rss_2.0Sciendo RSS Feed for Silvae Geneticahttps://sciendo.com/journal/SGhttps://www.sciendo.comhttps://sciendo-parsed.s3.eu-central-1.amazonaws.com/647376194e662f30ba53f282/cover-image.jpghttps://sciendo.com/journal/SG140216https://sciendo.com/article/10.2478/sg-2024-0013<abstract> <title style='display:none'>Abstract</title> <p>Genotype × environment (G×E) interaction is a major challenge in selecting superior genotypes based on growth traits in <italic>Eucalyptus</italic> since phenotypic variability is significantly affected by environmental heterogeneity. The aim of the present investigation was to understand the relationship between wood property traits and fibre biometry in the bi-parental mapping population of <italic>E. camaldulensis × E. tereticornis</italic> across three locations and identify stable genotypes based on multiple traits to improve prediction accuracy in breeding programs. High broad-sense heritability was documented for fibre parameters indicating a good prospect of these traits for genotype selection in hybrid breeding programmes in <italic>Eucalyptus</italic>. Significant positive correlation of fibre parameters with cellulose, acoustic velocity, DMoE and negative correlation with lignin reiterate that the fibre traits can be improved by the selection of genotype for improved wood property traits. Multi-Trait Stability Index (MTSI) and weighted average of absolute scores of the genotype index (WAASB) short-listed four genotypes (C343, C327, C246 and C161) with improved wood property traits and the mean of selected genotypes for all traits was significantly higher than the grand mean of the overall genotypes. The identified superior and stable genotypes with improved wood properties and fibre biometry can be used in plantation programs or as genitors in breeding programs.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00132024-08-09T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0012<abstract> <title style='display:none'>Abstract</title> <p><italic>Juglans</italic> is an economically important genus distributed all over the world. Due to its high value, there is a large interest in genetic markers for population genetic analyses and the certification of reproductive material. Using chloroplast genomes of different <italic>Juglans</italic> species, we developed a highly polymorphic and reliable chloroplast SSR marker set of eleven cpSSRs. It was successfully tested in five different Juglans species. Genetic differentiation among species and provenances within species was assessed. We were able to define a total of nine different chloroplast haplotypes using the novel cpSSR markers with up to four different haplotypes within a single <italic>Juglans</italic> species. Due to the cost and labor effective character of SSR markers, when compared to other available methods, such as whole chloroplast genome sequencing or SNP analyses, this novel cpSSR marker set will contribute to future population genetic studies in the <italic>Juglans</italic> genus.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00122024-07-22T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0010<abstract> <title style='display:none'>Abstract</title> <p>This study aimed to test near-infrared spectroscopy to assess insect damage to oak acorns collected from a seed orchard of <italic>Quercus acuta</italic> in Jeju Island, Korea. A total of 550 acorns were sorted into 362 sound and 178 unsound (insect-damaged) acorns, followed by near-infrared spectroscopy. To minimize spectral data errors, preprocessing techniques such as first derivative, multiplicative scatter correction, standard normal variate, and Savitzky-Golay filter were applied, along with multivariate analysis methods like partial least squares. Then the model performance, including accuracy and precision, was evaluated using the Variable Importance in Projection. The near-infrared wavelength of the acorns showed strong absorption peaks at 660~720nm and a slight downward trend at 900~1000nm. The most effective model for distinguishing unsound acorns was Savitzky-Golay filtering treatment applied in the 400~1000nm range and used partial least squares, showing prediction accuracy of 86 % (p&lt;0.05). The performance was significantly influenced by absorption points at 660~720nm and 960~1000nm, with the latter range believed to be affected by changes in moisture and carbohydrates due to insect damage. The former range showed lower classification capability due to chlorophyll and color variation but affected the model performance when used with near-infrared wavelength range. These findings can narrow down the scope of investigation for future research using wider wavelength ranges or multispectral analysis.