Frontiers in Plant Science最新文献

Durum wheat, a globally significant crop for high-quality pasta production, remains vulnerable to unseasonal freezing events, a risk that is intensified with climate variability. To address this challenge, we combined genome-wide association studies (GWAS), genomic prediction, and marker-assisted selection to improve both freezing tolerance and grain quality in durum wheat. A panel of 250 diverse accessions, comprising cold-adapted lines from Eastern Europe and high-quality genotypes from Southern Europe, was genotyped using a 25K SNP array. Clear genetic differentiation by geographical origin and growth habit highlighted contrasting allelic patterns for adaptation and quality traits. Phenotypic evaluations were carried out in experimental field trials over two consecutive growing seasons in Italy and Russia to assess the freezing tolerance and quality performance of the genetic materials. GWAS identified five significant marker-trait associations (MTAs) for freezing tolerance on chromosomes 2A, 2B, 3B, 4A, and 5A. Notably, a strong MTA on chromosome 5A (physical position 488.2 Mb) individually explained up to 27% of the phenotypic variance (PVE), co-localizing with the critical Fr-A2 cold-stress regulatory locus. Significant associations for grain-quality traits were localized on a 1B chromosome hotspot (541-652 Mb). A multi-trait genomic selection model integrating freezing tolerance, grain weight, and gluten traits enabled the identification of optimal parental lines, resulting in measurable gains across simulated generations. From the top-ranked crosses, BC₂F₂ populations were developed and genotyped with KASP markers targeting validated MTAs. Lines carrying favorable alleles for both freezing tolerance and gluten strength were successfully selected, confirming the predictive accuracy of the model. The integration of GWAS, diversity-preserving genomic prediction, and functional marker validation offers a robust and scalable pipeline for breeding cold-resilient, high-quality durum wheat, providing tangible tools to adapt Mediterranean and similar wheat systems to increasing climate variability.

Introduction: Plant mitochondrial genomes (mitogenomes) are known for their structural complexity, particularly within the Orchidaceae. To understand the evolutionary dynamics in the endangered genus Calanthe, this study provides the first complete mitogenome assembly for the endangered species Calanthe sieboldii, a species of horticultural and conservation importance.

Methods: A hybrid sequencing approach combining Nanopore long reads and BGI short reads was used for denovo assembly. The genome was annotated, and we performed comparative analyses of repetitive sequences, interorganellar DNA transfer, codon usage, RNA editing, synteny, and phylogeny.

Results: The 644,236 bp mitogenome exhibits a highly fragmented architecture, comprising 21 independent circular chromosomes ranging from 19.9 to 48.7 kb. We annotated 39 unique protein-coding genes, 23 tRNA genes, and 3 rRNA genes. The genome is characterized by a high density of repetitive sequences and a massive influx of chloroplast DNA, with mitochondrial-plastid sequences accounting for 12.72% of the total length. Comparative synteny analysis with other orchid species revealed an almost complete loss of gene order, highlighting extreme structural rearrangement. Despite this plasticity, core molecular features, such as codon usage and predicted RNA editing patterns, remain conserved. Phylogenetic analysis robustly placed C. sieboldii within the Orchidaceae.

Discussion: This study decodes a complex multichromosomal mitogenome, reinforcing the paradigm of dynamic structural evolution in orchids and providing a vital genomic resource to support conservation efforts and evolutionary research on the Calanthe genus.

