Melilotus albus and M. officinalis are closely related legume species with potential value as stress-resilient resources for dry and marginal environments. However, whether they exhibit similar physiological and multi-omics response organization under continuous drought remains unclear. In this study, physiological, transcriptomic, and metabolomic analyses were integrated to compare drought-tolerant and drought-sensitive accessions of the two species at 0, 4, and 8 d of continuous drought. Both species showed coordinated changes in osmolyte accumulation, antioxidant defense, photosystem adjustment, and secondary metabolic remodeling, but differed in response rhythm and regulatory emphasis. Across the selected accession pairs, M. albus was mainly associated with sustained soluble sugar accumulation and relatively moderate photosystem changes, whereas M. officinalis showed a clearer tendency toward POD-associated defense and photoprotective adjustment. Comparative analyses across physiological and omics layers suggested that drought-response divergence became more clearly concentrated at the middle stage within the sampled period. Integrative analysis further indicated that phenylpropanoid- and flavonoid-related remodeling represented a major shared response direction in both species. However, this shared direction was organized differently, with M. albus showing changes across the phenylpropanoid backbone and multiple flavonoid-related branches, whereas M. officinalis showed a more focused pattern involving lignin-related and selected flavonol-related branches. These findings suggest that closely related Melilotus resources may differ in temporal coordination and secondary metabolic organization under continuous drought, providing useful information for understanding their response characteristics in dry and marginal environments.

The influence of global climate change on endangered species is of growing concern, especially for rosewood species that are in urgent need of protection and restoration. Ecological niche models are commonly used to evaluate probable species’ distribution under climate change and contribute to decision-making to define efficient management strategies. A model was developed to forecast which habitat was most likely appropriate for the Dalbergia odorifera. We screened the main climatic variables that describe the current geographic distribution of the species based on maximum entropy modelling (Maxent). We subsequently assessed its potential future distribution under moderate (RCP2.6) and severe (RCP8.5) climate change scenarios for the years 2050 and 2070. The precipitation ranges of the wettest month and the warmest quarter are the primary limiting factors for the current distribution of D. odorifera among the climatic predictors. Climate change will be expected to have beneficial effects on the distribution range of D. odorifera. In conclusion, the main limits for the distribution of D. odorifera are determined by the level of precipitation and human activities. The results of this study indicate that the coasts of southern China and Chongqing will play a key role in the protection and restoration of D. odorifera in the future.

Acer griseum (Franch.) Pax is an endangered species endemic to China, mainly scattered in the Qinling–Daba Mountains. The genetic diversity of 17 natural populations were analyzed by nuclear DNA (nDNA) and chloroplast DNA (cpDNA) to explore the driving forces for its microevolution. A high level of genetic diversity (nDNA: He = 0.296, cpDNA: Ht = 0.806) was found in A. griseum. Genetic variation was mainly within populations (92.52%) based on nDNA, while it was mainly among populations (96.26%) based on cpDNA. The seventeen populations were divided into two groups, corresponding to the subtropical zone (Group I) and temperate zone (Group II), with haplotype 4 (Hap4) and Hap5 being the most common haplotypes, respectively. Consequently, genes associated with heat and heavy metal stress were identified in Group I, while genes related to salt and drought stress were identified in Group II. Haplotype differentiation was driven by the heterogeneous microenvironment caused by the uplifting of the Qinling-Daba Mountains, which was a vital source of its high genetic diversity. Furthermore, the uplifted Qinling–Daba mountains may bridge high pollen flow among populations, whereas rivers can result in low seed flow among populations, which has led to the incongruent genetic structure between nDNA and cpDNA. This study represents a new perspective that geological events, especially orogeny, play an important role in plant microevolution through the establishment of maternal genetic structure and provides a meaningful conservation strategy for A. griseum. Overall, the Qinling–Daba Mountains not only are cradles for the genetic diversity of A. griseum but also provided refugia for it during the Quaternary glacial period.