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00102024-07-06T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0011<abstract> <title style='display:none'>Abstract</title> <p>There are many challenges involved in obtaining high-quality DNA from tissues/cells, especially when using plants as the raw material. Three different DNA extraction protocols were employed in order to isolate high quality of genomic DNA from <italic>Pyracantha crenulata</italic> leaves. <italic>P. crenulata</italic> is a complex, versatile, and evergreen shrub species in Rosaceae family which is ecologically, economically and culturally important. This species produces valuable antioxidants like polyphenols, polysaccharides and secondary metabolites which interfere with DNA extraction thus making molecular marker based studies difficult in this species. This study aimed to develop a simple, rapid, cost-effective and highly efficient protocol for <italic>P. crenulata</italic> leaves rich in salts and phenols. The results demonstrated that modified CTAB (double buffer) protocol is very effective in overcoming the challenges that could impede next-generation sequencing analysis. The yield of the extracted DNA was excellent ranging from 368 to 410 ng/μL DNA with A260/280 ratio ranging from 1.80 to 1.84. The extracted DNA was amenable to PCR amplification making it suitable for DNA-based molecular marker studies. None procedures have been published for the purpose up this species, therefore, double buffer based extraction protocol is reported for the first time in <italic>P. crenulata</italic> and might prove useful in other species of family Rosa-ceae. This study describes an effective DNA isolation method that is appropriate for frequent population genetic screening. In conclusion, the double buffer protocol showed the most efficient and effective approach for extracting DNA from phenol rich, fresh, mature, and dry leaves.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00112024-07-06T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0009<abstract> <title style='display:none'>Abstract</title> <p>Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step in these genome projects is the successful extraction of high-molecular-weight DNA in high quality and sufficient quantity, which is imperative for long-read sequencing. The extraction of high-molecular-weight DNA in trees has been limited and difficult to conduct. To achieve successful extraction, modification of the protocol for tree species is necessary. Here, we present a protocol for high-molecular-weight DNA extraction from the broadleaved tree species <italic>Fraxinus excelsior</italic> and from the conifer species <italic>Taxus baccata</italic>. The protocol is based on nuclei isolation and is divided into two main steps, i.e. nuclei separation based on the nuclei isolation buffer and DNA extraction using the Nanobind® plant nuclei kit by Pacific Biosciences (PacBio). The protocol can be applied to different tree species to obtain high-molecular-weight DNA in high quality, which can be used for Oxford Nanopore Technologies (ONT) and PacBio sequencing. ONT sequencing using four high-molecular-weight DNA preparations from <italic>Fraxinus excel-sior</italic> resulted in different read length N50 values (12.91-38.19 kb) and total base output (5.81-23.17 Gb), emphasizing the complex nature of the sequencing pipeline of high-molecular-weight DNA. PacBio HiFi sequencing of <italic>Taxus baccata</italic> produced circular consensus sequencing reads with an average length of 12.9 kb and an N50 of 13.59 kb. Altogether, this study presents a protocol to obtain high-molecular-weight DNA from different challenging tree species and discusses several important points that can be considered when adapting the protocol to additional species.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00092024-07-06T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0008<abstract> <title style='display:none'>Abstract</title> <p>Forest tree breeding faces challenges due to long generation times and high costs. To address these issues, the concept of “breeding without breeding” (BwB) offers the opportunity to accelerate breeding cycles by using naturally generated half- sib and full-sib families. An isolated population of trees may provide an ideal environment to identify full-sib families for genetic mapping without the need for controlled pollination. In this study, paternity analysis based on genotyping of 16 SSR markers in 1232 seedlings identified three large full-sib families of <italic>Quercus rubra</italic> (Qr_N - Qr_W with 576 siblings, Qr_N - Qr_S with 175 siblings and 124 siblings in the family Qr_P - Qr_11). Paternity assignments were effectively corroborated by segregation analysis, resulting in large F₁ full-sib families for further experiments such as Quantitative Trait Locus (QTL) mapping.