Circular RNAs (circRNAs) serve as key post-transcriptional regulators in plant stress adaptation. Here, we comprehensively characterize the circRNA landscape of cotton (Gossypium arboreum) under multiple abiotic stresses condition using RNase R-enhanced sequencing. Through a stringent KNIFE-based algorithm pipeline, we identified 4,365 high-confidence circRNAs. Mechanistically, circRNA biogenesis was associated with long flanking introns and exhibited complex patterns of alternative splicing, revealing conserved production propensities but dynamic splice sites across species. Nuclear circRNAs frequently exhibited expression patterns decoupled from their host genes, typically in a stress-specific manner. By integrating miRNA-seq data, we constructed a circRNA-miRNA-mRNA regulatory network and found it centered mainly on cotton-specific miRNAs. Notably, we discovered an extraordinary dominance of chloroplast-derived circRNAs, accounting for over 80% of the total circRNAs repertoire. These chloroplast circRNAs clustered dominantly at clustering at the 3' terminus of the photosynthetic gene psbA gene, suggesting a specialized post-transcriptional regulatory mechanism within the chloroplast. This study provides a high-resolution cotton circRNA atlas and highlights psbA-derived circRNAs as potential molecular targets for improving environmental resilience in crop.

Plasmopara viticola, an obligate biotrophic oomycete, is the causal agent of downy mildew in grapevine (Vitis vinifera) and a major constraint to viticulture worldwide. Here, we report the first high-quality whole-genome assembly of an Indian P. viticola isolate (PV01), generated using a hybrid sequencing approach combining Illumina and Oxford Nanopore platforms. The assembled genome spans 84.09 Mb across 182 contigs, with an N50 of ~971 kb and 97% BUSCO completeness, and encodes 12,404 predicted protein-coding genes, diverse transposable elements, and lineage-specific expansions. Functional annotation revealed a rich repertoire of effectors, including RXLR, CRN, and apoplastic effectors, as well as putative virulence-associated and secretory proteins likely involved in host manipulation and immune suppression. Comparative ortholog analysis across P. viticola isolates and representative oomycetes identified a conserved core genome alongside 164 PV01-specific orthogroups, reflecting isolate-level diversification. Dual RNA-seq analysis of infected grapevine leaves revealed strong suppression of chloroplast- and photosynthesis-associated pathways in the host, coupled with induction of defense-related genes, including PR proteins, WRKY transcription factors, calcium signaling components, and JA/ET-mediated pathways. Concurrently, P. viticola displayed infection-stage-specific expression of effectors, apoplastic proteases, vesicle trafficking components, and genes associated with autophagy suppression and redox homeostasis. Together, these integrated genomic and transcriptomic analyses provide insights into the molecular mechanisms underlying P. viticola pathogenicity and grapevine immune modulation.

Salinity and alkalinity stress is one of the main factors limiting the yield of rice. The damage to growth caused by alkaline stress is more severe than the damage caused by neutral salt stress. At present, there are limited genetic resources QTLs and genes available for rice breeders to improve alkalinity tolerance. To reveal new alkaline tolerance loci, we phenotyped 1,002 F_2:3 lines from Teng-Xi144 (TX144, alkalinity-sensitive)×Long-Dao19 (LD19, alkalinity-tolerant) for seedling survival and ion contents under 0.15% Na₂CO₃. Five traits were phenotyped under 0.15% Na₂CO₃ to identify major QTLs for alkalinity tolerance at the seedling stage (ATS). Using QTL-seq resequencing technology and a high-density linkage map based on 4,326 SNP markers, we identified qATS6 as a major QTL affecting seedling alkalinity tolerance, which could explain 15.33% of phenotypic variation, respectively. Within the 0.69 Mb interval, annotation, expression profile analysis, qRT-PCR and sequence analysis revealed a CDS single nucleotide polymorphism (SNP) in LOC_Os06g40640 (OsAld-Y) that differentiated parental responses to alkalinity stress. OsAld-Y has been reported to be a functional gene related to chloroplast development. Using CRISPR-Cas9 gene editing technology, we determined that OsAld-Y significantly enhanced alkalinity tolerance at the seedling stage. This study identified OsAld-Y as an alkalinity tolerant gene, and a SNP in the CDS region of OsAld-Y can be used to identify transcription factors that interact with it. This provides a theoretical basis for finding the molecular mechanism of OsAld-Y upstream and downstream regulation of alkalinity tolerance and molecular design breeding in the future.

Introduction: Accurately assessing the natural recovery processes of forest ecosystems remains a key challenge in restoration ecology. The concept of dark diversity-the set of species absent from a site but belonging to its habitat-specific species pool-provides a novel lens for this assessment.

