Influence of physical properties of peat-based potting mixes substituted with parboiled rice hulls on plant growth under two irrigation regimes Abstract This study was conducted to investigate the effects of physical properties of peat-based substrate mixtures partially substituted with parboiled rice hulls (PRH) on plant growth and performance. Thirteen substrate mixtures were formulated by substituting 0, 20, 30, 40, 50, 60, or 70% peat with either parboiled ground rice hulls (GRH) or whole rice hulls (WRH) (by volume) in commercial potting mix (CPM) containing 70% peat, 20% perlite, and 10% vermiculite. All substrate mixtures consisted of mainly medium-sized (2.0–0.25 mm) particles. However, regardless of the mixing ratio, GRH significantly increased the medium-sized particles especially with diameters of 2.0–0.71 mm, while WRH increased both the medium- and coarse-sized (> 2.0 mm) particles. A higher mixing ratio of PRH increased air space and decreased container capacity but to a greater extent by WRH compared to GRH. Similarly, bulk density was increased with a higher mixing ratio of both types of PRH, but to a greater degree by GRH. Total porosity of GRH-containing substrates was similar to that of CPM within the range of 30–70%. The substrate mixtures containing PRH did not have the same physical properties as the CPM at any mixing ratio, but the values of some GRH-containing mixtures were within or close to the suggested ranges for greenhouse substrates. Considering the maximum substitution of PRH for peat, the substitution with 40% GRH (GRH-40) was selected for a plant growth study in comparison to CPM. Petunia (Petunia × hybrida) ‘Easy Wave Neon Rose’ and zinnia (Zinnia elegans) ‘Benary’s Giant Golden Yellow’ were grown in pots containing CPM and GRH-40 at two irrigation levels: high (25–30%, by volume) and low (20–25%). Overall, shoot DW of both plant species was reduced in GRH-40, but root DW was maintained similar to those in CPM. The low irrigation level more significantly reduced shoot DW of petunia grown in CPM than in GRH-40, relative to their counterparts with the high irrigation level (20 and 7%, respectively); however, root growth of plant species grown in GRH-40 was either maintained or tended to be maintained even at the low irrigation level compared to their high irrigation counterparts. The water use efficiency of plants grown in GRH-40 was not significantly different from those in CPM regardless of irrigation level. These results indicate that GRH-40 provides desirable physical properties and water release characteristics, allowing more available water for plants under low irrigation levels than CPM. We concluded that substituting peat with 40% GRH in a commercial potting mix is a sustainable approach to produce petunia and zinnia.

Soilless tomato grown under nutritional stress increases green biomass but not yield or quality in presence of biochar as growing medium Abstract Biochar has been reported to improve soil fertility and growing medium performance. However, the role that biochar plays in plant nutrition is not completely understood, especially in plants grown under nutritional stress. Recent research indicates that the addition of biochar increases produce yield of tomato grown under salinity stress and drought; however, little information is available about the effects of biochar on fruit quality parameters. The use of biochar as a growth substrate in an intensive greenhouse cropping system may have the capacity of replacing non-renewable and less sustainable growing media like peat and in addition being a strategy to optimize chemical fertilisation. This work aimed to investigate the effects of biochar, as a potential candidate to replace peat, on tomato growing in soilless conditions under nutritional stress. Plant biomass accumulation, leaf fluorescence and chlorophyll, fruit yield and fruit quality parameters were measured as performance indicators. Biochar increased the green biomass, but it did not significantly affect yield or most quality parameters, apart from potassium content in ripe fruits. These results suggest that biochar has great potential as a peat alternative material and plant growth promoter, but no ability to improve tomato yield, under nutritional stress.

Discovery of PTE -1, Tourist -like miniature inverted repeat transposable element (MITE), and its activation in transgenic Brassica rapa ssp. pekinensis plants Abstract Miniature inverted-repeat transposable elements (MITEs) are class II, non-autonomous DNA transposons that occupy a large portion of the genome, most in an inactive state. Because transposition of MITEs can have a broad impact on the structure and function of the genome, it is important to identify activated MITEs and analyze their propensity for transposition. However, to date the activity of only a few MITEs has been analyzed. In this study, MITE activation during the transformation processes in Chinese cabbage was analyzed by using next-generation sequencing. Using genome wide analysis, we found PTE-1 was activated during the transformation process. The active transposition of PTE-1 was analyzed by PCR amplification. We determined the sequence of PTE-1 by cloning the PCR products. Based on its target site duplications sequence and terminal inverted repeats structure, we inferred that the element belongs to the Tourist family. The characteristics of PTE-1, including structure and copy number, were identified by bioinformatics approaches. The results suggest that PTE-1 activation could be induced by the transformation process and reveal the first detection of activated MITE in tissue culture derived from Brassica rapa plants.