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00082024-06-07T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0007<abstract> <title style='display:none'>Abstract</title> <p><italic>Balfourodendron riedelianum</italic> is an important timber species of South America used in civil construction and carpentry. Knowing the genetic variation, heritability and correlation between traits is an essential prerequisite for guiding selection of the best genotypes in tree improvement. In this study, growth (diameter and height) and wood density (mean, pith, middle and bark position) traits were investigated in 30-year-old trees planted in a <italic>B. riedelianum</italic> provenance and progeny test established in two sites, Luiz Antônio (LA) and Pederneiras (PE), in São Paulo State (Brazil). ANOVA results showed significant differences between sites for all traits, among provenances and families for wood density traits in the LA site and among families for growth traits in PE. Provenance x site and family x site interactions were significant for almost traits, and genetic correlation between sites was low for all traits (0.17–0.20). Genetic variation (<italic>CV</italic>_g) was higher (4.0–5.4 %) and mean family heritability (<italic>h</italic>_m²) was lower for growth (0.12–0.20) compared to wood density (<italic>CV</italic>_g: 2.3–3.8%, <italic>h</italic>_m²: 0.31–0.59) traits. Genetic correlation was significantly positive and ranged from moderate to high between growth traits (0.47–0.68) and between wood density traits (0.42–0.83) and non-significant between growth and wood density (-0.22–0.30) traits. An analysis of different radial positions showed that heritability tended to increase from pith to the bark position. Our results show a lower environmental effect on wood density traits, allowing the possibility of selecting superior provenances and families with high wood quality in breeding programs in both sites.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00072024-06-05T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0006<abstract> <title style='display:none'>Abstract</title> <p><italic>Podocarpus lambertii</italic> (Podocarpaceae) is an endangered conifer, endemic to Brazil and occurring in continuous forest and forest-grassland landscapes from the Araucaria Forest. Aiming to support conservation efforts for <italic>P. lambertii</italic> populations and gain insights into the preservation of forest-grassland mosaics in southern Brazil, we assessed the spatial pattern, genetic diversity, and fine-scale genetic structure (FSGS) within a population situated in a forest-grassland mosaic. The study was conducted in a 9-ha plot in forest-grassland mosaic. All <italic>P. lambertii</italic> individuals with height ≥ 0.1 m were sampled and the population was stratified into four demographic categories (Seedling, Juvenile, Immature, and Reproductive). For each of these categories, we used 13 allozyme markers to evaluate the spatial pattern, genetic diversity and FSGS. All individuals occurred inside the forest-patches, presenting an aggregated pattern of distribution. Low genetic diversity was recorded for all categories and for the population (<inline-formula> <alternatives> <inline-graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_sg-2024-0006_eq_001.png"/> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mover accent="true"><mml:mi>H</mml:mi><mml:mo>⌢</mml:mo></mml:mover></mml:mrow><mml:mi>E</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi> </mml:mi><mml:mn>0.046</mml:mn></mml:mrow></mml:math> <tex-math>{\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\frown$}}\over H} _E} = \,0.046</tex-math> </alternatives> </inline-formula>), as well as a high number of rare alleles (20). Positive and significant FSGS was estimated only for the Juveniles (<inline-formula> <alternatives> <inline-graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_sg-2024-0006_eq_002.png"/> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mover accent="true"><mml:mi>θ</mml:mi><mml:mo>⌢</mml:mo></mml:mover></mml:mrow><mml:mrow><mml:mi>x</mml:mi><mml:mi>y</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mi> </mml:mi><mml:mn>0.012</mml:mn></mml:mrow></mml:math> <tex-math>{\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\frown$}}\over \theta } _{xy}} = \,0.012</tex-math> </alternatives> </inline-formula>) up to maximum distance of 7.1 m, and the minimum viable area for the long-term conservation of Reproductive genetic diversity was approximately 68 ha. The set of our findings suggests that conservation actions need to enhance connectivity among forest-patches to prevent the loss of rare alleles due to genetic drift. Additionally, we highlight the significance of preserving forest-patches as repositories of species diversity and as crucial connectors between populations.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00062024-05-31T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0005<abstract> <title style='display:none'>Abstract</title> <p>Genetic variation and performance of up to 40-year-old Norway spruce (<italic>Picea abies</italic> (L.) Karst.) families from half-diallel crosses made in natural populations where studied, and the results were compared with results from nursery test of seedlings (1-2 years from seed) and short-term farm-field tests at 6-10 years from seed. The diallel analyses revealed significant levels of additive genetic variance for growth and phenology traits. The non-additive genetic variance was generally small to moderate. Strong genetic correlations for growth performance were found between the short-term and long-term trials but not between the nursery and long-term trials. Similarly, genetic correlations for phenology traits were strong between short-term trials and long-term trials, whereas the nursery tests generally did not predict phenology at older age well. The findings indicate that early selection for growth and adaptive traits based on short-term trials is effective for improvement of long-term performance in field if the test site is not outside the normal range of deployment of the reproductive material.