Search Results (797)

Globally, Central Asian wild fruit forests are critical repositories of wild fruit germplasm resources and provide essential ecosystem services. However, their habitats are facing escalating degradation risks driven by climate warming, shifting precipitation regimes, and intensifying anthropogenic disturbances. Accurately quantifying climate-driven spatiotemporal variations in habitat suitability for keystone wild fruit tree species is therefore an essential prerequisite for formulating targeted conservation and management strategies in arid and semi-arid landscapes. In this study, we applied the maximum entropy (MaxEnt) model to simulate the current (2000–2020 baseline) and future (2030s, 2050s, 2070s) potential suitable habitats of two dominant wild fruit tree species, Malus sieversii (Ledeb.) M.Roem. and Prunus cerasifera Ehrh., in the Ili Valley, a core distribution area of Central Asian wild fruit forests in northwestern China. We integrated rigorously screened species occurrence records with key environmental predictors and characterized future climate conditions using three Shared Socioeconomic Pathways (SSPs; SSP126, SSP245, and SSP585) spanning low to high radiative forcing levels. The model exhibited excellent predictive performance (AUC > 0.85), confirming the robustness and reliability of our habitat suitability simulations. Elevation and annual precipitation were identified as the dominant environmental variables governing habitat suitability for both species, highlighting the critical role of terrain–hydroclimate interactions in maintaining viable dryland refugia for wild fruit forests. Under the baseline climate scenario, the total area of suitable habitats reached 24.014 × 10³ km² for Malus sieversii and 18.990 × 10³ km² for Prunus cerasifera. Future climate projections revealed a consistent and significant contraction trend in suitable habitats for both species, with the magnitude of habitat loss escalating with increasing radiative forcing and longer projection time horizons. Specifically, under the high-emission SSP585 scenario by the 2070s, the suitable habitat area is projected to decline by 7.579 × 10³ km² for Malus sieversii and 9.883 × 10³ km² for Prunus cerasifera relative to the baseline. Our findings delineate climate-vulnerable hotspots of wild fruit forests and provide a robust spatial scientific basis for prioritizing in situ conservation, targeted habitat restoration, and anthropogenic disturbance regulation to support the long-term persistence of these irreplaceable wild fruit germplasm resources under accelerating global climate change. Full article

KNOTTED1-LIKE HOMEOBOX (KNOX) genes are conserved transcription factors that play crucial roles in plant growth, development, and stress responses. However, systematic characterization of the KNOX family in Malus sieversii, a valuable germplasm resource with outstanding stress tolerance and flavonoid accumulation, remains lacking. In this study, we performed a genome-wide identification of the KNOX gene family in M. sieversii and identified 21 MsiKNOX genes. Phylogenetic analysis classified these genes into three subfamilies (Class I, II, and M), with structural features and motif compositions consistent with those of their orthologs in Arabidopsis thaliana and cultivated apple. Chromosomal localization revealed an uneven distribution across 13 chromosomes, and synteny analysis indicated both conserved evolution and lineage-specific expansion of the KNOX family in M. sieversii. Promoter cis-element analysis suggested that MsiKNOX genes are potentially involved in responses to multiple abiotic stresses and hormone signaling. Expression profiling under ABA and GA treatments showed that most MsiKNOX genes responded differentially to these phytohormones. Notably, MsiKNOX09 was significantly upregulated by ABA and downregulated by GA, and was further shown to physically interact with the anthocyanin-associated MsiMYB1 in yeast two-hybrid and split-luciferase assays. These findings provide a comprehensive overview of the KNOX gene family in M. sieversii and suggest that MsiKNOX09 acts as a hormone-responsive regulator and may participate in MsiMYB1-mediated regulatory pathways. Full article

