rss_2.0Silvae Genetica FeedSciendo RSS Feed for Silvae Geneticahttps://sciendo.com/journal/SGhttps://www.sciendo.comSilvae Genetica Feedhttps://sciendo-parsed.s3.eu-central-1.amazonaws.com/647376194e662f30ba53f282/cover-image.jpghttps://sciendo.com/journal/SG140216Identification of three large full-sib families of for genetic mapping in an isolated planting outside the species’ range in Germanyhttps://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 F<sub>1</sub> 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+00:00Genetic parameters and correlations in growth and wood density traits of based on provenance and progeny testinghttps://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><sub>g</sub>) was higher (4.0–5.4 %) and mean family heritability (<italic>h</italic><sub>m</sub><sup>2</sup>) was lower for growth (0.12–0.20) compared to wood density (<italic>CV</italic><sub>g</sub>: 2.3–3.8%, <italic>h</italic><sub>m</sub><sup>2</sup>: 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+00:00Genetic diversity and fine-scale genetic structure of the conifer in a forest-grassland mosaic from Southern Brazilhttps://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+00:00Diallel crosses in V. Can early testing predict long-term performance?https://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+00:00Structure, diversity, and genetic delimitation of two species endemic to eastern Mexicohttps://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+00:00Age trends of genetic variation and early selection for growth traits in open-pollinated familieshttps://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+00:00Genomic predictions and candidate single nucleotide polymorphisms for growth, form, and wood properties of teak cloneshttps://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+00:00Variation in the amount of pollen per male flower on https://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+00:00Patterns of genetic variation and the potential origin of sweet chestnut ( Mill.) stands far from its natural northern distribution edgehttps://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+00:00Microssatellite markers for plant variety protection of clonally propagated forest trees: a case study in teak ( L.f.)https://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+00:00Selection of suitable reference genes for miRNA expression normalization by quantitative RTPCR under abiotic stress in https://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, NaHCO<sub>3</sub>, 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, NaHCO<sub>3</sub>, 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 NaHCO<sub>3</sub> 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 NaHCO<sub>3</sub> stress.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00182023-10-28T00:00:00.000+00:00Drought stress-induced transcriptome changes in the context of functional interactionshttps://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+00:00Variations of growth and wood traits in standing trees of the third-generation families in Indonesiahttps://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+00:00Genomic DNA extraction and phenolic content of salty and tannic plant material of two mangrove tree species from the mexican pacific coasthttps://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+00:00Genetic diversity and structure of (Magnoliacea): A threatened species in eastern Mexicohttps://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+00:00 – a computer program to test genomic tools in breeding programshttps://sciendo.com/article/10.2478/sg-2023-0013<abstract> <title style='display:none'>Abstract</title> <p><italic>SNPscan breeder</italic> is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of a trait of interest, different mating designs and different selection criteria, i.e. pheno-types, breeding values from progeny tests, marker-assisted selection (MAS) and genomic selection (GS). The impact of breeding population size, mating design, selection intensity, genetic architecture, heritability and selection criteria on genetic gains, kinship, inbreeding and genetic diversity can be evaluated to optimize the breeding program. A special feature is the possibility for post-hoc analysis of different strategies to identify causal SNPs and allele effects within the frame of genome-wide association studies (GWAS). The proportion of true and false positive SNPs and the correlation of estimated and true allelic effects can be measured and the overall impact of their use for MAS on the success of the breeding program can be tested.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00132023-07-16T00:00:00.000+00:00An efficient repeat masking library for the genomic data of coconut and related treeshttps://sciendo.com/article/10.2478/sg-2023-0011<abstract> <title style='display:none'>Abstract</title> <p>Even though repeat masking using custom designed libraries significantly improves the genome annotation and gene prediction, such libraries for palm trees are yet to be designed and made accessible to the researchers. In this study, a repeat library was designed and validated for use in coconut and related palm genomes. Coconut genome with chromosome-level assembly was used to design independent libraries for tall and dwarf ecotypes, which were subsequently merged. Efficiency of the combined <italic>de novo</italic> library in genome annotation and gene prediction was assessed in comparison with the conventional libraries (Dfam+RepBase), using RepeatMasker. <italic>De novo</italic> library had 76.3 % efficiency in coconut genomes compared to 3.51 % in custom libraries and number of genes predicted was reduced from an average of 193,099 to 31,022. In date palm, oil pam and sago palm also, combined library gave higher repeat masking and reduced the number of genes predicted. The <italic>de novo</italic> library can be accessed at <ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.kau.in/repeat-libraries">http://www.kau.in/repeat-libraries</ext-link>.