Modulation of auxin signalling through DIAGETROPICA and ENTIRE differentially affects tomato plant growth via changes in photosynthetic and mitochondrial metabolism

Auxin modulates a range of plant developmental processes including embryogenesis, organogenesis, and shoot and root development. Recent studies have shown that plant hormones also strongly influence metabolic networks, which results in altered growth phenotypes. Modulating auxin signalling pathways may therefore provide an opportunity to alter crop performance. Here, we performed a detailed physiological and metabolic characterization of tomato (Solanum lycopersicum) mutants with either increased (entire) or reduced (diageotropica—dgt) auxin signalling to investigate the consequences of altered auxin signalling on photosynthesis, water use, and primary metabolism. We show that reduced auxin sensitivity in dgt led to anatomical and physiological modifications, including altered stomatal distribution along the leaf blade and reduced stomatal conductance, resulting in clear reductions in both photosynthesis and water loss in detached leaves. By contrast, plants with higher auxin sensitivity (entire) increased the photosynthetic capacity, as deduced by higher V_cmax and J_max coupled with reduced stomatal limitation. Remarkably, our results demonstrate that auxin‐sensitive mutants (dgt) are characterized by impairments in the usage of starch that led to lower growth, most likely associated with decreased respiration. Collectively, our findings suggest that mutations in different components of the auxin signalling pathway specifically modulate photosynthetic and respiratory processes.     

TrioMDR: Detecting SNP interactions in trio families with model-based multifactor dimensionality reduction

Single nucleotide polymorphism (SNP) interactions can explain the missing heritability of common complex diseases. Many interaction detection methods have been proposed in genome-wide association studies, and they can be divided into two types: population-based and family-based. Compared with population-based methods, family-based methods are robust vs. population stratification. Several family-based methods have been proposed, among which Multifactor Dimensionality Reduction (MDR)-based methods are popular and powerful. However, current MDR-based methods suffer from heavy computational burden. Furthermore, they do not allow for main effect adjustment. In this work we develop a two-stage model-based MDR approach (TrioMDR) to detect multi-locus interaction in trio families (i.e., two parents and one affected child). TrioMDR combines the MDR framework with logistic regression models to check interactions, so TrioMDR can adjust main effects. In addition, unlike consuming permutation procedures used in traditional MDR-based methods, TrioMDR utilizes a simple semi-parameter P-values correction procedure to control type I error rate, this procedure only uses a few permutations to achieve the significance of a multi-locus model and significantly speeds up TrioMDR. We performed extensive experiments on simulated data to compare the type I error and power of TrioMDR under different scenarios. The results demonstrate that TrioMDR is fast and more powerful in general than some recently proposed methods for interaction detection in trios. The R codes of TrioMDR are available at: https://github.com/TrioMDR/TrioMDR.     

Spatiotemporal distribution of growth releases and suppressions along a landslide body

Our study analyzes the growth response (release or suppression) of Norway spruce trees growing along a landslide zone in eastern Czech Republic. A total of one hundred and eighty-six increment cores were extracted from Norway spruce (Picea abies (L.) Karst.) individuals, which were affected by two different disturbances, the Girová landslide in May 2010 and an anthropogenic cut-off in the neighborhood of the landslide later the same year. Growth changes were analysed in three zones that were defined according to the type of effect the disturbance had on the surrounding vegetation. The aims of our study are to (i) detect growth changes in trees that survived the disturbances in 2010, (ii) evaluate the delay time of the growth reaction to the disturbances, (iii) compare how growth changes differed in response to the two different disturbance types (natural landslide vs. anthropogenic harvesting and deforestation), and (iv) investigate spatio-temporal differences in the growth changes. Our results indicate that tree growth changed in response to the altered environmental conditions following the 2010 disturbances. The changes vary depending on the intensity of the disturbance and its effect on the forest stand. Trees in Zone 1 responded with a slight growth release (14.6 % of responding trees), which was strongest after 2013. However, growth suppression (85.4 %) was the dominant reaction in Zone 1; with the majority of trees showing growth suppression in 2014, four years after the events. The strongest and most abrupt growth release (66.1 %) occurred in Zone 2 in 2011, after a one-year delay. Since 2010, we have observed a trend of growth suppression (33.9 %) in this zone. In Zone 3, following a one-year delay, growth release has occurred gradually in about a third of the trees (37.0 %). The majority of trees in this zone have responded with growth suppression (63.0 %) in 2010 and with a three-year delay after 2013. We also found differences in how tree growth responds to anthropogenic and landslide disturbances, as well as spatio-temporal differences related to the extent of post-disturbance changes.     