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00052024-04-13T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0004<abstract><title style='display:none'>Abstract</title> <p>In Mexico, <italic>Magnolia</italic> species of the section <italic>Macrophylla</italic> have been segregated based on phenotypic characteristics. However, the wide environmental variation throughout their distribution area in the eastern region of the country could be the main cause of the high degree of morphological variation among the taxa of this section. Therefore, it is necessary to carry out studies at the genetic level to confirm the taxonomic identity of these species. In the present study, the diversity and genetic structure of the populations of <italic>Magnolia rzedowskiana</italic> and <italic>M. zotictla</italic> were estimated using simple sequence repeat markers. We evaluated whether the taxonomic delimitation as independent species is consistent with their degree of genetic differentiation, comparing three regions of chloroplast DNA: trnH-psbA, ORF350, and rpl32-trnL. The DNA was obtained from four populations of the two species, which are distributed in the states of Hidalgo, Querétaro and San Luis Potosí. The populations presented intermediate–high genetic diversity (He = 0.52–0.60), limited gene flow (Nm = 0.62) and high genetic differentiation (Fst = 0.288), which may be related to their low density and strong geographic isolation, caused by the high degree of fragmentation of their habitat. The phylogenetic analysis and the genetic differentiation values indicate that each of the populations of the two <italic>Magnolia</italic> species analyzed behaves as an independent evolutionary unit, so the taxonomic delimitation of the three <italic>M. rzedowskiana</italic> populations must be reconsidered. The results obtained could be very useful for implementing management and conservation strategies for these populations in the short term.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00042024-04-04T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0003<abstract><title style='display:none'>Abstract</title> <p>The present study measured the growth traits of 98 open-pollinated half-sibling families from the second-generation clonal seed orchard of Chinese fir for 6 consecutive years from age 2 to 7, the change patterns of genetic variation in growth traits and genetic parameters were analyzed, and best linear unbiased prediction (BLUP) was used for early selection to determine the excellent families. The growth traits of Chinese fir revealed highly significant differences between families, indicating that there was significant genetic variation at the family level, which serves as the foundation for exceptional family selection. The heritabilities of family and individual for H (height) ranged from 0.61 to 0.65 and 0.41 to 0.46, respectively; for DGH (the diameter at ground height)/DBH (the diameter at breast height), they were 0.55 to 0.66 and 0.35 to 0.46, respectively; and for V (tree volume), they were 0.66 to 0.70 and 0.48 to 0.49, respectively. The growth traits of genetic control were at a greater level at age 5. The findings of the coefficient of variation analysis demonstrated that the phenotypic variation coefficient were larger than the genetic variation coefficient for three growth traits at various ages. The juvenile-mature genetic and phenotypic correlations revealed an increasing tendency with age, and mainly controlled by genetic factors. Compared to other age groups for growth traits, age 5 had greater phenotypic and genetic association coefficients, as well as greater efficiency of early selection. Based on the selection method of breeding value, nine families were selected with a 9.2 % selection rate.