Whole genome sequencing techniques are capable of providing insights into plant genetic adaptation to climate oscillations. Acer truncatum Bunge is a new resource tree for food with ornamental, timber and medicinal value. However, it has been listed as a near-threatened species because of the decreasing number of natural populations. In order to develop conservation strategies and sustainable innovative utilization for genetic resources, spatial pattern of genetic diversity and demographic history of A. truncatum from 13 natural populations, which cover the entire range, were analyzed by 9,086,353 single nucleotide polymorphisms (SNPs) through whole genome resequencing. The genetic diversity of natural populations was high (He = 0.289, I = 0.449), and genetic variations mainly resided within populations (82.47%) by AMOVA analysis. Cluster analysis showed that 13 natural populations mainly originated from three common gene pools. Therefore, it is recommended that the natural populations (LBGM, BTM, WLS and DQT) with high genetic diversity in different groups were given priority for in situ conservation and the genetic resources from these populations were collected for ex situ conservation. The effective population size of A. truncatum experienced two large-scale sharp contractions and currently decreased to its bottom in history. Nonetheless, A. truncatum could have expanded its effective population size to its historical peak after the last glacial period, indicating that it is highly resilient to fluctuations of temperature and humidity.

Rubus idaeus is one of the primary cultivated species of raspberries, renowned for its appealing color, distinctive flavor and numerous health benefits. WIP proteins, which contain three conserved amino acids (W: Tryptophan, I: Isoleucine, P: Proline) and four zinc finger motifs in a highly conserved C-terminal region, are members of the A1d subgroup of C2H2 zinc finger proteins. Drought is one of the main limiting factors of plant growth and development, which restricts the cultivation and utilization of raspberry in northwest China. In this study, to obtain candidate genes for drought resistance, we identified key related genes, RiWIPs, from R. idaeus and analyzed their bioinformation and tissue stress response expression to drought. We found that there are three RiWIPs in R. idaeus and they are located on chromosomes 3, 4 and 6 of R. idaeus, respectively. The open reading frames (ORFs) of the RiWIPs ranged from 870 to 1056 bp in length, encoding 289 to 372 amino acid residues. The proteins were highly conserved and feature diverse conserved motifs. The promoters of the RiWIPs contained abundant cis-elements related to growth, development and stress response. Tissue-specific expression analysis revealed that the RiWIPs were expressed in the leaves, stems and roots of both drought-susceptible and drought-tolerant cultivars, except for RiWIP2, which was only expressed in the roots of the drought-tolerant one. Under drought stress, the transcriptional activity of the RiWIPs was increased to different degrees with specificity in the leaves, stems and roots. Our study demonstrated the role of WIP genes in raspberry drought response and provided a marker gene, RiWIP2, for drought resistance and candidate genes for subsequent drought-resistant breeding of R. idaeus.

Magnolia sieboldii, an important ornamental tree native to East Asia, comprises two subspecies in distinct regions, with wild populations facing suboptimal survival. This study aimed to understand the potential habitat distribution of these subspecies under future climate-change conditions to support climate-adaptive conservation. The maximum entropy (MaxEnt) model was used with occurrence and environmental data to simulate the current and future suitable habitats under various climate scenarios. Precipitation in the warmest quarter played a crucial role in shaping the potential habitats of both subspecies; however, they exhibited different sensitivities to temperature-related variables and altitude. Magnolia sieboldii subsp. sieboldii is more sensitive to temperature seasonality and annual mean temperature, whereas Magnolia sieboldii subsp. japonica is more affected by altitude, mean temperature in the driest quarter, and isothermality. Currently, the subsp. sieboldii is predicted to have larger, more contiguous suitable habitats across northeastern China, the Korean Peninsula, and Japan, whereas the subsp. japonica occupies smaller, more disjunct habitats scattered in central and western Japan and the southern Chinese mountains. These two subspecies will respond differently to future climate change. Potentially suitable habitats for subsp. sieboldii are expected to expand significantly northward over time, especially under the SSP585 scenario compared with the SSP126 scenario. In contrast, moderately and highly suitable habitats for the subsp. japonica are projected to contract southward significantly. Therefore, we recommend prioritizing the conservation of the subsp. japonica over that of the subsp. sieboldii. Strategies include in situ and ex situ protection, introduction and cultivation, regional hybridization, and international cooperation. Our study offers valuable insights for the development of targeted conservation strategies for both subspecies of M. sieboldii to counteract the effects of climate change.