This study evaluated morphological variation in 45 accessions of cultivated Perilla frutescens var. frutescens (PFF) and var. crispa (PFC) collected from South Korea and Japan, together with their weedy counterparts, var. frutescens (WPFF) and var. crispa (WPFC) from South Korea, using ten quantitative and ten qualitative traits. Clear morphological differentiation was observed between cultivated and weedy forms in both varieties, particularly in pigmentation, plant fragrance, and seed-related traits. PFF cultivars were characterized by predominantly green pigmentation, a typical frutescens aroma, and significantly larger and heavier seeds, suggesting stronger phenotypic differentiation in leaf and seed utilization. In contrast, PFC cultivars showed substantial morphological overlap with WPFC and WPFF accessions, indicating comparatively weaker phenotypic differentiation. Principal component analysis showed that the first principal component (PC1) explained 25.7% of the total phenotypic variance and was strongly associated with five quantitative traits (plant height, inflorescence length, floret number, seed size, and 100-seed weight) and five qualitative traits (adaxial and abaxial leaf color, flower color, seed color, and seed hardness). Along PC1, PFF cultivars formed a well-defined cluster, whereas PFC cultivars and the weedy WPFF and WPFC accessions exhibited broader dispersion, reflecting greater morphological variability. These results provide morphological insights into the differentiation between cultivated and weedy Perilla accessions and indicate potential domestication-related patterns. However, these interpretations are based primarily on morphological observations, and further genetic and evolutionary studies will be necessary to clarify the domestication history of these taxa. The identified trait complexes provide a useful phenotypic foundation for marker-assisted breeding, informed cultivar selection, and effective germplasm conservation and management. Full article

To establish standardized DNA fingerprinting and molecular identification systems for mandarin citrus, we analyzed 69 mandarin accessions via fluorescent SSR capillary electrophoresis to construct DNA molecular fingerprints and unique molecular identity cards. Eighteen highly polymorphic SSR primer pairs were screened, yielding 239 genotype calls and 147 alleles. The number of amplified alleles per primer pair ranged from 4 to 18, with polymorphic information content (PIC) values varying from 0.411 to 0.650. Ten core primer pairs were further selected, achieving a discrimination rate of 65.2% (45 out of 69 accessions distinguished). Utilizing these fluorescent SSR markers, we established DNA molecular fingerprints and unique molecular identity cards for all 69 accessions. Among them, 45 accessions possessed unique fingerprints, whereas the remaining 24 indistinguishable accessions were clustered into six groups. Each cluster contained both wild (4 accessions total) and cultivated (20 accessions total) resources with high genetic similarity, which merits further investigation. This study provides a practical foundation for the authentication, conservation, and genetic relationship analysis of mandarin germplasm resources and establishes a technical framework for standardizing mandarin variety identification. Full article

Growth and egg production are the two most economically important traits in goose production systems. However, negative genetic correlations between these traits make it difficult to achieve balanced genetic improvement through selection. In this study, we analyzed whole-genome resequencing data from 1033 Zhedong White Geese to identify genetic variants related to birth weight (BW), body weight at 90 days (BW90), and egg number at 66 weeks of age (EN66). Single-trait genome-wide association studies (GWASs) identified 6, 5, and 5 lead SNPs significantly associated with BW, BW90, and EN66, respectively. By integrating network analysis, PLACO, and multivariate linear mixed models (mvLMMs), we further identified KCNAB2 and KCND3 as potential pleiotropic candidate genes influencing both growth and egg production. Notably, the variant at CHR25: 6006715, located within an intronic region of KCND3, was associated with increased BW (ZscoreBW = 4.44) and decreased EN66 (ZscoreEN66 = −3.55), showing strong pleiotropic significance (P_PLACO = 4.88 × 10⁻⁸). Collectively, these findings provide new insights into the genetic architecture underlying the antagonistic relationship between growth and egg production in geese and offer valuable genetic targets for developing breeding strategies that jointly optimize growth performance and reproductive efficiency. Full article

Background/Objectives: To establish a foundation for conserving and utilizing local frog germplasm resources in Zhejiang Province, for Quasipaa spinose, which has high commercial and nutritional value, a pan-genome analysis was performed. Methods: Herein, we characterized 405,263 SNPs for the giant spiny frog, Q. spinose, using the Illumina NovaSeq platform. Results: These loci were highly polymorphic in 59 individuals sampled from three different subpopulations, with 0.05 to 0.30 minor alleles per locus. The observed and expected heterozygosities were 0.2379 and 0.2683 (IBD), respectively. These polymorphic loci would be useful for assessing genetic diversity, population structure, gene flow, population assignment, and paternity in giant spiny frogs. Conclusions: Our investigation demonstrated that there are distinct genetic and evolutionary histories between Zhejiang and Jiangxi frogs. Phylogenetic inference effectively differentiated these three subpopulations based on their geographical origins, and the phylogenetic inference level of domesticated Zhejiang frogs was comparatively higher than that of the Jiangxi-derived population. Furthermore, by utilizing three selective signature methods, namely, Obs/Exp het, nucleotide diversity (Pi), and identical by state (IBS), across subpopulations, we concluded that these three breeds were from an identical population, and no genetic bottleneck occurred among these three lineages, in accordance with LD decay analysis. Finally, 2700 potential candidate genes were identified, including MAPK, calcium signaling pathway, Ras signaling pathway and regulation of actin cytoskeleton; we noted that the key genes associated with dilated cardiomyopathy or arrhythmogenic right ventricular cardiomyopathy in humans beings and GnRH signaling pathway-related genes (i.e., CD80, IFNA, and KCNK1) were highly enriched, which could impact cardiac function through immune-associated genes. Full article