Modeling the vertical foliage distribution of an individual <Emphasis Type="Italic">Castanopsis cuspidata</Emphasis> (Thunb.) Schottky,a dominant broad-leaved tree in Japanese warm-temperate forest

The vertical foliage distribution of Castanopsis cuspidata (Thunb.) Schottky was examined in trees of various sizes to clarify its variation in relation to tree size and the light environment in a stand. As indices of these parameters, we analyzed crown social position (CSP: percent of stand height) and specific leaf area (SLA). The vertical foliage distribution of trees was expressed by a Weibull function. The variation in the vertical foliage distribution of C. cuspidata could be categorized into three types using crown social position and light environment. In the first type, leaves were concentrated to the top 20% of the tree; such trees are canopy trees that can receive full sunlight. The second type had a large relative crown depth and an asymmetric distribution with the maximum foliage located near the top of the tree; such trees are suppressed trees whose crowns do not receive sufficient light. The third type had a large relative crown depth and a symmetric distribution; such trees occur in high light environments, although their crowns are in the understory layer. The differences in the vertical foliage distribution are related to the strategies used to capture light. Multiple regression analysis showed that CSP and SLA at the top layer of the tree explained successive changes in the vertical foliage distribution. These results will contribute to scaling-up the vertical foliage distribution to the community level in pure stands of C. cuspidata using an individual-based model.     

土壤干旱对元宝枫渗透调节能力的影响

采用盆栽控水法和P—V技术研究分析了不同土壤干旱(速度、程度)条件对元宝枫渗透调节能力的影响。结果表明,元宝枫具有很强的渗透调节能力．但该能力受土壤干旱的速度和程度影响,在缓慢干旱条件下,元宝枫叶片的ψw、ψ0、π100、RWC^0、ROWC^0均明显降低．其中与渗透调节能力直接相关的(π100可下调0．52MPa,ψ0下调1．51MPa。在快速干旱条件下π100和ψ0分别仅下凋0．20MPa和0．48MPa。△π100值也表明缓慢干旱条件下元宝枫渗透调节能力是快速干旱下的45倍。在缓慢干旱条件下．由轻度到中度干旱时其渗透调节能力显著增强(增加270％);由中度到严重干旱时．增加不明显(增加了24．5％)。从3种有机渗透调节物质含量与△π100值的动态变化可见,可溶性糖含量增加对渗透调节能力的贡献是第一位的．其次是Pro、游离氨基酸。     

Plant water relations at elevated CO2 -- implications for water-limited environments

Long-term exposure of plants to elevated [CO2] leads to a number of growth and physiological effects, many of which are interpreted in the context of ameliorating the negative impacts of drought. However, despite considerable study, a clear picture in terms of the influence of elevated [CO2] on plant water relations and the role that these effects play in determining the response of plants to elevated [CO2] under water-limited conditions has been slow to emerge. In this paper, four areas of research are examined that represent critical, yet uncertain, themes related to the response of plants to elevated [CO2] and drought. These include (1) fine-root proliferation and implications for whole-plant water uptake; (2) enhanced water-use efficiency and consequences for drought tolerance; (3) reductions in stomatal conductance and impacts on leaf water potential; and (4) solute accumulation, osmotic adjustment and dehydration tolerance of leaves. A survey of the literature indicates that the growth of plants at elevated [CO2] can lead to conditions whereby plants maintain higher (less negative) leaf water potentials. The mechanisms that contribute to this effect are not fully known, although CO2-induced reductions in stomatal conductance, increases in whole-plant hydraulic conductance and osmotic adjustment may be important. Less understood are the interactive effects of elevated [CO2] and drought on fine-root production and water-use efficiency, and the contribution of these processes to plant growth in water-limited environments. Increases in water-use efficiency and reductions in water use can contribute to enhanced soil water content under elevated [CO2]. Herbaceous crops and grasslands are most responsive in this regard. The conservation of soil water at elevated [CO2] in other systems has been less studied, but in terms of maintaining growth or carbon gain during drought, the benefits of CO2-induced improvements in soil water content appear relatively minor. Nonetheless, because even small effects of elevated [CO2] on plant and soil water relations can have important implications for ecosystems, we conclude that this area of research deserves continued investigation. Future studies that focus on cellular mechanisms of plant response to elevated [CO2] and drought are needed, as are whole-plant investigations that emphasize the integration of processes throughout the soil--plant--atmosphere continuum. We suggest that the hydraulic principles that govern water transport provide an integrating framework that would allow CO2-induced changes in stomatal conductance, leaf water potential, root growth and other processes to be uniquely evaluated within the context of whole-plant hydraulic conductance and water transport efficiency.     

