Natural Ecotypes Research Articles

Strong plastic responses in aerenchyma formation in F1 hybrids of Imperata cylindrica under different soil moisture conditions.

Hybrids can express traits plastically, enabling them to occupy environments that differ from parental environments. However, there is insufficient evidence demonstrating how phenotypic plasticity in specific traits mediates hybrid performance. Two parental ecotypes of Imperata cylindrica produce F1 hybrids. The E-type in wet habitats has larger internal aerenchyma than the C-type in dry habitats. This study evaluated relationships between habitat utilisation, aerenchyma plasticity, and growth of I. cylindrica accessions. We hypothesize that plasticity in expressing parental traits explains hybrid establishment in habitats with various soil moisture conditions. Aerenchyma formation was examined in the leaf midribs, rhizomes and roots of two parental ecotypes and their F1 hybrids in their natural habitats. In common garden experiments, we examined plastic aerenchyma formation in leaf midribs, rhizomes and roots of natural and artificial F1 hybrids and parental ecotypes and quantified vegetative growth performance. In the natural habitats where soil moisture content varied widely, the F1 hybrids showed larger variation in aerenchyma formation in rhizomes than their parental ecotypes. In the common garden experiments, F1 hybrids showed high plasticity of aerenchyma formation in rhizomes, and their growth was similar to that of C-type and E-type under drained and flooded conditions, respectively. The results demonstrate that F1 hybrids of I. cylindrica exhibit plasticity in aerenchyma development in response to varying local soil moisture content. This characteristic allows the hybrids to thrive in diverse soil moisture conditions.

Versatile Medium for the Isolation of Sulfur-Reducing Bacteria from Natural Ecotypes

Sulfate-reducing bacteria (SRB) are a diverse group of microorganisms that are commonly isolated from anoxygenic environments (lake depths, soil, or swamps) and are also found in the intestines of humans and animals. They are well known for outcompeting methanogens for common substrates thereby helping in the decrease of methane emissions and also playing a major role in sulfur cycling. Therefore, determining the cultivable methods for their isolation is important. Various media has been used for the cultivation and purification of SRB from natural wetlands. The luxuriant growth of SRB was observed in all the media tested, out of which the best suitable media to recover a maximum of colonies from the natural soil/sediment samples was discovered as a modified postage medium. The enumeration of the isolated SRB was done by the most probable number (MPN) technique. A total of twenty pure isolates of SRB were isolated from different ecotypes.

Testing the association of relative growth rate and adaptation to climate across natural ecotypes of Arabidopsis.

Ecophysiologists have reported a range of relationships, including intrinsic trade-offs across and within species between plant relative growth rate in high resource conditions (RGR) vs adaptation to tolerate cold or arid climates, arising from trait-based mechanisms. Few studies have considered ecotypes within a species, in which the lack of a trade-off would contribute to a wide species range and resilience to climate change. For 15 ecotypes of Arabidopsis thaliana in a common garden we tested for associations between RGR vs adaptation to cold or dry native climates and assessed hypotheses for its mediation by 15 functional traits. Ecotypes native to warmer, drier climates had higher leaf density, leaf mass per area, root mass fraction, nitrogen per leaf area and carbon isotope ratio, and lower osmotic potential at full turgor. Relative growth rate was statistically independent of the climate of the ecotype native range and of individual functional traits. The decoupling of RGR and cold or drought adaptation in Arabidopsis is consistent with multiple stress resistance and avoidance mechanisms for ecotypic climate adaptation and would contribute to the species' wide geographic range and resilience as the climate changes.

Ecology typological assessment of forest vegetation of the North-Eastern Forest-Steppe of Ukraine

