The Role of Viral Infection in Inducing Variability in Virus-Free Progeny in Tomato

The effect of virus-host interactions on subsequent generations is poorly understood. The evaluation of the effects of viral infection on inheritance of quantitative traits in the progeny of infected plants and elucidation of a possible relationship between chiasma frequency in the infected plants and variability of traits in the progeny were investigated. The current study involved genotypes of four intraspecific hybrids of tomato （Solanum lycopersicum L.）, their parental forms and two additional cultivars. Used as infection were the tobacco mosaic virus （TMV） and potato virus X （PVX）. The consequences of the effect of viral infection were evaluated based on chromosome pairing in diakinesis and/or by examining quantitative and qualitative traits in the progeny of the infected tomato plants. Tomato plants infected with TMV ＋ PVX were found to differ in chiasma frequency per pollen mother cell or per bivalent. Deviations have been observed for genotypes of both F1 hybrids and cultivars. At the same time, differences in mean values of the traits under study have only been found for progeny populations （F2-F4） derived from virus-infected F1 hybrids, but not in the case of progeny of the infected cultivars. The rate of recombinants combining traits of both parents increased significantly （2.22-8.24 times） in progeny populations of hybrids infected with TMV＋PVX. The above suggests that the observed effects could be the result of modification of recombination frequencies that can be manifested in heterozygous hybrids and make small contributions to variability in cases of ＇homozygous＇ tomato genotypes （i.e. cultivars）.     

Reprint of: Saprolegnia strains isolated from river insects and amphipods are broad spectrum pathogens

Saprolegnia species are destructive pathogens to many aquatic organisms and are found in most parts of the world. Reports based on phylogenetic analysis suggest that Saprolegnia strains isolated from aquatic animals such as crustaceans and frogs are close to Saprolegnia strains isolated from infected fish or fish eggs and vice versa. However, it has often been assumed that host specificity occurs for each individual isolate or strain. Here we demonstrate that Saprolegnia spp. can have multiple hosts and are thus capable of infecting different aquatic organisms. Saprolegnia delica, Saprolegnia hypogyna, and 2 strains of Saprolegnia diclina were isolated from aquatic insects and amphipods while S. delica, Saprolegnia ferax, Pythium pachycaule, and a Pythium sp. were isolated from the water of a medium to fast flowing river. The ITS region of the rRNA gene was sequenced for all isolates. In challenge experiments, all four isolates from insects were found to be highly pathogenic to eggs of Atlantic salmon (Salmo salar) and embryos of the African clawed frog (Xenopus laevis). We found that Saprolegnia spp. isolated from salmon eggs were also able to successfully establish infection in nymphs of stonefly (Perla bipunctata) and embryos of X. laevis). These results suggest that Saprolegnia spp. are capable of infecting multiple hosts, which may give them an advantage during seasonal variation in their natural environments.     

A meta-analysis on morphological,physiological and biochemical responses of plants with PGPR inoculation under drought stress

Plant growth-promoting rhizobacteria (PGPR) can help plants to resist drought stress. However, the mechanisms of how PGPR inoculation affect plant status under drought remain incompletely understood. We performed a meta-analysis of plant response to PGPR inoculation by compiling data from 57 PGPR-inoculation studies, including 2, 387 paired observations on morphological, physiological and biochemical parameters under drought and well-watered conditions. We compare the PGPR effect on plants performances among different groups of controls and treatments. Our results reveal that PGPR enables plants to restore themselves from drought-stressed to near a well-watered state, and that C4 plants recover better from drought stress than C3 plants. Furthermore, PGPR is more effective underdrought than well-watered conditions in increasing plant biomass, enhancing photosynthesis and inhibiting oxidant damage, and the responses of C4 plants to the PGPR effect was stronger than that of C3 plants under drought conditions. Additionally, PGPR belonging to different taxa and PGPR with different functional traits have varying degrees of drought-resistance effects on plants. These results are important to improve our understanding of the PGPR beneficial effects on enhanced drought-resistance of plants.     