Effects of elevated ozone on physiological, biochemical and morphological characteristics of eggplant Abstract Air pollutants are emitted from various anthropogenic sources into the atmosphere. Especially, ozone (O3) has become a critical problem since the average O3 concentration is increasing every year by about 0.5–2% across the world. O3 in the air affects plant growth because it mainly passes through the stomata of leaves into plants. This experiment was designed to identify the physiological, morphological, and biochemical responses of plants to O3. For the purposes of this study, eggplant (Solanum melongena L.), which is one of the most well-known crops produced in the world, was used. Eggplants were continuously subjected to 110 nmol mol−1 for 25 days using the phytotron. Following O3 treatment, the growth and biomass of the eggplant were reduced, and the photosynthetic rates were lower than those of the controls. In contrast, water use efficiency increased progressively on the leaves of the eggplant. Initial visible injures were observed at 15 days after O3 treatment. Stomatal density was reduced in response to the O3 treatment. With regard to biochemical responses, malondialdehyde content and relative ion leakage were higher than those of the control. Superoxide and hydrogen peroxide accumulation was observed on the leaf surface after 25 days of O3 treatment. These observations indicate that treatment with 110 nmol mol−1 O3 had negative effects on the physiological, morphological, and biochemical activities of eggplant. Further studies investigating the damage caused by exposure to different concentrations of O3 and for different periods of time are required.

Application of maximum quantum yield, a parameter of chlorophyll fluorescence, for early determination of bacterial wilt in tomato seedlings Abstract Bacterial wilt caused by Ralstonia solanacearum is a devastating disease that limits tomato seedling and fruit production. Monitoring and early detection are required to effectively manage and reduce the spread of this disease. Seedlings of 30 tomato accessions from three Solanum spp. that came from different countries were grown under greenhouse conditions. Seedlings at the 4-leaf stage were inoculated with R. solanacearum. Disease severity was monitored using the chlorophyll fluorescence parameter (maximum quantum yield; Fv/Fm) until 5 days post inoculation (dpi). Visual symptoms were recorded daily until 16 dpi, and compared with non-infected control seedlings. Fv/Fm started to decrease at 2 dpi in most of the accessions and reached the lowest values at 5 dpi. Visual symptoms started to appear at 3 dpi for 16 accessions, and all of the moderately resistant and susceptible accessions showed visual symptoms at 5 dpi excluding four highly resistant accessions showing non visual disease index at 5 dpi. Finally, 17 accessions were susceptible to R. solanacearum, resulting in visual disease indices (DI) at 3–4 dpi and Fv/Fm values between 0.00 and 0.55. These plants died at the end of the experiment. Nine accessions were moderately resistant to R. solanacearum, showing visual DI values of 1–2 and Fv/Fm values between 0.55 and 0.65. However, four accessions were highly resistant to bacterial wilt and had visual DI values of 0 and Fv/Fm values between 0.65 and 0.83. Furthermore, the resistant genotypes did not show any changes in their visual DI until 16 dpi. Collectively, these results indicate that, depending on the genotype, R. solanacearum infection can be precisely predicted 1–2 days before visual symptoms appear in tomato seedlings. The chlorophyll fluorescence parameter can also be used to accurately screen for moderately resistant accessions.

Genetic relationships and population structure of pears ( Pyrus spp.) assessed with genome-wide SNPs detected by genotyping-by-sequencing Abstract Pears (Pyrus spp.) are temperate trees and their fruits are consumed throughout the world, but their genetic relationships are difficult to identify due to low morphological diversity. We estimated the genetic relationships and population structure of 231 pear accessions using 10,186 genome-wide single nucleotide polymorphisms (SNPs) driven by genotyping-by-sequencing (GBS). In our phylogenetic tree and population structure analysis, the accessions were classified into two major groups (group I and II), which were characterized by European and Asian pears, and two subgroups in group II. Of the subgroups in group II, group II-1 contained P. pyrifolia and group II-2 consisted of P. bretschneideri, P. ussuriensis, and P. betulifolia. Principal component analysis classified the pears more precisely than the phylogenetic tree, and P. betulifolia, which belonged to group II-2, was divided into two additional groups. These results suggest that genome-wide GBS–SNPs are suitable to estimate the genetic diversity of pear germplasms, including Asian and European pears, and are also valuable for understanding the genetic structure and evolution of pears, predicting breeding materials, and genome-wide association studies. Furthermore, the information resulting from this study could be useful for the management of Korean pear germplasms and development of breeding materials.