Recently, significantly increases the need for a detailed study of various aspects of the modern natural, spontaneous and artificially generated phytodiversity as the main element of the formation and regeneration of natural ecotypes structural elements for building national ecological network. It is necessary to examine various aspects of the natural and spontaneous vegetation formed. Based on the ecological specifics of the North-Eastern Forest-Steppe of Ukraine, a detailed analysis of natural and artificially formed forests on the floodplain, pine terrace and plateau of the rivers of the Dnieper and Seversky Donets basins, as well as in ravine-beam systems is required. Peculiarities of forest vegetation conditions, distribution of tree species and ecological conditions of their growth are given. According to forest management data, the area of the North-Eastern Forest-Steppe covered with forest vegetation is 336110.3 ha. The distribution of forest areas by edatopes is as follows: trophotopes — oak wood (220640.2 ha, 65.64%), sugruds (54739.2 ha, 16.29%), subors (52174.5 ha, 15.52%) and pine forests (8556.4 ha, 2.55%); hygrotopes — fresh conditions (282960.3 ha, 84.19%), dry (35576.7 ha, 10.59%), damp (12179.5 ha, 3.62%), moist (4634.3 ha, 1.38%), wet (749.0 ha, 0.22%) and very dry conditions (10.5 ha, 0.003%). There are 38 types of forests areas covered with forest vegetation, which are dominated by fresh maple-linden forest (183442.0 ha, 54.58%), a slightly smaller area occupied by fresh oak-pine forest (47040.9 ha, 14.00%) and linden-oak-pine sugrud (33999.3 ha, 10.12%), as well as dry maple-linden forest (28697.7 ha, 8.54%). The composition of forest-forming species is quite diverse and is represented by 60 species of woody and shrubby plants. The main forest-forming species is Quercus robur (190153.9 ha, 56.58%). Pinus sylvestris (86212.1 ha, 25.65%) and Fraxinus excelsior (20318.5 ha, 6.05%) have slightly smaller areas, all other species occupy small areas. Research a variety of forest habitats will provide an opportunity to plan the conservation, reproduction and protection of phytodiversity, including species of sozophytes from different conservation lists, as well as to balance the provision of ecosystem services by tree and shrub plantations of the North-Eastern Forest-Steppe of Ukraine.

Ecological and typological assessment of forest vegetation of the Middle Dnieper (Forest-steppe of Ukraine)

The paper shows the importance of a detailed study of various aspects of modern phytodiversity as an essential element of preservation of natural ecotypes for building national ecological network in the system of pan-European network. To do this, it is necessary to explore various aspects of natural and spontaneously formed vegetation. Based on the ecological specifics of the Middle Dnieper (Forest-Steppe of Ukraine), a detailed analysis of natural and artificially formed forests on the Dnipro cliffs, in ravine-beam systems and on the Dnipro floodplain is required. Peculiarities of forest vegetation conditions, distribution of tree species and ecological conditions of their growth are given. According to forest management data, the area covered with forest vegetation is 251341.3 hectares. The distribution of forest areas by edatopes is as follows: trophotopes — subors (78083.2 hectares, 31.07%), sugruds (77232.6 hectares, 30.73%), oak wood (72520.6 hectares, 28.85%) and pine forests (23504.9 hectares, 9.35%); hygrotopes — fresh conditions (183792.4 hectares, 73.13%), dry (34938.5 hectares, 13.90%), damp (19038.7 hectares, 7.57%), moist (11401.1 hectares, 4.54%), wet (1896.0 hectares, 0.75%) and very dry conditions (274.6 hectares, 0.11%). There are 62 types of forests areas covered with forest vegetation, which are dominated by fresh oak-pine forest (68319.9 hectares, 27.18%) and hornbeam oak wood (32871.8 hectares, 13.08%), a slightly smaller area occupied by fresh pine forest (17568.3 hectares, 6.99%), hornbeam-oak-pine sugrud (16952.2 hectares, 6.74%), maple-linden forest (15144.4 hectares, 6.03%) hornbeam-pine (13775.4 hectares, 5.48%) and hornbeam (9334.3 hectares, 3.71%) sudibrovas and dry maple-linden forest (12810.9 hectares, 5.10%). The composition of forest-forming species is quite diverse and is represented by 71 species of woody and shrubby plants. The main forest-forming species are Pinus sylvestris (116592.9 hectares, 46.39%) and Quercus robur (60049.7 hectares, 23.89%). Robinia pseudoacacia (26406.0 hectares, 10.51%), Alnus glutinosa (11391.7 hectares, 4.53%) and Fraxinus excelsior (7835.5 hectares, 3.12%) have slightly smaller areas, all other species occupy small areas. Identifying all the diversity of forest habitats will provide an opportunity to plan the conservation, reproduction and protection of phytodiversity, including species of sozophytes from different conservation lists, as well as to balance the provision of ecosystem services by tree plantations of the Middle Dnieper.