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00032024-04-04T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0002<abstract> <title style='display:none'>Abstract</title> <p>Teak (<italic>Tectona grandis</italic>) is a premier hardwood timber, extensively cultivated throughout the tropics. The study aimed to undertake the first genomic selection of teak clones using single nucleotide polymorphism (SNP) markers and evaluate the prospects for prediction of stem volume (VOL), diameter (DBH), form Quality Score (QS), Specific Gravity (SG), and Heartwood Percentage (HW). Thirty-three elite teak clones from a genetic test in northern Costa Rica were genotyped at 10812 SNP loci and aligned to the teak reference genome sequence. The genomic relationship matrix revealed 7 cryptic groups of more highly related clones and within-group kinship values were consistent with full-sib families. Clone values for each of the 5 traits were calculated from 5-year field data for 26 of the geno-typed clones. Genomic prediction models were fitted to clone values using Bayesian Ridge Regression, BayesA, BayesB, BayesC, and Bayes Lasso. Predictive ability (PA) was greatest for DBH (up to 0.66), VOL (up to 0.63), SG (0.58), with 0.42 and 0.40 as the best PA for QS and HW, respectively. GWAS resulted in the discovery of 7 unique SNP markers for volume, 7 for DBH, 4 for QS, and 8 for SG. The small experimental size resulted in relatively large false discovery rates. Teak breeders are well positioned to benefit from the genomic tools and approaches to genotyping teak breeding and deployment populations on a large scale. Significant advantages are expected from widespread integration of genomic technologies into teak breeding systems to allow shortening of the breeding cycle.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00022024-03-16T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2024-0001<abstract> <title style='display:none'>Abstract</title> <p>It is important to evenly increase the amount of scattered pollen per clone for maintaining high genetic variation in clonal seed orchards. It is thus imperative to determine not only the number of male flowers per tree, but also the amount of pollen per male flower in each clone. In this study, the existence of annual variation on the fresh weight of male flowers (FW) and the clonal and annual variation, and ramets’ variation with the same or different tree ages on the weight of pollen per male flower (WP) were investigated using 21 <italic>Abies sachalinensis</italic> clones for 3 years. The results indicated that there were significant differences in FW and WP among clones each year and the relationships between FW and WP were linearly significant for every year. WP also showed significant annual variation, while the re was also significant variation in ramets. The clonal repeatability regarding WP was 0.37—0.47 for data obtained for 2 or 3 years and the generalized linear mixed models with the random effects of clone, year, and ramet indicated that the effect of clone more strongly affected WP than other effects. These results suggested that WP on <italic>A. sachalinensis</italic> is a trait that is considerably influenced by clonal characteristics; there is thus a need to characterize this trait in each clone when using seed orchards.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2024-00012024-02-24T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2023-0020<abstract> <title style='display:none'>Abstract</title> <p><italic>Castanea sativa</italic> Mill. is an important European tree species that has been used for timber and nut production since Greek and Roman times. In Germany, the species accounts for only a small proportion of forest stands but it is attracting increasing interest due to its possible potential for climate tolerance and resilience. However, the status of German sweet chestnut stands in terms of genetic diversity and adaptive potential is poorly investigated. We took a representative sample of 520 individuals from 13 stands in northern Germany (Mecklenburg Western Pomerania; MWP) and genotyped these at 11 genomic SSRs and EST-SSRs. In addition, we compared our data with the available literature, focusing on the possible origin of the MWP populations. The analysis of genetic structure identified three distinct genetic groups within MWP, suggesting different origins or seed mixtures of various provenances. The comparison with reference data at the EST-SSR FIR059 suggests that the MWP stands originate from the western gene pool. The genetic variation observed in most MWP stands is at approximately the same level as stands in the natural range. Therefore, these stands with high diversity seem to be particularly suitable for further production of seed and plant material in MWP. This study contributes to the understanding of the genetic diversity and origin of sweet chestnut stands outside their natural distribution in MWP. It provides valuable knowledge for the evaluation and conservation of genetic resources of this tree species, which is expected to receive more attention under warmer and drier conditions.