SSR analysis reveals molecular variation and genetic diversity in Malus sieversii with different stress resistance levels in China Abstract Malus sieversii, a valuable crop in Xinjiang, China, is an important natural resource for researching the genetic diversity and phylogenetic evolution of the genus Malus worldwide. Samples from 152 M. sieversii individuals with different symptom grades of deadwood were collected from Gongliu and Xinyuan and analysed with 21 pairs of simple sequence repeat (SSR) primers, revealing molecular genetic characteristics and phylogeny of different groups and individuals. The samples showed high genetic diversity at the species level (Na = 10.76, Ne = 4.37, H = 0.73, I = 1.65, Ho = 0.71, and He = 0.73). Variation was mainly found within groups with lower genetic differentiation (Fst = 0.092) and higher gene flow (Nm = 2.67). A total of 226 alleles were obtained, of which 25 exclusive alleles were from samples with < 40% deadwood rate, and 23 exclusive alleles were from samples with > 40% deadwood rate. Specific bands relating to individuals with deadwood rate < 10% (10 exclusive alleles) or > 60% (7 exclusive alleles) were amplified with 11 pairs of SSR primers. The number of exclusive alleles from M. sieversii plants collected in Gongliu was 52 and from those collected in Xinyuan was 24. Using unweighted pair-group method with arithmetic cluster analysis, the groups with different symptom grades from different sampling sites were shown to be clearly differentiated and formed several discrete subclades. Significantly, the six groups from Gongliu were further classified into two subclusters: Gongliu 1, including three groups with < 40% deadwood rate, and Gongliu 2, including three groups with > 40% deadwood rate.

DNA methylation levels in different tissues in tea plant via an optimized HPLC method Abstract DNA methylation is one of the most important events in epigenetics and significantly influences plant growth and development. In the present study, we established and optimized a high-performance liquid chromatography method for detecting the base composition in DNA in tea plant (Camellia sinensis L.) tissues by using saline buffers-free mobile phases. The DNA methylation level varied with tea plant tissue, cultivar, and growth stage. A relatively higher DNA methylation level was observed in tender leaf (38.34%) and pistil (38.19%) tissues, while a relatively low level was detected in capillary root (19.45%), stamen (19.61%), and old leaf (20.70%) tissues. The pattern of the methylation level formed a saddle curve during the growth of dormant buds in spring; the lowest point appeared at the stage of one leaf and a bud. The methylation level in the adventitious buds regenerated from the branch after pruning seemed to decrease with an increase in the degree of pruning. These DNA methylation levels might be associated with the development of tea plant.

Correction to: Comparative analysis and physio‑biochemical screening of an ex‑situ fig ( Ficus carica L.) collection The original version of this article unfortunately contained a mistake. Abderrahman Mekaoui was not listed among the authors. The corrected author list is given above. The original article has been corrected.

Isolation of putative pepper defense-related genes against the pathogen Phytophthora capsici using suppression subtractive hybridization/macroarray and RNA-sequencing analyses Abstract The oomycete Phytophthora capsici Leonian is one of the most economically important pathogens limiting pepper (Capsicum annuum) production in many regions around the world. Insights into the defense mechanisms of pepper against P. capsici would be helpful in the breeding of resistant cultivars. However, little is still known about the defense system in pepper against P. capsici. We used suppression subtractive hybridization (SSH) followed by macro-array screening to isolate the putative candidate defense genes (PSH, Phytophthora Subtractive Hybridization) in pepper that are differentially expressed between the resistant cultivar (CM334) and the susceptible cultivar (Chilsungcho) following P. capsici infection. A total of 72 PSH genes were identified and categorized based on their putative functions. Semi-quantitative RT-PCR analyses using 11 selected genes confirmed their differential expressions between the resistant and susceptible cultivars along the time course of infection with P. capsici. Furthermore, RNA-seq analyses were performed to understand the possible roles of PSH genes in the defense response to P. capsici as well as three viruses, including two tobacco mosaic virus strains and one Pepper Mottle Virus strain. We found that 37 genes out of 72 displayed differential expression in our RNA-seq-based heatmap between ‘CM334’ and ‘Chilsungcho’ upon pathogen infection. In particular, two genes, CA00g99220 and CA00g96010, and one gene, CA12g16620, were shown to be strongly and uniquely expressed in the resistant cultivar, CM334, against P. capsici and two viruses, respectively. Thus, we consider that this combined approach using SSH/macro-array screening and RNA-seq analyses is a relevant tool for isolation of candidate defense-related genes upon pathogen infection. Data in this study provide a good source for further study on the defense mechanisms against pathogens in chili pepper.