Search Results (575)

Terpenes are major determinants of tea aroma, and terpene synthases (TPSs) catalyze key steps in terpenoid biosynthesis. To capture gene-family variation beyond a single reference, we performed a pan-genome–based analysis of TPS genes across nine Camellia genomes (three wild tea relatives and six cultivated Camellia sinensis accessions) and integrated pan-transcriptome profiling across eight tissues. We identified 381 TPS genes; wild species contained more TPSs than cultivated accessions (mean 58.3 vs. 34.3), suggesting a putative contraction. Phylogenetic analysis with Arabidopsis TPSs classified Camellia TPSs into five subfamilies, dominated by TPS-b (149) and TPS-a (140), whereas TPS-c was rare (8). Gene-structure and physicochemical analyses revealed marked subfamily divergence, with TPS-c showing highly conserved coding-region length. Orthology clustering assigned 355 TPSs to 19 orthogroups, including five core groups (190 genes, 53.5%) and 14 dispensable groups (165 genes, 46.5%); core/non-core status was significantly associated with subfamily composition. Tandem and proximal duplication contributed most to TPS expansion (29.4% and 29.1%), and all orthogroups exhibited copy-number variation, with pronounced lineage-specific expansions. Ka/Ks analyses indicated pervasive purifying selection (median 0.516) but heterogeneous constraints among subfamilies. Finally, cultivated tea showed higher TPS expression in most tissues, especially mature leaf and stem, and TPS-g displayed the broadest and strongest expression. Together, these results provide a pan-genome resource for Camellia TPSs and highlight how domestication, duplication, and CNV shape terpene-related genetic diversity. Full article

PIN-LIKES (PILS) auxin transport genes play key roles in plant development, but their functions and molecular mechanism in soybean yield remain unclear. Here, we characterized the 44-member soybean GmPILS genes via comprehensive analyses. Phylogenetic analysis classified GmPILS into three subfamilies, with most proteins being hydrophobic, stable, and membrane-localized. Chromosomal distribution showed random scattering across 17 chromosomes, with gene duplication driving family expansion. Expression profiling identified GmPILS36 and GmPILS40 as seed-specific and differentially expressed between cultivated Suinong14 (SN14) and wild ZYD00006 (ZYD06) soybeans. Population genetic analyses revealed GmPILS40 experienced a domestication bottleneck without yield-related superior haplotypes, while GmPILS36 underwent selection during landrace-to-improved variety domestication. A coding region CC/TT natural variation in GmPILS36 (S/A substitution) was significantly associated with seed weight per plant and 100-seed weight, with the TT genotype conferring superior traits. This study provides insights into GmPILS genes’ evolution and identifies GmPILS36 as an important candidate gene for further functional study and investigation of the molecular mechanisms regulating soybean yield. Full article

Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is a fast-growing species widely utilized in construction, industrial raw materials. Owing to its broad application scope, research on Chinese fir is fragmented across multiple disciplines, making it difficult to grasp the overall research context and trends. Following the PRISMA guidelines, we retrieved articles related to Chinese fir published between 1942 and 2024 from Chinese databases (i.e., CNKI, Wanfang Data, and VIP Chinese Journal Database) and the Web of Science Core Collection (WOSCC). After removing duplicate and irrelevant records, a total of 7174 valid records were retained, including 5862 from Chinese databases and 1312 from WOSCC. The PRISMA-screened literature was imported into CiteSpace V.6.2.R4 for bibliometric analysis. Through keyword clustering, burst detection, and timeline mapping, we focused on analyzing the domestic resource distribution, research hotspots, and evolutionary trends of Chinese fir research. The results showed that research publications on Chinese fir have increased year by year, and international research started earlier and is more in-depth, while Chinese research covers a wider scope. Both follow two stages (germination and growth). Chinese research focuses on basic application areas such as seedling cultivation and plantation management; international research emphasizes ecological functions and biomass development. Global research exhibits convergence in the field of eco-environmental interactions; specifically, both domestic and international studies investigate the impacts of climate change (e.g., drought and global warming) and nitrogen deposition on the growth and functional evolution of Chinese fir. This study provides references for researchers, forestry policymakers, and planters. Full article