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00202024-01-27T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2023-0019<abstract> <title style='display:none'>Abstract</title> <p>Forest trees cultivars developed by breeders have been increasingly deployed as clones, following long generations of breeding and testing. An established protocol for distinctiveness, uniformity and stability (DUS) testing becomes an essential element for protecting the intellectual property rights associated with these clones. DUS testing with morphological descriptors has, however, shown limitations in categorically distinguishing cultivars, especially with narrow genetic base. DNA fingerprinting based on microsatellite markers has been a powerful tool to discriminate clones. Teak (<italic>Tectona grandis</italic>) is an economically valuable exotic timber species planted in Brazil. We assessed the individual and combined performance of a selected set of 21 teak microsatellites for identity analysis and parentage testing in a sample of 50 clones planted in Brazil. The clones displayed high genetic diversity attributable to their wide provenance origin. The 21 microsatellites combined provide high power of individual identification with a combined probability of identity of 1.84E-23 for unrelated individuals, and 4.82E-09 for full-sibs, and a power of paternity exclusion higher than 99.99999 % in all testing scenarios. Variable subsets of these 21 markers still provide abundant power of discrimination, although a recommended set should include a minimum of 12 markers with higher information content and reliable genotyping performance. Relatedness and genetic distance analyses revealed unexpected identities or significant recent shared ancestry among otherwise considered unique clones. These results advocate for the importance of including DNA markers, at least as discretionary complementary descriptors to the 22 morphological traits currently adopted for plant variety protection of teak cultivars in Brazil.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00192023-11-01T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2023-0018<abstract> <title style='display:none'>Abstract</title> <p>Suitable selection of endogenous controls is necessity for obtaining reliable qRT-PCR results. However, insufficient attention has been paid to the selection of endogenous controls for normalization in different stresses in plant, especially <italic>Larix olgensis</italic>. In this study, we screened candidate internal reference genes for miRNA expression normalization after subjecting <italic>Larix olgensis</italic> PEG-induced drought, NaHCO₃, or NaCl stress. Needles samples were collected at 0, 12, 24, 48 and 96 h after treatment. Four common housekeeping genes and 11 mature miRNAs that were found to be stably expressed in small RNA sequencing data of <italic>Larix olgensis</italic> were selected as candidate internal reference genes. Their expression levels were assessed by qRT-PCR. GeNorm and NormFinder were used to analyse the stability of gene expression from the candidate internal reference genes. Finally, the expression of some miRNAs was analysed after stress. The results showed that miRNAs exhibited better expression stability compared to the analysed ncRNAs. Under PEG, NaHCO₃, or NaCl stress, miR83321, miR43169, and miR74940 were identified as the most suitable internal reference genes, respectively. Under PEG stress, the expression of most miRNAs reached its highest level at 12 h, showing a trend of first increasing expression and then decreasing. Similarly, under NaHCO₃ and NaCl stress, the expression of most miRNAs reached its maximum levels at 48 h and 12 h, respectively. This indicates that most miRNAs more quickly respond to PEG and NaCl stress than NaHCO₃ stress.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00182023-10-28T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2023-0017<abstract><title style='display:none'>Abstract</title> <p>Molecular responses to drought stress have been mainly studied in deciduous tree species although conifers dominate boreal forests. Here, we analysed the transcriptional response of <italic>Picea abies </italic>(L.) H. Karst. needles after exposure to severe drought by quantitative RNA-sequencing. In total, 2,402 differentially expressed genes (DEGs) were identified, of which 1,186 were up- and 1,216 downregulated. The upregulated DEGs are mainly involved in responses to stress, nitrogen compound, water deprivation, and abscisic acid as well as in channel activity. Although only one bZIP was identified among the DEGs, several other transcription factors involved in ABA-dependent pathways such as MYB, bHLH and WRKY showed differential expression. AP2/EREBP transcription factors related to ABA-independent pathways were also identified as DEGs. A functional interaction network of the 40 most connected <italic>Arabidopsis thaliana </italic>homologs of all <italic>Picea abies </italic>DEGs placed the two top-hubs P5CS1 and P5CS2 in the center. P5CS1 is the key enzyme in the biosynthesis of proline known to be accumulated in plants under abiotic stress. Lignin synthesis and DNA-related processes, among others, are overrepresented in this network. Our data highlight interesting gene targets for functional studies and natural genetic variation analyses to support the future identification and selection of potential drought tolerant trees.