Embryonic stem cells represent a valuable germplasm resource with significant implications for breed conservation, development, and utilization. However, the scarcity of genetic resources in endangered species poses a fundamental constraint on obtaining gametes for embryonic stem cell derivation. Therefore, generating embryonic stem cells from somatic cell nuclear transfer blastocysts offers an optimal alternative for conservation cloning. In this study, we established ApèiJiaza somatic cell nuclear transfer ESCs (APNT-ESCs) from cloned embryos, using ApèiJiaza cattle ear fibroblasts as nuclear donors. APNT-ESCs could be passaged for over 30 generations in vitro, exhibiting high expression of key pluripotency markers, genomic stability, and the ability to form embryoid bodies and differentiate into cell types of all three germ layers. This research established an effective biotechnological framework for the genetic conservation of other endangered species lacking accessible gametes. Full article

Plant AT-rich sequence and zinc-binding (PLATZ) proteins are a class of plant-specific transcription factors that have been identified and functionally characterised in multiple species. However, the PLATZ gene family has not yet been systematically characterised in Populus euphratica. In this study, 19 PePLATZ genes were identified and classified into five subgroups. The analyses of gene structure, conserved motifs and protein domains indicated that the PLATZ family is highly conserved during evolution. Meanwhile, promoter cis-acting element profiling suggested their potential roles in stress-responsive transcriptional regulation. Transcriptomic and qRT-PCR analyses showed that PePLATZ1, PePLATZ6, PePLATZ8, PePLATZ14 and PePLATZ19 were highly expressed in the roots, stems and leaves of P. euphratica and were strongly induced by drought stress. PePLATZ8 localised to the nucleus and lacked transactivation activity but acted as a transcriptional repressor in planta. Transgenic poplar lines overexpressing PePLATZ8 exhibited significantly enhanced drought tolerance. Furthermore, after drought treatment, PePLATZ8-overexpressing plants accumulated high levels of H₂O₂ and exhibited significantly increased total superoxide dismutase activity, which likely contributed to improved drought tolerance. Together, the above findings deepen our understanding of the structure–function relationships of PePLATZ proteins and identify PePLATZ8 as a promising candidate gene for the molecular breeding of drought-resistant poplar germplasm. Full article

Outdoor ecological practice is essential for cultivating ecological literacy; however, there is currently a relative lack of comprehensive outdoor practical teaching case designs for class-based teaching. This study describes the design of an experimental teaching case for ecological education involving UAV-based field data collection. For the scheme, we selected the Xinhui Tangerine Peel Germplasm Resources Conservation Center in Jiangmen City, Guangdong Province as the study area, utilizing the DJI Phantom 4 RTK drone, which serves as the equipment for experimental teaching. The experiment is structured into three phases: indoor preparation, field execution, and data processing. Students from four groups collaboratively conducted aerial surveys across 24 partitioned plots, with flight altitudes stratified between groups to ensure safety and data integrity. (1) In the indoor preparation phase, appropriate single-flight operational units were defined. QGIS software (version 3.26.2) was employed for zonal mission planning, and suitable flight altitudes were estimated using contour data. (2) Field experiment phase. This involved conducting a comprehensive survey of the on-site environment, selecting suitable takeoff and landing points, dividing students into teams to carry out UAV-image-acquisition tasks, and assigning different altitudes for flight routes among the teams. (3) After the fieldwork, students processed imagery using Agisoft Metashape (version 2.0.1) to generate orthomosaics and digital surface models, and engaged in ecological interpretation of the results. The experimental design ensured orderly execution, complete data coverage, and active student participation. The results indicate the approach effectively enhanced students’ UAV operational skills, outdoor problem-solving abilities, and teamwork capabilities, while deepening their ecological understanding through real-world inquiry. This case provides a replicable model for integrating UAV technology into ecological education, contributing to the transformation of ecological awareness into actionable practice. Full article