ANTIBODY PREVALENCE TO AFRICAN SWINE FEVER VIRUS, MYCOBACTERIUM BOVIS, FOOT-AND-MOUTH DISEASE VIRUS, RIFT VALLEY FEVER VIRUS, INFLUENZA A VIRUS, AND BRUCELLA AND LEPTOSPIRA SPP. IN FREE-RANGING WARTHOG (PHACOCHOERUS AFRICANUS) POPULATIONS IN SOUTH AFRICA.

The warthog (Phacochoerus africanus) can be used as a model for investigating disease transmission at the human, wildlife, and livestock interface. An omnivore and scavenger, a warthog moves freely between natural ecotypes, farmland, and human communities and is susceptible to diseases of zoonotic, agricultural, and conservation concern. A retrospective study using 100 individual serum samples collected from May 1999 to August 2016 was performed to determine antibody prevalence to seven pathogens in warthogs from five locations in northeastern South Africa. Higher prevalence of antibodies to African swine fever virus and Mycobacterium bovis were detected in warthogs from the Greater Kruger National Park ecosystem in comparison to lower prevalence of antibodies to M. bovis and no antibodies to African swine fever virus in warthogs from uMhkuze Game Reserve. Low prevalence of antibodies to foot-and-mouth disease virus, Rift Valley fever virus, and influenza A virus was detected in all locations, and no antibodies against Brucella and Leptospira spp. were detected. No statistically significant difference in antibody prevalence was found between sexes for any disease. At the univariate analysis, M. bovis seropositivity was significantly different among age categories, with 49% (35/71) of adults found positive versus 29% (4/14) of juveniles and 9% (1/11) of sub-adults (Fisher's exact test, P=0.020), and between the sampling locations (Fisher's exact test, P=0.001). The multivariate model results indicated that juvenile warthogs had lower odds of testing positive to M. bovis antibodies than adults (juveniles' odds ratio [OR]=0.17, 95% confidence interval [CI]: 0.02-1.0), although this result was not statistically significant at the 5% level (P=0.052). For warthogs sampled at Satara Buffalo Camp, the odds (OR=0.22, 95% CI: 0.035-0.96) of being M. bovis antibody positive were significantly lower (P=0.043) than for warthogs sampled at Skukuza. Of particular interest in this study was the detection of warthogs seropositive for influenza A virus.

Reverse breeding: A modern plant breeding approach for hybrid recreation

Reverse breeding is a modern plant breeding method for producing complementing parental lines for any heterozygous plant through achaismatic meiosis (meiosis without crossovers). The achiasmatic meiosis leads to univalent segregation at meiotic metaphase-I and the generation of aneuploid gametes. These gametes are then regenerated as doubled-haploid (DH) plants. Each DH carries combinations of its parental chromosomes, and complementing DH pairs can be crossed to reconstitute the initial hybrid. In reverse breeding, the suppression of meiotic crossovers in a hybrid ensures the transmission of non-recombinant chromosomes to haploid gametes. The PAIR2 gene is required for homologous chromosome synapsis at meiosis-I in plants. An insertional mutation in the rice PAIR2 gene, the ortholog of Arabidopsis thaliana ASY1, results in a defect in homologous chromosome pairing during meiosis, display univalents at metaphase-I. Essentially, reverse breeding follows an approach akin to the generation of a DH population from an F1 hybrid, carrying a dominant-acting transgene that down-regulates the expression of Disrupted Meiotic cDNA1 (DMC1), resulting in inhibition of crossover recombination and thereby enabling intact-chromosome inheritance. In earlier reports on reverse breeding in A. thaliana, a hybrid was constructed of using two of its natural ecotypes (Col-0 and Laer-0), carrying an RNAi transgene targeting the meiotic recombinase (RecA homolog) DMC1 that prevented the formation of meiotic crossover recombination. This method mainly included steps: (i) the generation and selection of RNAi: DMC1 transformed lines; (ii) the generation of achiasmatic hybrids; (iii) the crossing of achiasmatic hybrids to GFP-tailswap to generate haploid chromosome substitution lines (CSLs); (iv) the generation of DHs by spontaneous doubling of haploid CSLs; and (v) the crossing of complementing CSLs to recreate the initial hybrid. The scope of reverse breeding could be envisioned for the improvement of agricultural crops, as it may enable the generation of parental breeding lines for the recreation of hybrid.

Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa.

Bioethanol production from lignocellulosic biomass has received increasing attention over the past decade. Many attempts have been made to reduce the cost of bioethanol production by combining the separate steps of the process into a single-step process known as consolidated bioprocessing. This requires identification of organisms that can efficiently decompose lignocellulose to simple sugars and ferment the pentose and hexose sugars liberated to ethanol. There have been many attempts in engineering laboratory strains by adding new genes or modifying genes to expand the capacity of an industrial microorganism. There has been less attention in improving bioethanol-related processes utilizing natural variation existing in the natural ecotypes. In this study, we sought to identify genomic loci contributing to variation in saccharification of cellulose and fermentation of glucose in the fermenting cellulolytic fungus Neurospora crassa through quantitative trait loci (QTL) analysis. We identified one major QTL contributing to fermentation of glucose and multiple putative QTL’s underlying saccharification. Understanding the natural variation of the major QTL gene would provide new insights in developing industrial microbes for bioethanol production.

Questing Ixodes ricinus ticks (Acari, Ixodidae) as a vector of Borrelia burgdorferi sensu lato and Borrelia miyamotoi in an urban area of north-eastern Poland

Green areas located within large cities, as natural ecotypes, are a convenient habitat for ticks and their use as recreational areas is associated with the potential risk of acquiring tick-borne diseases. This study estimated the I. ricinus tick density, prevalence of infection with Borrelia species and the diversity of these bacteria in a green urban area (Olsztyn) of north-eastern Poland, an endemic region of tick-borne diseases. The ticks were collected during spring and autumn of 2015, at sites differing in the degree of human pressure and habitat. Borrelia species detection, typing and a molecular phylogenetic analysis were carried out based on the sequenced flaB gene. The overall mean abundance of I. ricinus was 2.0 ± 1.55 ticks per 100 m2. The density of I. ricinus did not vary significantly between sites. According to semi-qualitative tick abundance categories, the collection sites were classified as ‘very low’ and ‘low’ tick abundance category. The overall infection rate of I. ricinus with Borrelia spirochaetes was 27.4%. The infection rate of adult ticks (42.0%) was three times higher than with nymphs (14.3%). Based on the restriction patterns and sequencing, B. afzelii (93.1%; 27/29), B. valaisiana 3.5% (1/29) and B. miyamotoi (3.5%; 1/29), related to the relapsing fever (RF) spirochaetes, were detected. No co-infections were found. Borrelia miyamotoi, detected for the first time in ticks in the north-eastern urban areas of Poland, was identical to isolates described as European-type. The Borrelia spirochaete infection rate of I. ricinus ticks in an urban area indicated a high risk of LB. Physicians should also be aware of B. miyamotoi infections among patients with a history of tick-bites in north-eastern Poland.

Natural ecotype of Arabidopsis thaliana (L.) Heynh (Chernobyl-07) respond to cadmium stress more intensively than the sensitive ecotypes Oasis and Columbia

Large areas polluted with toxic heavy metals or radionuclides were formed as a side product of rapid industrial development of human society. Plants, due to their sessile nature, should adapt to these challenging genotoxic environmental conditions and develop resistance. Herein, we evaluated the response of three natural ecotypes of Arabidopsis thaliana (L.) Heynh (Oasis, Columbia-0, and Chernobyl-07) to cadmium, using discovery gel-based proteomics. These accessions are differing by level of tolerance to heavy metal probably achieved by various exposure to chronic ionizing radiation. Based on the pairwise comparison (control versus cadmium-treated) we recognized 5.8–13.4% of identified proteins as significantly altered at the presence of cadmium. Although the majority of photosynthesis-related proteins were found to be less abundant in all ecotypes it was noted that in contrast to the sensitive variants (Col and Oas), the tolerant Che accession may activate the mechanism preserving photosynthesis and energy production. Also, proteins modulating energy budget through alternative route and mediating higher resistance to heavy metals were upregulated in this ecotype. Although we suggest that regulation of enzymes acting in peptide and protein synthesis, protection of the plants against various abiotic stresses, or those neutralizing the effects of reactive oxygen species are rather associated with general response to cadmium, they were found to be altered more intensively in the Che accession. Thus, the identified affected proteins may represent good candidate molecules for molecular breeding to improve tolerance of crops to heavy metal stress.

