BMC Plant Biology最新文献

Background: Pod shatter resistance is an important trait in Brassica species, significantly impacting the yield and profitability of growers. Identifying genomic regions and understanding genes underlying shatter resistance is a major objective of breeding programs. Brassica rapa, commonly known as rape or field mustard, is an ancestral species of Brassica napus and Brassica juncea - the most widely oilseed crops grown worldwide. In this study, we performed diversity analysis of B. rapa accessions, bulked segregant analysis based quantitative trait locus-sequencing (QTL-seq), and traditional quantitative trait locus (QTL) mapping in an F₂ population to identify genomic regions associated with pod shatter resistance in B. rapa.

Results: A considerable genetic variation for pod shatter resistance, measured as rupture energy (RE), varied from 0.63 to 3.49 mJ^(½) was revealed among 90 accessions of B. rapa. Cluster analysis based on 10,324 DArTseq markers showed that pod shatter-resistant accessions originated from diverse sources. We further investigated the genetic and anatomical bases of variation in pod shatter resistance from two contrasting parental lines, ATC90153 (maternal parent with high RE) and ATC91215 (paternal parent with low RE). Bulked segregant resequencing analysis of parental lines and two pooled samples, prepared from 10 resistant and 10 sensitive lines to pod shatter, identified three genomic regions for shatter resistance on chromosomes A06 and A09. Traditional QTL analysis validated marker-pod shatter resistance associations on chromosomes A06 and A09 in the same F₂ population using a linkage map based on 23,274 DArTseq markers. Physical positions of significantly associated markers and the priori pod dehiscence genes on the B. rapa reference genome sequence suggested BEE1/PEROXIDASE/TCP8 on A06 and ADPG1/SHP1/MYB116 genes on A09 as potential candidates for pod shatter resistance. Sequence comparison of parental lines identified sequence variants (194 SNPs and 74 InDELs on A06, and two SNPs and two InDELs on A09) in the promoter and downstream regions of B. rapa genes within the QTL.

Conclusions: We identified QTLs and priori candidate genes associated with variation in pod shatter resistance on chromosomes A06 and A09 in B. rapa. This study provides potential gene targets to understand molecular mechanisms and improve pod shatter resistance in Brassica crops.

Background: Hemarthria compressa, a widely cultivated forage grass, is critical for supporting livestock production and maintaining the ecological balance in grassland ecosystems. Enhancing its stress resistance and productivity is crucial for sustainable grassland utilization and development. Silicon (Si) and Selenium (Se) are recognized as beneficial nutrients that promote plant growth and stress tolerance, and modulate of plant-microorganism interactions. However, the intricate linkages between the endophytes shifts and host grass growth induced by Si/Se amendments are poorly understood. In this study, a pot experiment was conducted to examine the effects of foliar-applied Si/Se on the growth and nutritional quality of H. compressa grass, as well as the composition, diversity and potential functions of endophytic bacteria in leaves.

Results: Both Si and Se treatments significantly improved grass biomass by approximately 17%. Nutritional quality was also improved, with Si application increased plant Si and neutral detergent fiber contents by 25.6% and 5.8%, while Se significantly enhanced the grass Se content from 0.055 mg kg^-1 to 0.636 mg kg^-1. Furthermore, Si/Se amendments altered the structure of the leaf endophytic bacterial community, resulting in an increased alpha diversity and a more modularized co-occurrence network. Moreover, both Si and Se treatments enriched plant growth-promoting bacterial genera such as Brevundimonas and Truepera. Metabolic function analysis revealed that Si application promoted chlorophyllide biosynthesis by 152%, several carbon metabolism pathways by 35-152%, and redox-related pathways by 57-93%, while the starch biosynthesis pathway was downregulated by 79% of the endophytic bacterial community. In contrast, Se application mainly enhanced starch degradation, CMP-legionamine biosynthesis by 71% and TCA cycle-related pathways by 23-58%, while reducing L-threonine metabolism by 98%. These specific functional changes in the endophytic bacteria induced by Si/Se amendments were closely linked with the observed growth promotion and stress resistance of the host H. compressa grass.

Conclusions: Si and Se amendments not only enhanced the growth and nutritional quality of H. compressa grass, but also altered the community structure and functional traits of endophytic bacteria in grass. The enrichment of beneficial endophytes and the modification of community metabolic functions within the endophytic community may play important synergistic effects on improving grass growth.