Leaf traits from stomata to morphology are associated with climatic and edaphic variables for dominant tropical forest evergreen oaks

热带森林优势种青冈叶片气孔、解剖和形态性状与气候、土壤因子的关联 了解优势树种叶片多水平的功能性状沿海拔梯度的变化及其内在关联,有助于预测优势种应对气候变化的响应与适应。本文研究了青冈属树种叶片气孔、解剖和形态性状沿海拔梯度的变化及其与环境调控因子的关联,探究了其生态策略是否随海拔发生改变。在海南尖峰岭热带森林,沿海拔梯度(400–1400 m)采集了6种常绿青冈：竹叶青冈(Cyclobalanopsis bambusaefolia)、雷公青冈(C. hui)、托盘青冈 (C. patelliformis)、饭甄青冈(C. fleuryi)、吊罗山青冈(C. tiaoloshanica)和亮叶青冈(C. phanera)叶片,用于气孔、解剖和形态性状的测定。研究结果表明,随海拔升高,青冈树种叶片气孔密度、气孔孔隙度指数和叶面积显著增加,但海绵组织厚度比和干物质含量则显着降低。叶片气孔、解剖和形态性状沿海拔梯 度的变化主要受年均温、年降水量和土壤pH 值调控。在低海拔和高海拔处,青冈属采取“耐受”和“竞 争”策略,而在中海拔处,则是“竞争”策略。土壤磷含量和土壤pH 值随海拔的变化可能是驱动其生态 策略转变的主要原因。该结果揭示,热带森林优势树种青冈可通过从气孔细胞-组织解剖结构-叶片水平功能性状的改变来响应环境变化。     

Tree seedling response to LED spectra: implications for forest restoration

We found that different spectra, provided by light-emitting diodes or a fluorescent lamp, caused different photomorphological responses depending on tree seedling type (coniferous or broad-leaved), species, seedling development stage, and seedling fraction (shoot or root). For two conifers (Picea abies and Pinus sylvestris) soon after germination (≤40 days), more seedling growth was related to a lower ratio of red-to-far-red (R:FR) light. As growth continued to 120 days, spectra with a greater complement of blue light yielded more growth. Roots showed more plasticity to light spectra than shoots. In general for the evergreen broad-leaved Quercus ilex, spectra with additional R:FR than for conifers yielded more growth in the first 57 days. Subsequently as seedlings grew, shoot growth appeared to be influenced less by light source than roots, with root length showing the greatest responses. Our results suggest that manipulating light spectra to foster desired seedling traits may be another tool for use in the production of high-quality seedlings as defined through the Target Plant Concept. Such seedlings are needed for restoration of the two billion hectares of degraded forestland, especially on harsh sites such as those found in the Mediterranean region, and to sequester carbon to mitigate climate change.     

Multiple trade‐offs regulate the effects of woody plant removal on biodiversity and ecosystem functions in global rangelands

Woody plant encroachment is a major land management issue. Woody removal often aims to restore the original grassy ecosystem, but few studies have assessed the role of woody removal on ecosystem functions and biodiversity at global scales. We collected data from 140 global studies and evaluated how different woody plant removal methods affected biodiversity (plant and animal diversity) and ecosystem functions (plant production, hydrological function, soil carbon) across global rangelands. Our results indicate that the impact of removal is strongly context dependent, varying with the specific response variable, removal method, and traits of the target species. Over all treatments, woody plant removal increased grass biomass and total groundstorey diversity. Physical and chemical removal methods increased grass biomass and total groundstorey biomass (i.e., non‐woody plants, including grass biomass), but burning reduced animal diversity. The impact of different treatment methods declined with time since removal, particularly for total groundstorey biomass. Removing pyramid‐shaped woody plants increased total groundstorey biomass and hydrological function but reduced total groundstorey diversity. Environmental context (e.g., aridity and soil texture) indirectly controlled the effect of removal on biomass and biodiversity by influencing plant traits such as plant shape, allelopathic, or roots types. Our study demonstrates that a one‐size‐fits‐all approach to woody plant removal is not appropriate, and that consideration of woody plant identity, removal method, and environmental context is critical for optimizing removal outcomes. Applying this knowledge is fundamental for maintaining diverse and functional rangeland ecosystems as we move toward a drier and more variable climate.     

Variation in male‐built nest volume with nesting‐support quality,colony, and egg production in whiskered terns

Nest building can represent an energetically costly activity for a variety of animal taxa. Besides, the determinants of within‐species variation in the design of nests, notably with respect to natural and sexual selection, are still insufficiently documented. Based on an observational study, we examined the influence of nesting conditions (nesting‐support quality, colony, laying date, and year) on male‐built nest volume and also its potential role as a postmating sexually selected display in the whiskered tern Chlidonias hybrida. This tern species is a monogamous colonial bird with obligate biparental care breeding on aquatic vegetation. Hence, large nesting platforms are expected to be a selective advantage because they would better withstand adverse environmental conditions and provide a secure structure for eggs. Nest size may also serve as a postmating sexual trait, and variation in egg production would be positively associated with nest size. We found that nest volume was adjusted to different environmental cues. A positive relationship was found between nest volume and nesting‐support quality, indicating that the leaf density of white waterlily is essential for nest stability. Variation in nest volume was not correlated to colony size but varied among colonies and years. Male‐built nest volume was also positively associated with mean egg volume per clutch but not with clutch size. The fitness consequences of building a large nest are yet to be studied, and additional investigations are recommended to better understand whether the activity of males early during breeding season (e.g., nest building and courtship feeding performance) really serves as postmating sexually selected signals.     

MITOCHONDRIAL GENOTYPES HAVE NO DETECTABLE EFFECTS ON MERISTIC TRAITS IN CUTTHROAT TROUT HYBRID SWARMS

Efforts to detect effects of cytoplasmic genes are confounded by the problem of partitioning nuclear and cytoplasmic effects. In this study we test for effects of mtDNA haplotype on development in hybrid populations of cutthroat trout (Oncorhynchus clarki) with randomly associated nuclear and mtDNA genotypes. We have previously described several intraspecific hybrid swarms formed by interbreeding of westslope cutthroat trout (O. c. lewisi) and Yellowstone cutthroat trout (O. c. bouvieri). Genetic distance between these subspecies is high (Nei's D = 0.30; mtDNA P = 0.02), and diagnostic alleles at multiple nuclear loci and two distinct mtDNA haplotypes are present in the hybrids. Historical associations between alleles at nuclear loci and between cytotypes and nuclear alleles have largely decayed. We test for differences in meristic characters between fish with alternate mtDNA haplotypes. Counts and fluctuating bilateral asymmetry for these characters have been previously shown to be sensitive indicators of genetic differences that affect development. No differences were found between mtDNA types in meristic counts or fluctuating asymmetry. Therefore, the alternate mtDNA haplotypes had no detectable effect on development as measured by meristic counts in these hybrid populations. However, diagnostic alleles at one nuclear allozyme locus (CK-CI) were associated with several fin ray counts.     

REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

Background

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data.

Results

We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of recombination detection algorithms. A newly generated NGS dataset from a genetic cross of Toxoplasma gondii allowed us to demonstrate our pipeline. REDHORSE successfully extracted the relevant genetic markers and was able to transform the read alignments from NGS to the genome to generate multiple sequence alignments. Recombination detection algorithm in REDHORSE was able to detect conventional crossovers and double crossovers typically associated with gene conversions whilst filtering out artifacts that might have been introduced during sequencing or alignment. REDHORSE outperformed other commonly used recombination detection algorithms in finding conventional crossovers. In addition, REDHORSE was the only algorithm that was able to detect double crossovers.

Conclusion

REDHORSE is an efficient analytical pipeline that serves as a bridge between genomic alignments and existing recombination detection algorithms. Moreover, REDHORSE is equipped with a recombination detection algorithm specifically designed for Next-generation sequencing data. REDHORSE is portable, platform independent Java based utility that provides efficient analysis of genetic crosses based on Next-generation sequencing data. REDHORSE is available at http://redhorse.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1309-7) contains supplementary material, which is available to authorized users.     

Effects of germination time on seed morph ratio in a seed-dimorphic species and possible ecological significance

Background and Aims Diaspores of heteromorphic species may germinate at different times due to distinct dormancy-breaking and germination requirements, and this difference can influence life history traits. The primary aim of this study was to determine the effect of germination time of the two seed morphs of Suaeda corniculata subsp. mongolica on life history traits of the offspring.Methods Germinated brown and black seeds were sown on the 20th of each month from April to September in a simulated but near-natural habitat of the species. Phenological and vegetative traits of the maternal plants, and number, size and germination percentage of the offspring were determined.Key Results Germinated seeds sown late in the year produced smaller plants that had a higher proportion of non-dormant brown than dormant black seeds, and these brown seeds were larger than those produced by germinated seeds sown early in the year. The length of the seedling stage for brown seeds was shorter than that for black seeds, and the root/shoot ratio and reproductive allocation of plants from brown seeds were more variable than they were for plants from black seeds. Late-germinating brown seeds produced larger plants than late-germinating black seeds.Conclusions Altering the proportion of the two seed types in response to germination timing can help alleviate the adverse effects of delayed germination. The flexible strategy of a species, such as S. corniculata, that produces different proportions of dimorphic seeds in response to variation in germination timing may favour the maintenance and regeneration of the population in its unpredictable environment.