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00172023-10-26T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2023-0016<abstract> <title style='display:none'>Abstract</title> <p>The breeding of a fast-growing tree species, <italic>Acacia mangium</italic> Willd. has entered the third-generation cycle in Indonesia. To fulfill timber industry needs, wood traits, as well as growth traits, should be improved by conducting appropriate tree breeding programs for this species. In the present study, growth and wood traits were measured for the 10-year-old third-generation <italic>A. mangium</italic> from 40 half-sib families originating from four sub-lines from two provenances. The mean values of ten families in each sub-line ranged from 17.7 to 21.8 cm for stem diameter, 14.3 to 16.2 m for tree height, 3.60 to 3.77 km/s for stress-wave velocity, and 19.9 to 20.9 mm for Pilodyn penetration, respectively. The broad-sense heritability values in each sub-line ranged from 0.014 to 0.444 for stem diameter, 0.000 to 0.208 for tree height, 0.261 to 0.715 for stress-wave velocity, and 0.171 to 0.484 for Pilodyn penetration, respectively. These results suggested that families with higher density and Young’s modulus of wood, suitable for solid wood production, can be selected from the third-generation <italic>A. mangium</italic>. Stem diameter significantly correlated with the other three measured traits, while phenotypic correlation coefficients between stem diameter and stress-wave velocity or Pilodyn penetration were very low. In addition, no significant phenotypic correlations were found between other measured traits. Furthermore, positive- or non-significant genetic correlations were found between growth and wood traits in all sub-lines. Thus, it is concluded that the selection of families with good growth characteristics will not always reduce the wood properties of this species.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00162023-10-18T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2023-0015<abstract> <title style='display:none'>Abstract</title> <p>Mangroves, unique tree and shrub species inhabiting coastal saline environments, exhibit distinctive ecological and morpho-physiological traits, including forming pure intertidal stands and possessing specialized mechanisms for salt excretion and aerial root respiration. These species produce valuable antioxidants, such as phenols and tannins, with significant pharmacological, ecological, and toxicological implications. This study aimed to develop a highly efficient DNA extraction protocol for mangrove leaves rich in salt and tannins. The commonly used CTAB extraction protocol and a commercial DNA extraction kit were modified to enhance DNA purity and yield. The antioxidant capacity of the samples was assessed using various protocols. The results demonstrated that the modified commercial kit outperformed other methods in extracting DNA from mangrove leaves, effectively overcoming challenges associated with high salt and phenolic compounds that could impede next-generation sequencing (NGS) analysis. Furthermore, the findings revealed an inverse relationship between tannin concentration and DNA extraction yield. This study offers a valuable resource for DNA extraction protocols from tannin-rich plant materials. In conclusion, the modified commercial kit represents the most efficient and effective approach for extracting DNA from tannin-rich mangrove leaves.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00152023-09-21T00:00:00.000+00:00https://sciendo.com/article/10.2478/sg-2023-0014<abstract> <title style='display:none'>Abstract</title> <p>This study analyzes the diversity and genetic structure of seven natural populations of <italic>Magnolia mexicana</italic> (Yoloxóchitl), an endangered and endemic species distributed in the Mexican Sierra Madre Oriental. The objective of the analysis is to generate basic information for the development of management and conservation programs for this species. The variation and genetic structure were estimated based on 12 SSR markers. The results indicate that the expected heterozygosity was 0.63±0.02 and the allelic richness was 1.21±0.05. The analysis of molecular variance (AMOVA) showed that variation between individuals explains 49 % of the total variation, and variation within individuals explains 36 %. The technical Neighbor joining and the ordination diagram of the canonical discriminant analysis show that the populations are made up of two genetic groups mostly. By contrast with the model Bayesian grouping (obtained with the STRUCTURE program) indicated the formation the six genetics groups. Recent bottleneck effects were observed in all localities, except in Duraznillo, El Cajón, and Zapotla. The relationship between genetic and geographic distances was not significant, which rules out a structure determined by isolation; the results suggest that the diversity and genetic structure of the species are affected by local factors such as habitat fragmentation, land use change, and excessive use of the flowers and fruits of <italic>M. mexicana</italic> by the inhabitants. Therefore, it is a priority to implement management and conservation programs to guarantee their survival.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00142023-08-02T00:00:00.000+00:00en-us-1