Background: Panax notoginseng (PN) is a medicinal plant containing essential ginsenosides. Given the therapeutic significance of ginsenosides, we delved into the mechanisms of ginsenoside Rb3 biosynthesis in PN flowers. We examined this process from the pre-differentiation stage to the end of flowering, aiming to uncover the biochemical pathways underlying ginsenoside production in PN.

Results: Budding stage (T2) was found critical for enhanced Rb3 production. Transcriptomic analysis revealed a marked shift in gene expression beginning at T2, with upregulation in pathways associated with secondary metabolite production. Gene set enrichment analysis (GSEA) illuminated the upregulation of genes involved in terpenoid backbone biosynthesis, amino acid degradation, and terpenoid modifications, specifically at T2. We correlated the fluctuating hormone levels with the activity of the transcription factor MYC2 to underscore hormonal influence on ginsenoside biosynthesis. Biosynthesis pathway reconstruction revealed the dominance of the mevalonate pathway. Critical enzymes such as ACAT, PPDS, DDS, and LUP4 were vital in precursor biosynthesis and modification. Notably, key genes such as HMGCS, FDPS, and DDS, as well as transcription factors MYC2, MYB124, and MYB61.1, showed a concerted surge in activity at T2.

Conclusions: These findings provide insights into the complex gene networks and molecular pathways that regulate ginsenoside biosynthesis, thereby promoting the medicinal properties of PN.

Background: Effective nitrogen (N) fertilizer management can improve photosynthetic performance of maize and enhance the grain yield. However, the effects of the deep placement of N on post-silking photosynthetic performance in maize and its relationship with grain filling are limited. The study was a split-plot design with N application rates as the main plots and N placement depths as sub-plots. The N application rates consisted of 225, 191.25, and 157.5 kg ha^- 1 and N placement depths consisted of 5 and 15 cm, respectively. The growth parameters, photosynthetic capacity, subcellular ultrastructure, antioxidant system in maize leaves, and grain filling characteristics were measured.

Results: Increasing the N placement depth counteracted the adverse effects of reduced N availability on the leaf area index, leaf area duration, and photosynthetic performance of plants. Compared to 225 kg N ha^- 1 applied underground at 5 cm, a 15% reduction in the N application rate at 15 cm reduced oxidative stress through the activation of antioxidative enzymes, which enabled plants to maintain their chloroplast ultrastructure, achieving 20.7% higher chlorophyll content, 7.8% higher photosynthetic rate per unit of leaf area, and 5.6% higher leaf area index during the later growth period. It also facilitated enhancing the growth rate during maximum filling and extending the active filling duration of grains.

Conclusions: Overall, reducing the recommended N application rate of 225 kg ha^- 1 by 15% but applying it at a depth of 15 cm might delay plant senescence and extend grain filling active time, improved photosynthetic performance in late growth period, and finally increased grain weight and grain yield of maize.

Background: Potentilla L. and Dasiphora L. are predominantly perennial herbs, occasionally manifesting as annuals or shrubs, primarily found in the northern temperate zone. However, taxonomic classification within this group remains contentious, particularly regarding genus boundaries and species delineation. Therefore, this study sequenced and analyzed the complete plastid genomes of 19 species from Potentilla and Dasiphora, comparing them with five previously published plastid sequences. Our objectives included reconstructing phylogenetic relationships within Potentilla and Dasiphora and investigating cytonuclear discordance among them.

Results: These plastid genomes were highly conserved in structure, GC content, and overall genome composition, comprising 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Notably, all Dasiphora plastid genomes lacked the unique intron for rpl2. Comparative genomic analyses revealed that variations in plastid genome size were due to differences in the lengths of the LSC, SSC, and IR regions. The IR region was predominantly conserved, while non-coding regions exhibited higher variability than coding regions. We screened SSR and identified seven highly variable loci that serve as potential molecular markers, offering valuable insights into the intergeneric relationships between Potentilla and Dasiphora. Phylogenetic analyses based on nuclear (ITS, ETS) and cytoplasmic (plastid, mitochondrial) genes confirmed the monophyly of Potentilla and Dasiphora, with results largely consistent with previous studies and supported by robust reliability metrics. We identified cytonuclear conflicts within Potentilla, which frequently disrupt its monophyly. We hypothesize that these conflicts may result from interspecific hybridization or incomplete lineage sorting events during the evolutionary history of the genus.

Conclusions: This study offers a theoretical foundation for advancing molecular identification and phylogenetic research on Potentilla and Dasiphora species. However, future work could benefit from greater detail on the criteria for selecting mitochondrial gene sequences and nrDNA datasets.

Seagrasses maintain cellular water balance by regulating ion concentrations and accumulating organic osmolytes, enabling them to survive in the fluctuating salinity of intertidal environments. However, the molecular mechanisms underlying seagrass responses to salinity changes remain relatively understudied. To address this, we conducted a multi-omics analysis of Ruppia sinensis under low, moderate, and high salinity conditions to uncover the mechanisms behind its adaptation to salinity fluctuations. Our research revealed that the transition from low to high salinity significantly altered the physiological characteristics of R. sinensis. Simultaneously, the species enhanced its ability to cope with and adapt to salinity fluctuations by increasing antioxidant enzyme activity. Integration of multi-omics data further indicated that under high salinity conditions, R. sinensis synthesizes more flavonoids to bolster its adaptive capacity. Additionally, the phenylpropanoid metabolic pathway appears to play a crucial role in the response of R. sinensis to changes in water salinity.

Background: Pepper (Capsicum annuum L.) is a vegetable crop of significant economic importance, but its yield and quality are severely affected by the combined stress of low temperature and low light (LL), particularly in greenhouse environments. Despite this, the physiological and molecular mechanisms underlying pepper's response to LL stress remain poorly understood. In this study, we conducted physiological and transcriptomic analyses on two pepper genotypes: Y2, a LL-sensitive genotype, and Y425, a LL-tolerant genotype. These genotypes were subjected to LL stress conditions (10 °C/5°C, 100 µmol m⁻²s⁻¹) and control (CK) conditions (28 °C/18°C, 300 µmol m⁻²s⁻¹).

Results: Three days after treatment, the phenotypes of the two pepper genotypes began to show clear distinctions, with Y425 seedlings exhibiting greater root length, shoot fresh weight, and root fresh weight compared to Y2. Additionally, comparative transcriptome analysis of leaf samples from both genotypes identified a total of 13,190 differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis revealed that genes associated with photosynthesis, osmotic stress response, reactive oxygen species response, and other GO terms potentially contribute to LL tolerance. Moreover, three key pathways involved in the response to LL stress were identified: photosynthesis-antenna proteins, zeatin biosynthesis, and circadian rhythm pathways. The key DEGs in these pathways were expressed at higher levels in Y425 as compared with Y2. Furthermore, physiological indicators such as chlorophyll fluorescence parameters, chlorophyll content, osmoregulatory substances, and antioxidant enzyme activities decreased under LL stress; however, the reduction was significantly greater in Y2 compared to Y425, further validating the molecular findings from the transcriptome analysis.

Conclusion: This study identified significant physiological and transcriptomic differences in two pepper genotypes under LL stress. It highlighted key pathways and provide novel insights into the molecular and physiological mechanisms of pepper's LL tolerance. These results emphasize the importance of optimizing greenhouse conditions for better crop productivity.

Background: Rheum pumilum, an endemic species on the Qinghai-Tibetan Plateau (QTP), serves as an ideal material for investigating the phylogeography of alpine plants. This study employs chloroplast DNA fragments (trnL-F, trnS-G, and matK) to delve into how Rh. pumilum adapted to the extreme environmental changes on the QTP, during its evolutionary process through phylogenetic geographical analysis, revealing its population differentiation and historical dynamics.

Results: The examination of 39 haplotypes across 26 populations of Rh. pumilum reveals distinct regional distribution, reflecting a phylogeographic pattern resembling "alpine-island". The total genetic diversity of Rh. pumilum is remarkably high (Ht = 0.910), with the majority of genetic variation primarily occurred among populations (84.5%) with limited gene flow, indicating geographic isolation influenced by diverse habitats of plateau. The geographic isolation model is further supported by various analytical methods, including AMOVA analysis, UPGMA dendrogram, PCoA, Structure analysis, and Mantel test. Micro-refugia for Rh. pumilum during the Quaternary ice ages are supported by haplotype network and genetic diversity analysis. The absence of a typical "star-shape" pattern in the overall haplotype network suggests that Rh. pumilum likely maintains a stable state without experiencing rapid expansion, which has been supported by mismatch distribution analysis. Ecological Niche Modeling (ENM) indicates sensitivity of Rh. pumilum to humidity, temperature and altitude, aligning with a historical distribution resembling a "displacement refugia" model during the Quaternary ice ages. The involvement of Rh. kialense and Rh. sublanceolatum in the origin and gene introgression of Rh. pumilum is suggested, possibly as maternal ancestors of closely related haplotypes. Haplotype divergence of Rh. pumilum approximately 11 million years ago, with notable divergence peaks observed during the late Miocene, as well as the Pliocene, Pleistocene and Holocene.