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00112023-07-16T00:00:00.000+00:00SNPs Detection and Genetic Analysis of via Genotyping-by-Sequencinghttps://sciendo.com/article/10.2478/sg-2023-0012<abstract> <title style='display:none'>Abstract</title> <p><italic>Chionanthus retusus</italic> is one of the well-known ornamental trees in East Asia and America. Not only its value in the market but also had the potential as a source for producing antioxidant. However, due to uncontrolled exploitation, the number of wild <italic>C. retusus</italic> in China is decreasing rapidly. The genetic study of <italic>C. retusus</italic> is limited. In order to investigate the genetic diversity and the distribution of <italic>C. retusus</italic> in China, 47 samples from 8 different provinces have been sequenced via restriction site-associated DNA sequencing (RAD-seq). Totally, 31, 402 high-quality single nucleotide polymorphisms (SNP) were obtained. According to the phylogenetic tree and the principal component analysis, the samples were divided into four populations, including 3 major populations and 1 hybrid population. Population1 were the samples from Jiangsu and Yunnan province and the Population2 were mainly from northern and northeast of China including Liaoning and Hubei province, while the Population4 were from Shandong and Henan province, which were in central China. As the admixture showed, the population3 were the offspring of the other 3 populations by hybridization. The mean heterozygosity of Chinese Fringe tree from different province is 0.42 %, with the highest heterozygosity, which is as high as 0.63 %, from Jiangsu province and the lowest heterozygosity, which is only 0.19, from Henan province. This is the first report about the genetic diversity and relationship of <italic>Chionanthus retusus</italic>, which will provide value information for further genetic study, genomic study, conservation and breeding.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00122023-07-16T00:00:00.000+00:00Clonal fertility and heritability in strobilus production, and gene diversity of seed crops in a second-generation seed orchard of https://sciendo.com/article/10.2478/sg-2023-0010<abstract> <title style='display:none'>Abstract</title> <p>Variation of female and male strobilus production among clones over 4 consecutive years was estimated, and genetic variance, heritability, and genetic correlation in strobilus production were investigated in the second-generation seed orchard of <italic>Pinus thunbergii</italic>. This seed orchard was created with grafts selected according to the volume growth of their offspring. The production of female strobili continued to increase, whereas the production of male strobili fluctuated throughout the investigated period. The number of female strobili was highest in rich cone years, but the production of male strobili was not the same in rich or poor years. The maleness index showed a balance between female and male parents that occurred when male strobilus production was in rich or poor years. The parental balance curve for female strobilus production was closer to the expectation (i.e., more equal contribution) than that for male strobilus production in all years. The analysis of variance revealed significant differences among clones in female and male strobilus production over the four-year period. The narrow-sense heritability was higher in male strobilus production than female strobilus, implying that male strobilus production was under genetic control. The Pearson’s correlation was positive and mostly significant, indicating that female strobilus production was reflected in male strobilus production. The effective parent number was lowest in moderate and good years for cone production. The loss of gene diversity in seed crops was lower than expected based on clonal fertility variation.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00102023-07-15T00:00:00.000+00:00Genetic diversity and mating system of in three localities along the lower Solimões River in Central Amazoniahttps://sciendo.com/article/10.2478/sg-2023-0008<abstract> <title style='display:none'>Abstract</title> <p><italic>Euterpe precatoria</italic> is a Neotropical palm from South and Central America and is hyperdominant in Amazonia, where it is increasingly important in the Brazilian market for açaí. Genetic diversity, population structure and mating system of <italic>E. precatoria</italic> were characterized with 10 microsatellite markers in three localities (Codajás, Manacapuru, and Manaquiri) along the lower Solimões River, Amazonas, Brazil. Leaves of 63 mature palms were collected, as well as fruits from 30 of these to analyze 20 seedlings per progeny. Genetic differentiation across localities was substantial (<italic>G</italic><sub>S</sub><sup>′</sup> = 0.304) for mature palms, suggesting that gene flow is restricted between localities due to isolation by distance. Inbreeding was significant in progenies from all populations (ranging from 0.059–0.076), but not for mature palms, suggesting selection for heterozygosity during maturation to the adult stage. The outcrossing rate was high (0.917–1.0), confirming that the species is predominantly allogamous. Matings were not random due to the occurrence of biparental inbreeding (0.021–0.079) and correlated matings (0.059–0.424), so open-pollinated progenies present mixtures of self-sibs, half-sibs, full-sibs, and self-half-sibs, resulting in mean effective population size within progenies (2.23–3.06) lower than expected for a random mating population. The mating system’s characteristics are those expected in a predominantly allogamous hyper-abundant palm and suggest that human management of these often-anthropogenic populations is unlikely to reduce genetic diversity in the short term if done <italic>in situ</italic>, as practiced by Indigenous Peoples and local communities. Intensification will require careful attention to maintain genetic diversity.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.2478/sg-2023-00082023-07-11T00:00:00.000+00:00en-us-1