogene and in later assemblages. During the Quaternary, aquatic plant communities suffered from the effects of eutrophication, paludification and acidification, which were the result of the combined impact of glaciation and anthropogenic disturbance.

Anthropogenic radionuclides in atmospheric air over Switzerland during the last few decades.

The atmospheric nuclear testing in the 1950s and early 1960s and the burn-up of the SNAP-9A satellite led to large injections of radionuclides into the stratosphere. It is generally accepted that current levels of plutonium and caesium radionuclides in the stratosphere are negligible. Here we show that those radionuclides are present in the stratosphere at higher levels than in the troposphere. The lower content in the troposphere reveals that dry and wet deposition efficiently removes radionuclides within a period of a few weeks to months. Since the stratosphere is thermally stratified and separated from the troposphere by the tropopause, radioactive aerosols remain longer. We estimate a mean residence time for plutonium and caesium radionuclides in the stratosphere of 2.5-5 years. Our results also reveal that strong volcanic eruptions like Eyjafjallajökull in 2010 have an important role in redistributing anthropogenic radionuclides from the stratosphere to the troposphere.

Adaptive diversity in heterogeneous environments for populations regulated by a mixture of soft and hard selection

The stable co-existence of two haploid genotypes or two species is studied in a spatially heterogeneous environment submitted to a mixture of soft selection (within-patch regulation) and hard selection (outside-patch regulation) and where two kinds of resource are available. This is analysed both at an ecological time-scale (short term) and at an evolutionary time-scale (long term). At an ecological scale, we show that co-existence is very unlikely if the two competitors are symmetrical specialists exploiting different resources. In this case, the most favourable conditions are met when the two resources are equally available, a situation that should favour generalists at an evolutionary scale. Alternatively, low within-patch density dependence (soft selection) enhances the co-existence between two slightly different specialists of the most available resource. This results from the opposing forces that are acting in hard and soft regulation modes. In the case of unbalanced accessibility to the two resources, hard selection favours the most specialized genotype, whereas soft selection strongly favours the less specialized one. Our results suggest that competition for different resources may be difficult to demonstrate in the wild even when it is a key factor in the maintenance of adaptive diversity. At an evolutionary scale, a monomorphic invasive evolutionarily stable strategy (ESS) always exists. When a linear trade-off exists between survival in one habitat versus that in another, this ESS lies between an absolute adjustment of survival to niche size (for mainly soft-regulated populations) and absolute survival (specialization) in a single niche (for mainly hard-regulated populations). This suggests that environments in agreement with the assumptions of such models should lead to an absence of adaptive variation in the long term.

Final Report on the Portable Computerized Assessments of Sleepy Drivers in Operational Environments, June 29, 2011

Excessive daytime sleepiness underpins a large number of the reported motor vehicle crashes. Fair and accurate field measures are needed to identify at-risk drivers who have been identified as potentially driving in a sleep deprived state on the basis of erratic driving behavior. The purpose of this research study was to evaluate a set of cognitive tests that can assist Motor Vehicle Enforcement Officers on duty in identifying drivers who may be engaged in sleep impaired driving. Currently no gold standard test exists to judge sleepiness in the field. Previous research has shown that Psychomotor Vigilance Task (PVT) is sensitive to sleep deprivation. The first goal of the current study was to evaluate whether computerized tests of attention and memory, more brief than PVT, would be as sensitive to sleepiness effects. The second goal of the study was to evaluate whether objective and subjective indices of acute and cumulative sleepiness predicted cognitive performance. Findings showed that sleepiness effects were detected in three out of six tasks. Furthermore, PVT was the only task that showed a consistent slowing of both ‘best’, i.e. minimum, and ‘typical’ responses, median RT due to sleepiness. However, PVT failed to show significant associations with objective measures of sleep deprivation (number of hours awake). The findings indicate that sleepiness tests in the field have significant limitations. The findings clearly show that it will not be possible to set absolute performance thresholds to identify sleep-impaired drivers based on cognitive performance on any test. Cooperation with industry to adjust work and rest cycles, and incentives to comply with those regulations will be critical components of a broad policy to prevent sleepy truck drivers from getting on the road.

Anthropogenic disturbance as a driver of microspatial and microhabitat segregation of cytotypes of Centaurea stoebe and cytotype interactions in secondary contact zones.

BACKGROUND AND AIMS: In a mixed-ploidy population, strong frequency-dependent mating will lead to the elimination of the less common cytotype, unless prezygotic barriers enhance assortative mating. However, such barriers favouring cytotype coexistence have only rarely been explored. Here, an assessment is made of the mechanisms involved in formation of mixed-ploidy populations and coexistence of diploid plants and their closely related allotetraploid derivates from the Centaurea stoebe complex (Asteraceae). METHODS: An investigation was made of microspatial and microhabitat distribution, life-history and fitness traits, flowering phenology, genetic relatedness of cytotypes and intercytotype gene flow (cpDNA and microsatellites) in six mixed-ploidy populations in Central Europe. KEY RESULTS: Diploids and tetraploids were genetically differentiated, thus corroborating the secondary origin of contact zones. The cytotypes were spatially segregated at all sites studied, with tetraploids colonizing preferentially drier and open microhabitats created by human-induced disturbances. Conversely, they were rare in more natural microsites and microsites with denser vegetation despite their superior persistence ability (polycarpic life cycle). The seed set of tetraploid plants was strongly influenced by their frequency in mixed-ploidy populations. Triploid hybrids originated from bidirectional hybridizations were extremely rare and almost completely sterile, indicating a strong postzygotic barrier between cytotypes. CONCLUSIONS: The findings suggest that tetraploids are later immigrants into already established diploid populations and that anthropogenic activities creating open niches favouring propagule introductions were the major factor shaping the non-random distribution and habitat segregation of cytotypes at fine spatial scale. Establishment and spread of tetraploids was further facilitated by their superior persistence through the perennial life cycle. The results highlight the importance of non-adaptive spatio-temporal processes in explaining microhabitat and microspatial segregation of cytotypes.

Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis.

The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression.