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Abies koreana E.H.Wilson (Korean fir), an endangered high-altitude conifer native to South Korea, is facing severe population decline due to climate change and low germination rates. While ecological factors have been studied, the genetic and epigenetic mechanisms underlying its seed development are still poorly understood. DNA methylation, regulated by MET1 and CMT2, plays a critical role in the stability of gene expression during seed development. This study investigates the expression patterns of MET1 and CMT2 across 12 developmental stages, from pre-germination to post-germination, with a focus on shoot and root tissues. RNA-seq data were analyzed to identify MET1 and CMT2, and expression patterns were validated using RT-qPCR. MET1 showed high sequence conservation with conifers such as Pinus sylvestris, indicating potential conservation of CG methylation mechanisms among conifer species. CMT2 showed lower sequence conservation across species, indicating reduced evolutionary conservation compared to MET1. Tissue-specific analysis showed MET1 being predominantly active in shoots during cotyledon development, while CMT2 was upregulated in roots at later stages. These findings highlight the dynamic and tissue-specific roles of DNA methylation in the seed development of A. koreana, contributing to a better understanding of the genetic and epigenetic mechanisms involved in its germination and early growth.

We used hyperspectral analysis to distinguish between acorns of Japanese red oak (Quercus acuta Thunb.) and ring-cup oak (Quercus glauca Thunb.), two closely related species of the evergreen oaks. To accomplish this, 631 Japanese red oak acorns and 505 ring-cupped oak acorns were collected from the seed orchard in Jeju Island, Korea, and hyperspectral imaging was performed. Two types of hyperspectral devices, Corning and Korea Spectral Products (KSP), were used to calibrate images and extract regions of interest. Average spectra were obtained from the extracted regions of interest, and morphological variables were added to the Corning data to form a dataset. Partial least square (PLS) was used as the learning model, Standard normal variate, Multiplicative scatter correction, and Savitzky-Golay filtering were applied as preprocessing techniques, and competitive adaptive reweighted sampling and successive projection algorithm were applied as variable selection techniques ; and the combination of preprocessing method, the number of PLS components, and the number of selected variables were optimized.. The lightweight model was generated from the selected variables, and the performance was improved by combining the morphological variables. As a result, the lightweight model based on Corning dataset showed 45~85% accuracy, and the lightweight model based on the KSP dataset showed 75~90% accuracy. The model utilizing morphological variables in the Corning-based lightweight model showed a high accuracy of 98-100%, so we were able to discriminate the acorns of evergreen oaks between Q. acuta and Q. glauca. The results of this study are expected to serve as a basis for future model development for seed classification of hybrid oak acorns.

Chamaecyparis obtusa (Siebold & Zucc.) Endl., commonly known as Japanese cypress or hinoki cypress, is widely cultivated for its high-quality timber and ornamental use. Despite its economic and ecological importance, the species faces challenges in adapting to various climates, necessitating the distribution of high-quality seeds and seedlings. This study aims to enhance the genetic improvement and stability of seed production by analyzing fertility characteristics and genetic traits from two clonal seed orchards of C. obtusa in two locations (Gochang and Seogwipo), South Korea. We examined patterns of strobilus and cone production from 2020 to 2022, assessed effective parent numbers, genetic diversity, and heritability estimates, and analyzed parental contribution for the reproductive traits. Results indicated significant annual variation in strobilus and cone production among clones, with higher male fertility variance than female parents. The effective parent number and genetic diversity were generally maintained sustainably, though Seogwipo showed slightly lower diversity. The study underscores the need for management practices to balance clonal contributions, and sustain long-term productivity and genetic diversity in the seed orchards of C. obtusa. Future research should focus on understanding environmental influences on clonal contributions and refining selection criteria for superior clones in the advanced generation breeding program.

Fertility variation, defined as a difference in the ability to create progeny (i.e., reproductive success) among individuals, was reviewed using the related available theoretical and practical literature in an attempt to contribute to and improve future studies on the subject. Fertility variation is a useful guide for various purposes such as gene conservation, seed production programs, forest genetic resource (i.e., seed sources) management, other forestry practices (e.g., regeneration), and evolutional and physiological studies. Many papers and proceedings have been published, including both theoretical and practical approaches, on how fertility variation has improved in the last two decades. Large variations in fertility were widely reported among populations within species and among species. We reviewed the literature and combined our diverse knowledge to examine fertility variations and their linkage parameters. Fertility variations and their related parameters (e.g., gene diversity, status number, effective parent number, parental–balance curves) estimated based on reproductive characteristics have been studied for many years using easy and cheap surveys that are used for different purposes in forest sciences. Their importance is increasing and their use is becoming more widespread because of these advantages, leading to improvements in research papers. While many research papers have recently been published on fertility variations and linkage parameters, a review paper has not been published to date. Therefore, a review paper is needed based on a literature survey and unpublished experience, as a guide for future studies.

This research examines the impact of varied acorn yields on the effective population size of Turkey oak (Quercus cerris L.) as assessed through the fertility averages of zygotic parents. We selected two distinct populations from the species’ natural habitats based on their good and poor acorn production rates to investigate acorn production, growth attributes, and their interrelationships over three years of production and two years of growth data. Results showed that the population with good acorn production exhibited greater growth attributes and acorn yields compared to the poor acorn production population. Acorn production had lower coefficients of variation compared to growth attributes. Fertility variation in both populations was moderate, with a decrease in the effective number of parents from the population with abundant acorn production to the one with limited acorn production. The presence of mixed seeds from diverse populations had a detrimental impact on fertility variation and related metrics. Nonetheless, this study suggests that regions with limited acorn production still have the potential for natural regeneration due to their larger effective population size when coupled with appropriate forestry practices such as selective acorn harvesting to enhance genetic diversity. These findings emphasize the importance of accounting for fertility variation in the selection and management of seed sources, even within the context of a limited area and three years of data. Further research should be conducted in larger populations and over longer periods to draw more comprehensive conclusions.

This study aimed to test near-infrared spectroscopy to assess insect damage to oak acorns collected from a seed orchard of 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<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.

The purpose of the study is to investigate long-term changes on lymphoscintigraphy and their association with clinical factors in breast cancer-related lymphedema (BCRL) patients. This single-center cohort study included BCRL patients who underwent baseline and follow-up lymphoscintigraphy. The percentage of excessive circumference (PEC) of the affected upper limb compared with the unaffected side was used as an indicator of the clinical severity of BCRL. Each 99m Tc-phytate lymphoscintigraphy image was categorized according to the Taiwan lymphoscintigraphy staging system. Clinical parameters and the lymphoscintigraphy stage at baseline and follow-up were compared and analyzed. Eighty-seven patients were included. Baseline and follow-up lymphoscintigraphies were performed at median 7 (interquartile range [IQR]: 2‒14) and 78 (IQR: 49‒116) months after surgery, respectively. Both lymphoscintigraphy stage and PEC showed variable change with overall increases in their severity. Stepwise multivariable analysis revealed follow-up lymphoscintigraphy stage ( P  = 0.001) to be independent variables for PEC at follow-up, however, baseline lymphoscintigraphy stage was not. The clinical courses of BCRL and patients’ lymphoscintigraphy patterns showed diverse changes over long-term follow-up. In addition to initial lymphoscintigraphy for diagnosis, lymphatic remapping by follow-up lymphoscintigraphy can be useful to visualize functional changes in the lymphatic system that may guide the optimal management in BCRL.

Background Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results We report two high-quality de novo genomes ( Capsicum baccatum and C. chinense ) and an improved reference genome ( C. annuum ) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum . In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Transposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.