Conclusion: These findings suggest a correlation between genetic diversity, haplotype lineage divergence and key geological and climatic events, notably the uplift of the QTP, monsoon climate changes, and the climatic oscillations during the Quaternary ice ages. This study might provide valuable insights into the formation mechanisms of plant diversity on the QTP, crucial for biodiversity conservation and sustainable species development in extreme environments.

Background: Tinospora sagittata, a member belongs to the genus Tinospora of Menispermaceae family. Its tuberous roots have been used as traditional Chinese medicine (TCM) for pharmacological properties and are commonly known name as "Jin Guo Lan". Although its plastome and nuclear genome had been sequenced, its mitochondrial genome has not been explored, which significantly hampers conservation efforts and further research for this species. In addition, previous efforts based on multiple molecular markers providing profound insights into an intergeneric phylogenetic framework for Burasaieae and sampled species of T. sagittata are placed in a superclades, species delimitation of T. sagittata still need to be comprehensively evaluated.

Results: Flow cytometry revealed that Tinospora sagittata has two cytotypes and a wide range in genome sizes. We further sequenced and assembled the organelle genomes of T. sagittata, including the mitogenome (513,210-513,215 bp) and plastome (163,621-164,006 bp). The plastomes were highly similar in gene content and exhibited a typical quadripartite structure, but a translocation as well as two inversions were detected in mitogenomes. The repeats patterns in both organelles are generally similar, but significant difference in the codon bias of the genes of Tinospora organelle genomes. Interesting, both organelle genomes had shown that inter-gene spacer regions could be used as effective molecular markers for further phylogenetic analyses and species identification. Comprehensive analysis of protein coding genes of organelle genomes showed that significant difference in Ka, Ks, and Ka/Ks values among the organelle genomes. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Ranunculales described in the APG IV system.

Conclusions: We provided a high-quality and well-annotated organelle genome for Tinospora sagittata. The study present here advances our understanding of the intricate interplay between plastome and mitogenome. Moreover, our results also laid the foundation for further studying the course, tempo and mode of organelle genome evolution of Menispermaceae.

Background: The basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and responses to environmental changes. The mangrove plant Kandelia obovata, native to subtropical and tropical coastal intertidal zones, has evolved various adaptive mechanisms to cope with unstable muddy substrates, tidal fluctuations, saltwater intrusion, and intense ultraviolet radiation. This study aims to provide a comprehensive characterization of the bZIP gene family in K. obovata and investigate its functional roles in response to environmental stresses.

Results: In the K. obovata genome, 66 bZIP genes were identified and named KobZIP1 to KobZIP66, categorized based on their chromosomal locations. These KobZIP genes exhibited diversity in physicochemical properties, such as protein length, molecular weight, and isoelectric point, and were all predicted to localize to the nucleus. Phylogenetic and structural analyses classified the KobZIP genes into 12 subfamilies, with subfamily A containing the majority of members. Gene structure analysis revealed variations in the number and position of exons and introns among subfamilies, reflecting their evolutionary history and potential functional diversity. Conserved motif analysis showed that all bZIP family members contained motifs in the basic and hinge regions, with subfamily D displaying the greatest motif diversity. Promoter region analysis identified various cis-acting elements associated with responses to phytohormones (ABA, GA, ET, IAA, MeJA, SA) and environmental stress. The expression patterns of KobZIP genes across different tissues and under various abiotic stress conditions were analyzed using transcriptomic data and experimental validation.

Conclusion: This study provides a comprehensive characterization and functional analysis of the bZIP gene family in K. obovata, offering new insights into their roles in plant development and environmental adaptation. The expression profiles of KobZIP genes during root development and post-embryonic stages, along with their responses to ABA, low temperature, and salt stress, underscore their potential significance in the adaptation of mangrove plants to the intertidal environment.