Decoupling photo- and thermoperiod by projected climate change perturbs bud development, dormancy establishment and vernalization in the model tree Populus

BackgroundThe performance and survival of deciduous trees depends on their innate ability to anticipate seasonal change. A key event is the timely production of short photoperiod-induced terminal and axillary buds that are dormant and freezing-tolerant. Some observations suggest that low temperature contributes to terminal bud initiation and dormancy. This is puzzling because low temperatures in the chilling range universally release dormancy. It also raises the broader question if the projected climate instabilities, as well as the northward migration of trees, will affect winter preparations and survival of trees.ResultsTo gauge the response capacity of trees, we exposed juvenile hybrid aspens to a 10-h short photoperiod in combination with different day/night temperature regimes: high (24/24 °C), moderate (18/18 °C), moderate-low (18/12 °C) and low (12/12 °C), and analysed bud development, dormancy establishment, and marker gene expression. We found that low temperature during the bud formation period (pre-dormancy) upregulated dormancy-release genes of the gibberellin (GA) pathway, including the key GA biosynthesis genes GA20oxidase and GA3oxidase, the GA-receptor gene GID1, as well as GA-inducible enzymes of the 1,3-β-glucanase family that degrade callose at plasmodesmal Dormancy Sphincter Complexes. Simultaneously, this pre-dormancy low temperature perturbed the expression of flowering pathway genes, including CO, FT, CENL1, AGL14, LFY and AP1. In brief, pre-dormancy low temperature compromised bud development, dormancy establishment, and potentially vernalization. On the other hand, a high pre-dormancy temperature prevented dormancy establishment and resulted in flushing.ConclusionsThe results show that pre-dormancy low temperature represents a form of chilling that antagonizes dormancy establishment. Combined with available field data, this indicates that natural Populus ecotypes have evolved to avoid the adverse effects of high and low temperatures by initiating and completing dormant buds within an approximate temperature-window of 24-12 °C. Global warming and erratic temperature patterns outside this range can therefore endanger the successful propagation of deciduous perennials.

Emergence and Initial Growth of the Seedlings of Euterpe oleracea Mart. Seeds of Different Ecotypes in Function on the Substrate

In Brazil, the assai (Euterpe oleracea Mart.) is a native palm of the Amazon biome, being exploited in an extractive and predatory way to obtain palm heart and processed pulp. In recent years, there has been an increase in the exploitation of commercial plantations in the country, since extractivism and management of native areas are not able to meet growing demand. In this way, companies of the sector and public institutions have invested in new technologies, such as the improvement of plants, which has increased the demand for good quality seeds, coming from natural ecotypes. Thus, the objective of this work was to evaluate seeds of E. oleracea from three ecotypes regarding the emergence and initial growth of the seedlings in different substrates to guide future plant selection. Seed lots from three assai berry ecotypes were evaluated for water content, seedling emergence, first count, seedling emergence speed index, seedling length and dry mass. The experimental design was completely randomized, with four repetitions of 50 seeds, sown on different substrates. In the physiological characteristics of the seeds and seedlings, there are differences of the three E. oleracea ecotypes. These ecotypes make it possible to identify and select assai palm’s mother plants of Luiz Domingues (IG) and Maracanã (V) natives of areas of the igapó and várzea, respectively, as producers of better quality seeds and seedlings in an alternative substrate (composed of sand, agricultural soil and cattle manure in a proportion of 2:2:1) and, commercial substrate (FORTH® compound of pinus and gray bark), respectively.

Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana.

Increasing evidence for epigenetic variation within and among natural plant populations has led to much speculation about its role in the evolution of plant phenotypes. However, we still have a very limited understanding of the evolutionary potential of epigenetic variation, in particular in comparison to DNA sequence-based variation. To address this question, we compared the magnitudes of heritable phenotypic variation in epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana-lines that mainly differ in DNA methylation but only very little in DNA sequence-with other types of A. thaliana lines that differ strongly also in DNA sequence. We grew subsets of two epiRIL populations with subsets of two genetic RIL populations, of natural ecotype collections, and of lines from a natural population in a common environment and assessed their heritable variation in growth, phenology, and fitness. Among-line phenotypic variation and broad-sense heritabilities tended to be largest in natural ecotypes, but for some traits the variation among epiRILs was comparable to that among RILs and natural ecotypes. Within-line phenotypic variation was generally similar in epiRILs, RILs, and ecotypes. Provided that phenotypic variation in epiRILs is mainly caused by epigenetic differences, whereas in RILs and natural lines it is largely driven by sequence variation, our results indicate that epigenetic variation has the potential to create phenotypic variation that is stable and substantial, and thus of evolutionary significance.