Sugar beet, one of the most important natural sources of sugars in the world, is well known as a recalcitrant crop for genetic transformation. In the present study, several key components of Agrobacterium-mediated transformation of sugar beet have been studied. The correct choice of explant and plant regeneration potential of domestic breeding lines was evaluated; however, most attention was paid to the search for the most efficient selectable marker gene and selection agents. To produce transgenic plants, we applied a method based on the agrobacterial inoculation of wounded morphogenic structures previously initiated on in vitro cultivated leaves. Four selective marker genes conferring antibiotic or herbicide resistance were evaluated. In the case of selection using kanamycin or G418 (nptII gene controlled by the nos promoter), no transgenic plants were obtained, while the addition of the aminoglycoside antibiotic hygromycin (hpt gene, driven by the nos promoter) to the medium ensured the successful production of transgenic plants from three breeding lines with a frequency ranging from 1.5 to 5.1%. The selection of transgenic tissues using herbicides such as phosphinothricin and glyphosate after transformation with the bar and cp4-epsps genes (both controlled by the CaMV 35S promoter) also ensured the obtaining of transgenic plants, but the transformation efficiency was significantly low, reaching only 1.0 and 0.4%, respectively. Primary transgenic sugar beet plants grown in the greenhouse demonstrated enhanced resistance to herbicides in dosages commonly used in the field. In addition, after self-pollination of the primary T0 transgenic lines, homozygous T2 offspring were successfully selected, which demonstrated stable resistance to glyphosate due to the constitutive expression of the introduced cp4-epsps gene. Full article

European plum (Prunus domestica L.) is widely cultivated worldwide, with China producing 6.8 million t annually (55% of the global total output). However, the Kashgar region of Xinjiang, China’s primary production area, has experienced outbreaks of brown spot disease caused by Alternaria alternata (Fr.) Keissl. Outbreaks of this disease severely hinder both domestic and global development of the European plum industry. Because this pathogen has a strong latent infection capability during the early stages of disease development, its early detection is important. We develop two detection methods targeting the ITS sequence of A. alternata: LAMP-Cresol Red chromogenic visible endpoint detection and LAMP-SYBR Green I real-time fluorescent detection. Both methods demonstrate high specificity for A. alternata, enabling stable detection of the pathogen in various plant samples; detection limits reach the femtogram (fg) level, significantly surpassing conventional PCR detection capabilities. Development of these highly efficient and precise early detection methods provides a solid foundation for sustainable development of China as a global hub of the European plum industry, and contributes significantly to global disease prevention, control, and industrial stability for this crop. Full article

Annual wild soybean, the ancestor of cultivated soybean, underwent a significant increase in seed oil content during domestication. To elucidate the genetic basis of this change, a chromosome segment substitution line population (177 lines) constructed with cultivated soybean NN1138-2 as recipient and wild soybean N24852 as donor was used in this study. Phenotypic evaluation across three distinct environments led to the identification of two major QTL/segments, qOC14 on chromosome 14 and qOC20 on chromosome 20, which collectively explained 39.46% of the phenotypic variation, with individual contributions of 17.87% and 21.59%, respectively. Both wild alleles exhibited negative additive effects, with values of −0.35% and −0.42%, respectively, consistent with the inherently low oil content of wild soybeans. Leveraging transcriptome and genome data from the two parents, two candidate genes were predicted. Notably, Glyma.14G179800 is a novel candidate gene encoding a PHD-type zinc finger domain-containing protein, and the hap-A haplotype exhibits a positive effect on oil content. In contrast, Glyma.20G085100 is a reported POWR1 gene, known to regulate protein and oil content. Our findings not only validate the role of known gene but, more importantly, unveil a new candidate gene, offering valuable genetic resources and theoretical targets for molecular breeding of high-oil soybean. Full article

Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato. Full article

Pesticides have been extensively used in agriculture, forestry, and veterinary medicine under intensive production systems. Unfortunately, pesticide pollution resulted in a significant decline in non-target organisms, for instance, in detritivores such as necrophagous insects. Even formulations proposed as less harmful alternatives, such as neonicotinoids like imidacloprid (IMI), have been demonstrated to permeate the trophic chain and trigger severe consequences on non-target species. Here, the intra- and inter-generational effects of a sublethal dose of IMI were explored in the necrophagous greenbottle fly, Lucilia sericata (Meigen, 1826) (Diptera: Calliphoridae). This is because it has been demonstrated that the carcasses of domestic and wild animals can be contaminated with levels of these neonicotinoids. Transgenerational effects, extending up to three generations after a focal application of the pesticide on laboratory-cultivated F₁ flies, were investigated in this study. Morphological, demographic, and phenological features were evaluated through various analyses, including general linear mixed models (GLMM) and Haldane units analyses. Although GLMM showed no significant differences between treatments for the multiple traits observed, a significant directional microevolutionary trend of increased average imago and pupal size was identified for the IMI treatment through Haldane unit analysis. This microevolutionary change falls within the threshold of transgenerational phenotypic plasticity, a crucial mechanism for adaptive responses to environmental stressors. Among the possible explanations for this pattern, it is proposed that this is a likely consequence of the triggering of an epigenetic hormetic transgenerational change. This may contribute to explaining the development of adaptation and resistance towards pesticide formulations in a few generations after focal exposure. In addition to this idea, other possible mechanisms and consequences that explain the observed pattern are discussed. Overall, this experiment highlights the concerns of pesticide spillover consequences, even from sublethal doses of these formulations. Full article

Background: Chili pepper (Capsicum annuum L.), a globally cultivated and ancient domesticated crop, carries considerable significance in agriculture. While radiation-induced mutagenesis has found application in this crop, the mutagenic efficacy and molecular-level impacts of 7Li ion beam radiation remain poorly elucidated. Methods: We irradiated pepper with a beam of 7Li ions to create a mutant, which showed good economic traits, and phenotypic and physio-biochemical characterization were combined with proteomic and metabolomic profiling to delineate the mutagenic mechanisms. Quantitative real-time PCR (qRT-PCR) was further utilized to assess the biological impact and underlying response pathways. We used this to evaluate the biological impact and the reaction mechanisms behind it. Results: 7Li beam radiation positively influenced morphology and physiological traits, notably chlorophyll and anthocyanin content. Leveraging proteomic profiling detected 6082 proteins, including 355 differential proteins (139 upregulated, 216 downregulated), enriched in 4 KEGG pathways. Based on GO and KEGG network analysis, 250 metabolites were quantified, with 120 being differentially abundant (112 upregulated, 8 downregulated), enriched in 9 metabolic pathways. Furthermore, qRT-PCR results revealed that differentially expressed genes were consistent with the corresponding metabolomic data. Joint analysis revealed the coordinated enrichment of differential metabolites and proteins in pathways related to amino acid and carbohydrate metabolism. These findings suggest that these active pathways in pepper are related to its response to ion beam radiation. Overall, this study is a valuable resource for subsequent genomic research on peppers and 7Li ion beam radiation research. Full article

Background/Objectives: Identifying archaeobotanical wheat remains is central to reconstructing the evolutionary history of cereal crops. Beyond documenting agricultural practices, such analyses provide critical evidence of phylogenetic diversity, lineage persistence, and local extinction events within the genus Triticum L. This study applies advanced computational morphometrics to reveal deep-time changes in wheat species distribution, including the disappearance of taxa now phylogeographically confined to central Asia. Methods: We developed a machine learning framework integrating Random Forest compared with logistic regression to classify morphometric data from 848 dry and 340 experimentally carbonized modern grains representing multiple wheat taxa (genus Triticum), alongside 15 archaeobotanical T. turgidum subsp. parvicoccum and 38 T. aestivum var. antiquorum. This probabilistic classifier was then applied to 2463 archeological wheat grains, including 48 from Punta de los Gavilanes and 517 from Almizaraque (southeastern Spain, 3rd–2nd millennium BC). Results: The analysis identified Triticum sphaerococcum and other phylogenetically distinct wheat taxa—today restricted to central and south Asia—among western European Bronze Age assemblages. These findings indicate that lineages now regionally extinct once formed part of a broader cultivated gene pool spanning into the western Mediterranean. Morphometric evidence highlights that past wheat diversity encompassed multiple clades and morphotypes absent from modern European germplasm. Conclusions: Our results demonstrate substantial phylogenetic turnover in wheat over the past 4000 years, marked by regional extirpations and contraction of once-widespread lineages to central Asia. This provides rare archeological evidence for the tempo and mode of cereal phylogeography, illustrating how domesticated lineages underwent extinction and range restriction akin to wild taxa. By integrating computational morphometrics with archaeobotanical evidence, this study establishes a scalable framework for tracing cryptic phylogenetic diversity, refining models of wheat domestication and assessing long-term genetic erosion in cultivated plants. Full article