Photosynthetic Assimilation of Sun versus Shade Norway Spruce [Picea abies (L.) Karst] Needles Under the Long-Term Impact of Elevated CO2 Concentration

The long-term impact of elevated concentration of CO₂ on assimilation activity of sun-exposed (E) versus shaded (S) foliage was investigated in a Norway spruce stand [Picea abies (L.) Karst, age 14 years] after three years of cultivation in two domes with adjustable windows (DAW). One DAW was supplied with ambient air [AC, ca. 350 µmol(CO₂) mol^–1) and the second with elevated CO₂ concentration [EC = AC plus 350 µmol(CO₂) mol^–1]. The pronounced vertical profile of the photosynthetic photon flux density (PPFD) led to the typical differentiation of the photosynthetic apparatus between the shaded and sun needles. Namely, photon-saturated values of maximal net photosynthetic rate (P _Nmax) and apparent quantum yield () were significantly higher/lower for E-needles as compared with the S-ones. The prolonged exposure to EC was responsible for the apparent assimilatory activity stimulation observed mainly in deeply shaded needles. The degree of this stimulation decreases in the order: S-needles dense part > S-needles sparse part > E-needles dense part > E-needles sparse part. In exposed needles some signals on a manifestation of the acclimation depression of the photosynthetic activity were found. The long-term effect of EC was responsible for the decrease of nitrogen content of needles and for its smoother gradient between E- and S-needles. The obtained results indicate that the E- and S-foliage respond differently to the long-term impact of EC.     

次生栎林蒸腾强度与生态因子的关系

采用多元回归分析和灰色关联分析方法,探讨下蜀次生栎林蒸腾强度与生态因子的相关关系。研究认为用二次工咕次多项式回归方程和指数回归方程拟合更能反映各生态因子在整个生长季中与蒸腾强度关系的性质。影响蒸腾强度的主要生态因子是温度和净辐射;其次是空气相对湿度和土壤热流通量;风速和土壤含水率的影响很小。灰色关联分析与多元回归分析的结论一致。研究结果为进一步阐明次生栎林的结构和功能提供了理论基础。     

Weighted p-value adjustments for animal carcinogenicity trend test

A typical animal carcinogenicity experiment routinely analyzes approximately 10-30 tumor sites. Comparisons of tumor responses between dosed and control groups and dose-related trend tests are often evaluated for each individual tumor site/type separately. p-Value adjustment approaches have been proposed for controlling the overall Type I error rate or familywise error rate (FWE). However, these adjustments often result in reducing the power to detect a dose effect. This paper proposes using weighted adjustments by assuming that each tumor can be classified as either class A or class B based on prior considerations. The tumors in class A, which are considered as more critical endpoints, are given less adjustment. Two weighted methods of adjustments are presented, the weighted p adjustment and weighted alpha adjustment. A Monte Carlo simulation shows that both weighted adjustments control the FWE well. Furthermore, the power increases if a treatment-dependent tumor is analyzed as in class A tumors and the power decreases if it is analyzed as in class B tumors. A data set from a National Toxicology Program (NTP) 2-year animal carcinogenicity experiment with 13 tumor types/sites observed in male mice was analyzed using the proposed methods. The modified poly-3 test was used to test for increased carcinogenicity since it has been adopted by the NTP as a standard test for a dose-related trend. The unweighted adjustment analysis concluded that there was no statistically significant dose-related trend. Using the Food and Drug Administration classification scheme for the weighted adjustment analyses, two rare tumors (with background rates of 1% or less) were analyzed as class A tumors and 11 common tumors (with background rates higher than 1%) as class B. Both weighted analyses showed a significant dose-related trend for one rare tumor.