以 219 个叶子花栽培品种为研究对象,在 140 对引物中筛选出 20 对多态性高的简单重复序列(SSR)荧光标记引物对219 个品种进行扩增,共扩增出 414 条带型,平均每对引物扩增出 20.7 条;20 对引物的多态性信息含量(PIC)为 0.189～0.823,平均值为 0.696,当PIC>0.50 时可以认为该引物为高度多态性信息引物;20 对引物在 219 个品种中共检测出 219 个等位基因,平均每对引物检测出 10.95 个;20 对引物在 219 个品种组成的群体中,其平均有效等位基因数为 4.212 个,平均Shannon多样性指数为 1.633,平均观测杂合度为 0.430.在构建叶子花品种分子身份证方面,通过SSR标记技术,根据PIC的高低选择引物组合,采用数字与英文大小写字母相结合的方法,对不同长度的扩增片段进行赋值,最终用 20 对引物构建了 219 个叶子花品种的分子身份证,并通过在线软件进一步转换成唯一可识别的品种信息二维码.叶子花品种分子身份证和信息二维码的构建,可避免出现由于品种繁多及命名混乱而导致的同名异物和同物异名的现象,促进品种知识产权保护,做到种质可追溯.

[目的]筛选多态性高、通用性强等的SSR位点,评估筛选所得SSR位点的组合在山茶属品种中的鉴别能力;在保持最大鉴别能力的基础上,确定可用于山茶属品种鉴别所需的最少SSR位点的组合,提高品种鉴别效率.[方法]本研究以 111份山茶属品种为材料,结合凝胶电泳、荧光毛细管电泳、位点多态性分析和位点组合品种鉴别力(VDP)分析等方法,筛选评价SSR位点并对SSR位点组合的品种鉴别力进行分析与评价.[结果]本研究筛选获得17个SSR位点,占筛选位点总数的 30.9%,在 111份山茶属品种中,共检测到 166个等位基因,单位点基因型数量范围为 6～35,均值为 23.353个,观测等位基因数(Na)范围为 3～15,均值为 9.765个,多态性信息含量(PIC)的范围为0.447～0.835,均值为 0.696,位点缺失率的范围为 0～4.50%,均值为 0.90%.当差异位点数=1时,17个SSR位点在全部品种(系)、红山茶组品种和金花茶组无性系中达到的R-VDP最大值均为1,可将SSR位点数量分别缩减到11、10、5个,分别占筛选所得位点数的 64.7%,58.8%和 29.4%;当差异位点数=2时,17个SSR位点在全部品种(系)、红山茶组品种和金花茶组无性系中达到的R-VDP最大值分别为 0.964,0.952和 1.000,可将SSR位点数量分别缩减到 12、12、和 7个,分别占筛选所得位点数的 70.6%、70.6%和 41.2%;当差异位点数=3时,17个SSR位点在全部品种(系)、红山茶组品种和金花茶组无性系中达到的R-VDP最大值分别为 0.946,0.929,1.000,可将SSR位点数量分别缩减到 8、7和 8个,分别占筛选所得位点数的 47.1%、41.2%和 47.1%.当差异位点数≤6时,17个SSR位点组合对山茶属测试品种(系)群的R-VDP最大值可保持相对稳定的水平.[结论]本研究筛选验证获得 17个多态性高、通用性强等的SSR位点;这些位点的组合在山茶属品种(系)群中均表现出良好的品种鉴别能力;确定了山茶属不同类群品种(系)鉴别所需的最少SSR位点的组合,构建了一套山茶属SSR位点组合品种鉴别能力分析评价的体系,为山茶属品种鉴别及相关标准的制定等奠定了基础.