This study applies integrated LCA–LCC to 1 L of bottled beer at a representative small Japanese brewery using 2024 operational data. Following ISO 14040/44, the cradle-to-gate boundary covers raw materials (excluding agricultural cultivation while including transport and preprocessing), brewing, packaging, and thermal sterilization. The baseline global warming impact is 0.52 kg CO₂e/L and the cost is JPY 487/L, with single-use glass and labor identified as dominant hotspots. As beer is produced from malt, hops, yeast, and water, this study focuses on how alternative production strategies mitigate sustainability hotspots within this process. Three alternative production scenarios were evaluated within this integrated LCA–LCC model. Scenario 1 (local rice substitution) replaces 30% of the fermentable extract from imported malt with domestically grown rice, changing only ingredient transport and preprocessing within the truncated cradle-to-gate boundary (crop cultivation remains excluded), and yields 0.55 kg CO₂e/L and JPY 492/L, i.e., a slightly higher global warming impact and cost than the baseline. Scenario 2 (direct sales expansion) assumes that 50% of the beer is sold on site via draft, thereby reducing single-use glass bottles and fuel for pasteurization and achieving 0.29 kg CO₂e/L (−44%) and JPY 435/L (−11%) in the deterministic model, the best combined environmental and economic performance among the modeled options. Scenario 3 (joint logistics) models cooperative brewing and shared distribution, which improve labor efficiency and modestly reduce transport intensity, delivering 399 JPY/L in the deterministic model; however, Monte Carlo analysis yields a higher expected cost and indicates that these cost savings are not robust. One-way sensitivity analysis identified packaging and labor as the dominant drivers of both environmental and economic performance, while Monte Carlo simulation confirmed the relative insignificance of electricity-related parameters and reinforced the comparative robustness of Scenario 2. Together, these results highlight the most effective leverage points for a sustainable transition in Japan’s craft beer sector, offering the greatest leverage for a more sustainable transition in Japan’s craft brewing sector. Full article

Substrate composition plays a vital role in the soilless cultivation of Helleborus; high-quality substrates can create optimal growth conditions and enhance plant quality. However, knowledge regarding suitable substrates for Helleborus remains limited. The aim of the study was to test the effects of different substrates on growth of potted Helleborus × hybridus seedlings. In total, 12 treatments were formulated by mixing organic components (moss peat, cocopeat, domestic peat) with inorganic particles (perlite, kanuma soil, vermiculite) at a 1:1 ratio, using moss peat moss as the control. The results indicated that substrates of moss peat + vermiculite (1:1) and cocopeat + vermiculite (1:1) significantly promoted plant height, shoot number, leaf number, and root development. The treatment with domestic peat + perlite + kanuma soil + vermiculite (3:1:1:1) yielded the highest soluble protein content, whereas the CK group showed the highest soluble sugar content. A comprehensive evaluation by Principal Component Analysis (PCA) identified moss peat + vermiculite (1:1) as the optimal substrate, followed by coir + vermiculite (1:1). Considering economic costs and environmental protection factors, the cocopeat + vermiculite (1:1) mixture demonstrated superior potential. Collectively, our study clarifies the effects of different substrate compositions and provides new insights for achieving cleaner and more efficient soilless cultivation of Helleborus. Full article

Agrivoltaic (APV) systems co-locate agricultural production and photovoltaic (PV) electricity generation on the same land to maximize land use efficiency. This study proposes an integrated assessment framework that jointly evaluates crop yield and electricity generation in APV systems. Unlike many previous APV studies that estimated crop responses from empirical PAR–photosynthesis relationships, this framework explicitly couples a process-based rice growth model (DSSAT-CERES-Rice) with irradiance and PV performance simulations (Honeybee-Radiance and PVlib) in a single workflow. The five-stage framework comprises (i) meteorological data acquisition and processing; (ii) 3D modeling in Rhinoceros; (iii) calculation of module front and rear irradiance and crop height irradiance using Honeybee; (iv) crop yield calculation with DSSAT; and (v) electricity generation calculation with PVlib. Using bifacial PV modules under rice cultivation in Gochang, Jeollabuk-do (Republic of Korea), simulations were performed with ground coverage ratio (GCR) and PV array azimuth as key design variables. As GCR increased from 20% to 50%, crop yield reduction (CYR) rose from 12% to 33%, while land equivalent ratio (LER) increased from 128% to 158%. To keep CYR within the domestic guideline of 20% while maximizing land use, designs with GCR ≤ 30% were found to be appropriate. At GCR 30%, CYR of 17–18% and LER of 139–140% were achieved, securing a balance between agricultural productivity and electricity generation. Although PV array azimuth had a limited impact on crop yield and electricity generation, southeast or southwest orientations showed more uniform irradiance distributions over the field than due south. A simple economic assessment was also conducted for the study site to compare total annual net income from rice and PV across GCR scenarios. The proposed framework can be applied to other crops and sites and supports design-stage decisions that jointly consider crop yield, electricity generation, and economic viability. Full article