Five species, many genotypes, broad phenotypic diversity: When agronomy meets functional ecology.

Current ecological theory can provide insight into the causes and impacts of plant domestication. However, just how domestication has impacted intraspecific genetic variability (ITV) is unknown. We used 50 ecotypes and 35 cultivars from five grassland species to explore how selection drives functional trait coordination and genetic differentiation. We quantified the extent of genetic diversity among different sets of functional traits and determined how much genetic diversity has been generated within populations of natural ecotypes and selected cultivars. In general, the cultivars were larger (e.g., greater height, faster growth rates) and had larger and thinner leaves (greater SLA). We found large (average 63%) and trait-dependent (ranging from 14% for LNC to 95.8% for growth rate) genetic variability. The relative extent of genetic variability was greater for whole-plant than for organ-level traits. This pattern was consistent within ecotypes and within cultivars. However, ecotypes presented greater ITV variability. The results indicated that genetic diversity is large in domesticated species with contrasting levels of heritability among functional traits and that selection for high yield has led to indirect selection of some associated leaf traits. These findings open the way to define which target traits should be the focus in selection programs, especially in the context of community-level selection.

Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location.

BackgroundIntraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant Arabidopsis thaliana at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted.ResultsWe analyzed the natural CNVs in the region overlapping MSH2 gene that encodes the DNA mismatch repair protein, and AT3G18530 and AT3G18535 genes that encode poorly characterized proteins. By applying multiplex ligation-dependent probe amplification and droplet digital PCR we genotyped those genes in 189 A. thaliana accessions. We found that AT3G18530 and AT3G18535 were duplicated (2–14 times) in 20 and deleted in 101 accessions. MSH2 was duplicated in 12 accessions (up to 12-14 copies) but never deleted. In all but one case, the MSH2 duplications were associated with those of AT3G18530 and AT3G18535. Considering the structure of the CNVs, we distinguished 5 genotypes for this region, determined their frequency and geographical distribution. We defined the CNV breakpoints in 35 accessions with AT3G18530 and AT3G18535 deletions and tandem duplications and showed that they were reciprocal events, resulting from non-allelic homologous recombination between 99 %-identical sequences flanking these genes. The widespread geographical distribution of the deletions supported by the SNP and linkage disequilibrium analyses of the genomic sequence confirmed the recurrent nature of this CNV.ConclusionsWe characterized in detail for the first time the complex multiallelic CNV in Arabidopsis genome. The region encoding MSH2, AT3G18530 and AT3G18535 genes shows enormous variation of copy numbers among natural ecotypes, being a remarkable example of high Arabidopsis genome plasticity. We provided the molecular insight into the mechanism underlying the recurrent nature of AT3G18530-AT3G18535 duplications/deletions. We also performed the first direct comparison of the two leading experimental methods, suitable for assessing the DNA copy number status. Our comprehensive case study provides foundation information for further analyses of CNV evolution in Arabidopsis and other plants, and their possible use in plant breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3221-1) contains supplementary material, which is available to authorized users.

Genetic variation for clonal propagation and trait association with field performance in sainfoin