In overlapping distribution areas of Sorbus pohuashanensis and S. discolor in North China (Mount Tuoliang, Mount Xiling and Mount Baihua), Sorbus individuals were found with pink fruit, which have never been recorded for the flora of China. Fourteen morphological characters combined with four chloroplast DNA markers and internal transcribed spacer (ITS) were used to analyze the origin of the Sorbus individuals with pink fruits and their relationship to S. pohuashanensis and S. discolor . PCA, SDA and one-way (taxon) ANOVA of morphological characters provided convincing evidence of the hybrid origin of Sorbus individuals with pink fruits based on a novel morphological character and many intermediate characters. Haplotype analysis based on four cpDNA markers showed that either S. pohuashanensis or S. discolor were maternal parents of Sorbus individuals with pink fruits. Incongruence of the position of Sorbus individuals with pink fruits between cpDNA and ITS in cluster trees supported by DNA sequence comparative analysis, implying former hybridization events between S. pohuashanensis and S. discolor . Multiple hybridization events between S. pohuashanensis and S. discolor might have contributed to the generation of Sorbus individuals with pink fruits. This study has provided insights into hybridization between species of the same genus in sympatric areas, which is of great significance for the study of interspecific hybridization.

Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. We generated 171.47 Gb PacBio long reads and 72.43 Gb Hi-C data and yielded an assembly of 10 pseudochromosomes with a total size of 690.99 Mb and Scaffold N50 of 65.76 Mb. The analysis of specific genes revealed that the triterpenoids represented by lupeol may play an important role in D. cultrata’s potential medicinal value. Using the new reference genome, we analyzed the resequencing of 19 Dalbergia accessions and found that D. cultrata and D. cochinchinensis have the latest genetic relationship. Transcriptome sequencing of D. cultrata leaves grown under cold stress revealed that MYB transcription factor and E3 ubiquitin ligase may be playing an important role in the cold response of D. cultrata. Genome resources and identified genetic variation, especially those genes related to the biosynthesis of phytochemicals and cold stress response, will be helpful for the introduction, domestication, utilization, and further breeding of Dalbergia species.

BACKGROUND:Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.RESULTS:A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.CONCLUSIONS:The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.

Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.

Acer L. (Sapindaceae) consists of approximately 200 species, with great ornamental and commercial values. However, due to a substantial divergence in inflorescence, leaf shape, and fruit shape during the process of long-term natural evolution, it is remarkably difficult to distinguish them by morphological features. Eight species with compound-leaved maples from Sect. Trifoliata, Pentaphylla, and Negundo play an important role in revealing the morphological variation of Acer. Hence, the complete chloroplast (cp) genomes of all eight compound-leaved maples native to Asia were characterized, and comparative genomic analysis was conducted to infer their phylogenetic relationships. A few differences were found in cp genome size and gene content among eight Acer species. The gene rps2 was only identified in A. griseum. The differences in the cp genome sequences among eight Acer species have been clearly demonstrated, where matK-rps16, trnE-trnT, ndhC-trnV, ccsA-ndhD, and ycf1-trnN were the most divergent regions. The phylogenetic analysis revealed that Acer was clustered into monophyly by 100% bootstrap values, with A. glabrum (Sect. Glabra) and A. pseudoplatanus (Sect. Palmata) as the most basic species. Except for A. henryi and A. negundo, seven compound-leaved maples and some simple-leaved maples were highly supported to cluster into one clade with A. sutchuenense as the primitive species of Sect. Trifoliata and A. pentaphyllum as a series (Ser. Pentaphylla) of Sect. Pentaphylla. Besides, it is speculated by plastid phylogeny reconstruction that A. cissifolium (Sect. Negundo) may have ancestral connections with A. triflorum (Sect. Trifoliata). Finally, we conjectured that compound-leaved maples may have evolved from simple-leaved maples.