Methods: In this study, we developed and applied an integrated diagnostic framework that synthesizes dark diversity, functional traits, and diagnostic species. We applied this framework to a chronosequence of recovering forest ecosystems in subtropical China, representing early, middle, and late recovery stages.

Results: Our results demonstrated that the Community Completeness Index (CCI), derived from dark diversity, increased significantly during recovery, with its stabilization indicating the approach to a stable state. The framework identified stagespecific early-warning species: the absence of light-demanding, acquisitive transitional species in the mid-stage signaled successful progression, while the absence of shade-tolerant, conservative climax species in the late-stage signaled potential degradation. Crucially, analysis using Dark Diversity Affinity (DDA) revealed that the functional traits of species (e.g., seed mass, mycorrhizal type, leaf economics) were the primary filters determining species absence, exhibiting a stronger influence than local environmental conditions. These filters shifted predictably across stages, from dispersal and establishment limitations early on to competitive interactions later.

Discussion: The proposed framework translates dark diversity theory into an actionable tool for restoration. It moves beyond simple observation to diagnose recovery success, pinpoint specific bottlenecks, and inform targeted interventions such as assisted dispersal or canopy management. This provides a mechanism-based approach for guiding precision restoration in forest ecosystems.

High temperatures may have a substantial impact on cellular meiosis, and subsequently affects plant reproduction, development, and yield over time. In this study, using overexpressed transgenic lines, we show that BrDMC1, a gene involved in meiotic recombination, regulates heat tolerance during the early pollen development stage in Brassica rapa. According to the expression pattern analysis, BrDMC1.A03 was not discovered at the transcriptional level, whereas BrDMC1.A01 was highly expressed in young flower buds in B.rapa. The Cis-acting element prediction revealed that BrDMC1.A01 contains a low-temperature responsive element, and GUS histochemical analysis revealed an increased staining ability following temperature stress. Under normal conditions, there were no significant cytogenetic or molecular differences between wild-type (WT) and overexpressed-BrDMC1 (OE-BrDMC1).After 24 h of treatment at 38°C, compared with WT, OE-BrDMC1 demonstrated dramatically increased pollen fertility, reduced aberrant chromosomal behaviors during meiosis, lowered reactive oxygen species (ROS) concentration, and boosted antioxidant enzymes SOD, POD, and CAT. Furthermore, genes involved in repair of DNA double-strand breaks (DSBs), as well as those that govern meiotic cell cycle transition, were considerably increased in OE-BrDMC1 under high temperature stress. These findings suggest that BrDMC1 could probably mediate heat tolerance during pollen meiosis, revealing the genetic basis for meiotic adaptation to high temperatures in B.rapa.

Introduction: The CrRLK1L family represents an important subgroup of plant receptor-like kinases (RLKs) that govern growth, signal transduction, reproduction, and stress adaptation.

Methods: In this study, we performed genome-wide identification, phylogenetic reconstruction, gene structure and motif analysis, evolutionary duplication analysis, promoter cis-element prediction, and tissue- and stress-specific expression profiling of SbCrRLK1L genes.

Results: A total of 28 SbCrRLK1L genes were identified and clustered into four well-supported subgroups with conserved structural features. Multiple duplication events, including WGD, TD, PD, DSD, and TRD, contributed to the expansion of this gene family. Promoter analysis revealed abundant cis-elements associated with hormonal regulation, stress responses, and development. Expression analysis showed that SbCrRLK1L1/8/17/24/25/26 were predominantly expressed in roots, while SbCrRLK1L1/8/17/24/25 were significantly regulated by drought and salt stress.

Discussion: The expression of specific SbCrRLK1L genes suggests their potential roles in root development. The strong transcriptional responsiveness to abiotic stress indicates that key SbCrRLK1L members may act as critical regulators in sorghum stress tolerance. Collectively, our findings provide a foundation for dissecting the functions of CrRLK1L genes in sorghum development and stress adaptation.