Clonal plant materials with identical genotypes may be used to precisely detect environmental effects and genotype x environment interactions resulting in a more accurate estimate of genetic parameters in plant genetic analysis. In sainfoin ( Onobrychis viciifolia ), knowledge on genetic variation for clonal propagation and its association with field performance is limited. Eleven natural ecotypes of sainfoin from wide geographical areas of Iran were used to evaluate genetic variation for clonal propagation and its association with related traits. From each ecotype 11‒21 genotypes were cloned via cuttings. Then, clones of a hundred genotypes from 10 ecotypes were transplanted to the field. High genetic variation was found between ecotypes of sainfoin for producing viable clones. The mean values for viable clones varied from 50% (Borujen ecotype) to 97% (Najafabad ecotype). The values of within-ecotype coefficient of variation were higher than the genetic coefficient of variation. The highest heritability estimates were obtained for sensitivity to powdery mildew, plant height and number of stems per plant. Dry matter yield (DMY) in the field was significantly and positively correlated with plant height and number of stems per plant, inflorescence length and growth score. An association between DMY and percent of viable clones was found indicating the possibility of selection during the early stages of clonal propagation. According to principal component analysis, Baft and Fereydunshahr ecotypes have potential for improving production of sainfoin if introduced into breeding programs. These issues warrant further study. Keywords: Clone viability, genetic variability, Onobrychis viciifolia, phenotypic correlation, principal component analysis. DOI: 10.17138/TGFT(4)38-46

Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.

Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general and condition-specific activities of the TFs and their regulatory relationships with the target genes (TGs), we have used a homogeneous stress gene expression dataset generated on ten natural ecotypes of the model plant Arabidopsis thaliana, during five single and six combined stress conditions. Knowledge-based profiles of binding sites for 25 stress-responsive TF families (187 TFs) were generated and tested for their enrichment in the regulatory regions of the associated TGs. Condition-dependent regulatory sub-networks have shed light on the differential utilization of the underlying network topology, by stress-specific regulators and multifunctional regulators. The multifunctional regulators maintain the core stress response processes while the transient regulators confer the specificity to certain conditions. Clustering patterns of transcription factor binding sites (TFBS) have reflected the combinatorial nature of transcriptional regulation, and suggested the putative role of the homotypic clusters of TFBS towards maintaining transcriptional robustness against cis-regulatory mutations to facilitate the preservation of stress response processes. The Gene Ontology enrichment analysis of the TGs reflected sequential regulation of stress response mechanisms in plants.

MORPHOLOGICAL AND MOLECULAR EVALUATION OF THE FAR EAST FRUIT GENETIC RESOURCES OF LONICERA CAERULEA L

Field studies of honeysuckle ( Lonicera caerulea L. s.l.) and material for investigation (91 herbarium accessions; 20 scion samples; and fruits for detailed morphological description, organoleptic and molecular analyses) have been collected in the north-eastern part of the area of honeysuckle distribution, in Kamchatka and Sakhalin regions. All coenopopulations have been characterized ecologically, geobotanically, and phytosociologically. Factors threatening natural coenopopulations have been estimated, and these data preconditioned recommendations for honeysuckle in situ conservation. Fruits of 20 Russian honeysuckle cultivars have been included in comparative molecular assessment together with fruits from natural ecotypes. As a result of AFLP analysis, all investigated material was divided into three groups: two groups include samples L. caerulea , collected in Kamchatka, and the majority of the investigated honeysuckle cultivated forms, while the third group unites only genotypes of the sakhalin plants.

Investigating the Association between Flowering Time and Defense in the Arabidopsis thaliana-Fusarium oxysporum Interaction

Plants respond to pathogens either by investing more resources into immunity which is costly to development, or by accelerating reproductive processes such as flowering time to ensure reproduction occurs before the plant succumbs to disease. In this study we explored the link between flowering time and pathogen defense using the interaction between Arabidopsis thaliana and the root infecting fungal pathogen Fusarium oxysporum. We report that F. oxysporum infection accelerates flowering time and regulates transcription of a number of floral integrator genes, including FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT) and GIGANTEA (GI). Furthermore, we observed a positive correlation between late flowering and resistance to F. oxysporum in A. thaliana natural ecotypes. Late-flowering gi and autonomous pathway mutants also exhibited enhanced resistance to F. oxysporum, supporting the association between flowering time and defense. However, epistasis analysis showed that accelerating flowering time by deletion of FLC in fve-3 or fpa-7 mutants did not alter disease resistance, suggesting that the effect of autonomous pathway on disease resistance occurs independently from flowering time. Indeed, RNA-seq analyses suggest that fve-3 mediated resistance to F. oxysporum is most likely a result of altered defense-associated gene transcription. Together, our results indicate that the association between flowering time and pathogen defense is complex and can involve both pleiotropic and direct effects.

Recipient of the 2014 molecular ecology prize: Johanna Schmitt.

Recipient of the 2014 molecular ecology prize: Johanna Schmitt.