Understanding the impact of multiple anthropogenic threats on tree species is urgently needed for estimating population decline and enabling coordinated and efficient conservation actions. We applied a spatially explicit framework to assess the vulnerability of three highly valuable Asian rosewood species (Dalbergia cochinchinensis, D. cultrata, D. oliveri) to five key threats across their native ranges in six countries of the Greater Mekong Subregion. All three species face significant threat levels from at least one of the five threats in more than 75% of their native ranges, including within existing protected areas. Overexploitation is the single most important threat (53–60%), followed by habitat conversion (17–41%) and fire (20–28%). About 21% of the distribution range of D. cultrata is under medium to very high threat from climate change, which is predicted to have less impact on D. oliveri and on D. cochinchinensis. Based on our threat assessment we delineated species-specific priority areas for conservation and restoration that we subdivided by ecoregions as a surrogate for adaptive variation within species. Half of the ecoregions were classified as priority for improving the conservation of adaptive variation in one or more of the species. We propose spatially explicit follow-up actions that include in situ conservation, restoration, and ex situ conservation to improve the effectiveness of current conservation measures to capture adaptive variation within species. Transboundary coordination will be important to effectively address conservation threats. The study can act as a model for regional planning for other valuable tree species.

[目的]本研究旨在分析刀状黑黄檀基因组基本特征,发掘一套多态性好、重现性高的基因组SSR分子标记并用于评估其野生种群遗传变异程度.[方法]利用二代测序(NGS)方法初步评估刀状黑黄檀基因组大小、杂合度和重复序列;利用MISA对基因组上潜在的SSR位点进行检索,解析SSR类型与特征;利用Primer Premier v 5.0设计合成300对引物,通过琼脂糖凝胶电泳、非变性聚丙烯酰胺凝胶电泳对潜在的SSR位点进行初筛与复筛,最后采用荧光标记毛细管电泳进行SSR位点多态性与种群遗传多样性分析.[结果]刀状黑黄檀基因组特征分析结果显示:其基因组大小约为706.92 Mb,杂合度为1.26％,重复序列比率为55.74％.通过筛选实验,发掘了27个具有良好多态性的SSR标记,并进行了验证.结果显示27个SSR位点共扩增得到117个等位基因,多态性信息含量(PIC)介于0.149～0.803.对3个野生种群遗传多样性分析结果显示:种群水平的平均期望杂合度(He)为0.504,遗传分化系数(FST)为0.034;AMOVA分析显示:种群间变异占比3.46％,种群内变异占比96.54％,这表明遗传变异主要来源于种群内.[结论]刀状黑黄檀基因组属于高杂合、高重复的复杂基因组,研究结果为制定基因组精细组装策略提供了参考依据;发掘与验证的27个SSR标记具有较好的多态性与扩增稳定性;3个野生种群具有中等遗传多样性和较低的遗传分化,本研究为开展刀状黑黄檀的种质资源收集保存与分析评价提供科学依据.

通过观测、评价52个三角梅品种的表型性状,为三角梅种质资源利用及新品种选育提供科学依据.本文以52个3年生三角梅品种为试材,采用表型性状方差分析、相关性分析、主成分分析和聚类分析等方法,对14个表型性状进行多样性分析和评价.研究结果发现52个供试品种表型多样性丰富,具体如下:(1)14个表型性状的遗传多样性指数范围为0.39～3.35,其中质量性状中遗传多样性指数最大的是苞片形状(H=1.68);数量性状中遗传多样性指数最大的是叶长(H=3.35);14个表型性状中遗传多样性指数H＞1的有10个.(2)7个数量性状变异系数均值为23.2％,其中节间长变异系数最大(34.0％).(3)14个表型性状可简化为4个主成分因子,各主成分因子分别主要代表叶长、叶宽、节间长、花序梗长、苞片长、苞片宽、苞片类型、叶形和苞片颜色等指标变量.(4)4个主成分累计方差贡献率达64.3％,其中第一主成分方差贡献率达28.6％;第一和第二主成分主要反映三角梅的数量性状特征,第三和第四主成分主要反映三角梅的质量性状特征;综合得分最高的9个品种为C39、C7、C33、C43、C48、C29、C22、C35、C26.(5)聚类分析结果表明,在欧式遗传距离20时可将52个三角梅品种分为4个类群;三角梅品种间表型性状变异大;叶片大小、苞片类型、叶形、苞片颜色等是三角梅品种分类和选育的最主要依据.