Seed physical dormancy, also known as hard-seededness, is a characteristic commonly found in higher plants, which functions to prevent water and oxygen from passing through the impermeable seed coat. Background: Notably, seed dormancy has emerged as a critical factor in the domestication of leguminous plants. Alfalfa (Medicago sativa L.) is a globally cultivated high-quality legume forage crop, while the seeds from different varieties maintain varying degrees of hard-seededness. However, the molecular mechanisms underlying physical dormancy in alfalfa seeds remain poorly understood. In particular, the regulatory mechanisms at the transcriptomic level remain unclear, which has hindered the breeding process of varieties with low hard-seededness. Methods: In this study, we performed global transcriptome analysis to discover the genes specifically expressed in the alfalfa seed coat and provide insights into alfalfa seeds’ physical dormancy domestication traits. RNA sequencing was performed on various alfalfa tissues, including roots, stems, leaves, flowers, and seed coats. Results: This analysis led to the identification of 4740 seed coat-specific expressed genes, including key genes such as KNOX4 (a class II KNOTTED-like homeobox gene), qHs1 (encoding endo-1,4-β-glucanase), GmHs1-1 (encoding a calcineurin-like metallophosphoesterase), and KCS12 (β-ketoacyl-CoA synthase). In addition, several seed coat-specific transcription factor families were identified, including ERF, B3, and NAC, among others. Furthermore, a comparison of gene expression profiles between seeds with and without physical dormancy revealed 60 upregulated and 197 downregulated genes associated with physical dormancy. Crucially, functional enrichment analysis demonstrated that these genes are predominantly associated with lipid metabolism pathways, particularly those involved in the formation of “monolayer-surrounding lipid storage bodies.” Conclusions: This key finding suggests that the establishment of physical dormancy is closely linked to the biosynthesis and deposition of specialized lipid-based layers in the seed coat, which likely constitute the primary barrier to water penetration. Our study thus provides fundamental insights and a valuable genetic resource for future functional studies aimed at deciphering and manipulating physical dormancy in alfalfa. Full article

Duolang sheep, a meat–fat dual-purpose breed indigenous to Xinjiang, China, has been cultivated traditionally by the local Uyghur people for its prolificacy and precocious sexual maturity, while little research on the population structure and trait inheritance characteristics of Duolang sheep is available. This study employed whole-genome resequencing data from a cohort of 60 Duolang sheep to dissect their genetic population structure and genes related to reproductive traits. A total of 1565 Gb of high-quality data with an average depth of 14.06× was generated. After SNP calling and quality control, 31,300,060 SNPs were identified. Following linkage disequilibrium (LD)-based pruning, a total of 4,479,177 high-quality SNPs were retained for subsequent analyses. Based on these SNPs, the internal genetic structure of the Duolang sheep population was elucidated, with 14 kinship outliers detected through principal component analysis (PCA). Furthermore, LD decay analysis revealed that the r² declined below 0.1 at approximately 10 kb, indicating a relatively low level of selection pressure in the population. Within the population, Tajima’s D and iHS methods detected 517,218 and 82,534 candidate SNPs under selection, respectively, with 24,453 SNPs overlapping between the two methods. By splitting Duolang sheep into single-lamb (n = 29) and multiple-lamb (n = 12) subgroups according to litter size, 267,654 SNPs were identified by XP-CLR, while 184,179 SNPs suffering from selection were detected by F_ST and 62,150 by XP-EHH. Functional enrichment analysis of selected genes reveals the selection directions (domestication, growth, and reproduction) and related candidate genes in the Duolang sheep population, including ESRRA, ESRRB, OXT, FSHR, ESR2, GNRHR, and BMPR1B. This study provides the first comprehensive genomic landscape of Duolang sheep, elucidating genetic signatures of its adaptive traits. Full article