Epigenetic diversity contributes to phenotypic plasticity and environmental responsiveness in Citrus spp. In this work, genome-wide DNA methylation was analyzed in 49 accessions representing six Citrus species, hybrids, varieties, and cultivars from the Greek National Germplasm Collection. Substantial variation in global DNA methylation was detected, while the epigenetic diversity indices did not differ significantly among taxa. The highest values were observed in Citrus × aurantium var. sinensis (orange) varieties (P_epi = 77.33%, Na = 1.55, h = 0.14, I_epi = 0.24), whereas the lowest were recorded in Citrus × aurantifolia (lime) (P_epi = 18.67%, Na = 0.37, h = 0.09, I_epi = 0.13), reflecting potential methylation restructuring impacted by hybridization and selection. Epigenetic and genetic diversity were significantly different. Principal coordinate analyses (PCoA) of epigenetic data revealed limited concordance to taxonomy, except for unmethylated loci, the latter exhibiting similar data to genetic (SSR) results in which groups reflected the taxonomic genealogy. Epigenetic and genetic distances were uncoupled, and associations between epigenetic diversity (P_epi, h, I_epi) and traits directly or indirectly related to fitness (fruit weight, dry matter content, ascorbic acid concentration), were weak. These findings indicate that epigenetic diversity represents an independent layer of variation in Citrus germplasm with potential relevance for breeding, conservation and environmental resilience. Full article

N. chui is an economically important marine fish species distributed along the coastal waters of China, renowned for its delicate flesh texture and high-quality dried swim bladder. However, its scientific name and taxonomic relationship with N. coibor have long remained controversial, hindering accurate resource assessment and germplasm management. To address this issue, we sequenced and annotated the first complete mitochondrial genome of N. chui (GenBank accession: PZ024444). The circular mitogenome is 16,504 bp in length and contains 37 typical genes, with gene arrangement, nucleotide composition (A + T content: 52.07%), and codon usage patterns consistent with general teleost characteristics. Phylogenetic analyses based on 13 concatenated protein-coding genes revealed that N. chui and N. coibor form a maximally supported monophyletic clade (bootstrap support = 100%), with a pairwise genetic distance of 0. These mitochondrial results strongly suggest that the two nominal taxa are very closely related and may represent the same species. However, formal taxonomic synonymy cannot be established on mitochondrial evidence alone and requires further evaluation through examination of type material and comparative morphological study. Gene-specific selection pressure analyses showed that most mitochondrial protein-coding genes were subject to purifying selection, with ATP8 exhibiting the highest mean ω among genes with ω < 1, whereas ND5 and ND6 showed elevated ω values that warrant cautious interpretation. This study provides essential mitochondrial genomic resources for future research on species delimitation, phylogeny, and conservation of this important sciaenid fish. Full article

This study analyzed seven foliar traits of Cedrela odorata L. (Meliaceae) in 87 individuals across three germplasm movement zones in Tabasco, Mexico (VIII: humid; XIV: intermediate; XXI: dry) to assess differentiation and climatic relationships. Leaf length, area, petiolule length, leaflet number, rachis length, width, and stomatal density were measured. Univariate tests, canonical correlation analysis, redundancy analysis, and a relative phenotypic plasticity index were applied. Significant morphological differentiation was found: zone XIV exhibited the largest leaves and longest rachises, zone VIII the highest stomatal density, and zone XXI smaller, more subdivided leaves. The first canonical axis (r = 0.846, p < 0.001) associated long and wide leaves with warm, humid conditions, while the second (r = 0.810, p < 0.001) linked stomatal density and width to temperature minimum. Climate explained 55.7% of morphological variation, primarily through water and temperature gradients. High plasticity in leaf area, rachis length, and stomatal density suggests adaptive flexibility, yet consistent inter-zonal differences indicate local adaptation. These results demonstrate a strong correspondence with Tabasco’s germplasm movement zones and providing morphological evidence to support reforestation and germplasm management strategies under variable climatic conditions. Full article

Codon usage bias is important for regulating protein translation efficiency and accuracy. The HSP90 gene, a pivotal gene in plants, maintains homeostasis in plant protein stress responses and organelle immune defense functions. We systematically examine codon usage preferences in six forage grass species and the regulatory mechanisms of the HSP90 gene in governing codon preference. A set of metrics is evaluated, including effective codon number (ENC), codon adaptation index, and relative synonymous codon usage. Neutral evolutionary trajectories reveal usage preferences for six plant codons, with natural selection serving as the primary driving factor. The correlation between the ENC–GC3 curve (ENC relative to third-position GC content in synonymous codons) and codon bias index reveals these genes to exhibit moderate codon bias. The phenomenon of evolutionary constraints is exemplified by a propensity for C/G-terminating codons, concomitant with a suppression of NUA/NCG codons (NUA is an abbreviation for UA dinucleotide, and NCG is an abbreviation for CG dinucleotide). Phylogenomic reconstruction reveals a conserved diversification pathway, positioning P. giganteum A. Rich. at the basal node of the evolutionary framework. This study identified through systematic assessment that natural selection is the primary evolutionary force driving the biased use of codons in grass HSP90 genes. This finding provides actionable insights for enhancing abiotic stress tolerance in forage germplasm through precise codon engineering. Full article

Sperm cryopreservation is pivotal for conserving fish germplasm, yet cryodamage-induced quality decline limits its application. This study focused on Sichuan bream (Sinibrama taeniatus), an endemic and economically important fish species in the upper Yangtze River. Based on an established cryopreservation protocol, we evaluated sperm quality using computer-assisted sperm analysis (CASA) and fertility assays, followed by a systematic assessment of structural and functional damage via flow cytometry (membrane integrity, mitochondrial potential, reactive oxygen species, and DNA fragmentation), enzymatic assays (energy metabolism and antioxidant enzymes), Western blotting, and ultrastructural observation. Finally, integrated proteomic and metabolomic analyses were employed to elucidate the underlying physiological mechanisms. The results demonstrated that freeze–thawing significantly impaired sperm motility, fertility, and ultrastructure, concurrently disrupting energy metabolism and the antioxidant system. Crucially, multi-omics revealed that these functional declines were linked to dysregulation in key pathways involving cytoskeleton organization, lipid metabolism, energy homeostasis, and oxidative stress, forming a coherent network from initial molecular perturbation to phenotypic dysfunction. This study provides a comprehensive characterization of sperm cryodamage in Sichuan bream, advancing the understanding of fish sperm cryobiology and informing targeted cryoprotection strategy development. Full article

Yeyong mustard is a mustard vegetable belonging to the Brassicaceae family and the Brassica genus. This study assembled, annotated, and analyzed the chloroplast genome of Brassica juncea L., aiming to clarify its systematic evolutionary relationship with other cruciferous plants. The study used the Illumina NovaSeq 6000 platform to sequence the entire chloroplast genome of leaf mustard, and systematically analyzed its genome structure, repeat sequences, nucleic acid diversity, and codon preferences using bioinformatics methods. At the same time, the phylogenetic relationships were constructed by combining the leaf chloroplast genome sequences of other cruciferous plants. The results showed that the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%, exhibiting a typical tetrad structure; a total of 132 coding genes were annotated, including 87 mRNA genes, 37 tRNA genes, and eight rRNA genes, and no pseudogenes were found. Codon preference analysis shows that leucine (Leu) has the highest frequency of use, with 32 codons having a relative synonymous codon usage (RSCU) greater than 1, mostly ending in A or U; there are 37 scattered repetitive sequences and 315 simple repetitive sequences in the genome. Ka/Ks analysis showed that the chloroplast genes of leaf mustard were subjected to purification selection as a whole, while genes such as nadhF and petD showed positive selection, which is speculated to be related to adaptive evolution. The results of the phylogenetic analysis further confirm that the chloroplast genome of leaf mustard has a typical tetrad structure and is relatively conserved. It is most closely related to mustard greens in terms of evolutionary relationship, followed by Brassica plants such as nori and turnip, and is also closely related to Brassica plants such as European rapeseed. This study elucidated the conservative characteristics and evolutionary patterns of the chloroplast genome in mustard leaves, providing theoretical support for the phylogenetic research of the Brassicaceae family and the development and utilization of germplasm resources. Full article