Plant Genome最新文献

Climate change is intensifying the frequency and severity of abiotic stresses that threaten global food security by reducing crop productivity. Among these, saline stress poses a serious threat to barley (Hordeum vulgare L.) production. These conditions are increasingly prevalent in arid and semiarid regions, as well as in regions with limited access to freshwater resources, making the identification of salt tolerance genes essential for breeding resilient varieties. In this study, we evaluated 400 genotypes from the barley nested association mapping population HEB-25 under control conditions and 40% seawater irrigation to simulate moderate-to-high salinity stress. A genome-wide association study (GWAS) was conducted to identify alleles from wild barley [H. vulgare L. subsp. spontaneum (C. Koch) Thell.] associated with enhanced salt tolerance. Phenotypic evaluation included germination percentage (Ger%), shoot length (SL), root length (RL), root-shoot length ratio, seedling fresh weight, seedling dry weight, and salt tolerance index of the different traits. The HEB-25 families exhibited significant variation in seedling responses to seawater-induced salinity, with contrasting effects on SL, RL, and dry weight. Compared to the elite parental Barke, several genotypes demonstrated high tolerance under seawater stress, maintaining stable Ger% and exhibiting the highest tolerance indices. Moreover, GWAS results identified 60 highly significant single nucleotide polymorphisms associated with seedling growth parameters under both conditions. These findings underscore the value of the HEB-400 panel as a genetic resource for dissecting salinity tolerance mechanisms, identifying stress-adaptive alleles lost during domestication and a source of pre-breeding material for developing genotypes with enhanced salinity tolerance.

Cupuassu (Theobroma grandiflorum) is a fruit tree native to the Brazilian Amazon and increasingly relevant to regional bioeconomies. Its cultivation is severely affected by witches' broom disease (WBD), caused by Moniliophthora perniciosa. While a chromosome-scale genome of the susceptible genotype C1074 is available, the lack of a resistant reference has limited investigation into the genomic basis of resistance. Here, we present the first chromosome-scale assembly of the WBD-resistant genotype C174 (415.8 Mb) and a comparative analysis with C1074 integrating structural variant detection, gene-duplication profiling, transposable-element (TE) annotation, and time-resolved host-pathogen transcriptomics. C174 exhibits distinctive tandem and dispersed duplications, genotype-specific TE insertions, and coordinated defense-gene expression, together with higher heterozygosity indicative of broader allelic diversity. Genome-wide, TEs show differential expression and spatial proximity to immune loci, suggesting potential regulatory importance. Although C1074 encodes more nucleotide-binding domain leucine-rich repeat receptors (541 vs. 434), most remain transcriptionally inactive, whereas C174 shows sequential activation of pattern-recognition receptors, mitogen-activated protein kinase components, transcription factors, and pathogenesis-related proteins. Within the Chromosome 6 previously identified resistance quantitative trait locus, two duplicated DUF4220/DUF594 genes (where DUF is domain of unknown function) unique to C174-orthologous to a maize gene implicated in fungal response before-are infection-induced and display signatures of episodic positive selection. Together, these results establish a high-quality genomic framework for exploring the molecular architecture of WBD response in T. grandiflorum. The datasets generated here-including the C174 and C1074 reference genomes, immune-related variant catalog, and prioritized defense-gene lists-constitute a comprehensive open resource for evolutionary, functional, and breeding research of Theobroma species.

Bread wheat (Triticum aestivum) remains a major source of food and calories globally, yet its vast genome, polyploidy, and high number of repetitive sequences make genomic research challenging in this crop. In this review, we discuss the progress and future perspectives of genome research in wheat. Current efforts focus on the establishment of genome assemblies, advances in functional genomics, advances in epigenetics, translational genetics, and CRISPR-Cas9 genome editing offers a powerful tool for site-specific genome editing for wheat improvement and functional genetic analysis. These approaches have elucidated the genetic basis of many important agronomic traits such as grain yield, biotic and abiotic stress, and wheat quality. Future aims are expected to expand to pan-genomics, the mechanism of wheat domestication, funnel the outputs of functional genomics for deployment in wheat breeding, multi-omics studies facilitate genetic dissection, and the era of big data: creation, integration and utilization, and artificial intelligence breeding.

Polyploid individuals of the subtropical forage grass Paspalum notatum Flüggé (bahiagrass) exhibit distinct phenotypes, including apomixis, enhanced vigor, gigas effects, and increased stress tolerance. While apomixis-based breeding programs supported by molecular tools have improved agronomic traits such as growth habit, forage dry matter, and lipid profile, a genome-wide understanding of ploidy-induced transcriptomic changes is still lacking. In this study, we aimed to generate a comprehensive reference catalog of transcripts differentially expressed in the leaves of diploid and tetraploid individuals, characterize genome responses to polyploidy, and identify candidate genes for breeding. Our results reveal distinct transcriptomic profiles in polyploids, with significant impacts on development, redox homeostasis, and photosynthesis-patterns consistent with those observed in other species. Gene ontology enrichment analyses highlighted key categories related to stress responses and signaling pathways. We also identified critical breeding targets, including transcription factors and hormone-related genes. Co-expression network analysis uncovered 532 master regulators affected by genome doubling, with non-random distribution across the genome and hotspot clustering in specific chromosomes. Overall, our findings provide novel insights into the molecular consequences of polyploidy in P. notatum, offering a valuable resource for molecular breeding programs aimed at improving stress tolerance, vigor, and other desirable traits.

SUMOylation is a protein post-translational modification that is essential for plant growth and response to changing environments. However, past work in this area has mainly focused on simple sequence similarity methods for discovering SUMOylation genes, often using orthologue mapping from yeast (Saccharomyces cerevisiae) or Arabidopsis (Arabidopsis thaliana). In this work, we employed a range of computational techniques and approaches to describe and characterize the SUMOylation machinery in Asian rice (Oryza sativa), a globally important stable crop, and where the SUMOylation system has been shown to play key roles in responses to biotic and abiotic stresses. We describe and analyze the Ubiquitin-Like Protease (ULP) system at the phylogenetic, transcriptional, and protein structural levels, with a focus on the rice reference genome, a well-annotated rice population reference panel (RPRP), and wild rice genomes. Our analysis revealed the expansion of ULPs in the reference genome and RPRP set (32-45 ULPs) compared to wild rice (9-36 ULPs), raising an intriguing hypothesis about the expansion of the ULP family being driven by selective breeding pressure. We provide evidence of potential functional ULPs and their possible roles in biotic and abiotic stress responses in cultivated rice. These insights offer valuable resources for future rice breeding and crop improvement.

Meiotic recombination is essential for generating genetic diversity, driving plant evolution, and enabling crop improvement, yet its uneven distribution across genomes constrains breeding efforts. Here, we investigated the multi-omic landmarks that shape the recombination landscape in Brassica napus by integrating epigenomic, genomic, and transcriptomic data with recombination maps derived from large multiparental rapeseed populations. Predictive machine learning accurately predicted recombination rates and hotspot location using only feature information. Recombination was generally suppressed in centromeres and other repeat-rich, methylated regions and enriched in gene-dense, transcriptionally active domains. Proxies for chromatin configuration-such as DNA methylation, transposable elements, or genes-consistently achieved the highest predictive power with the random forest algorithm. We discovered distinct recombination landscape patterns between subgenomes, with crossovers clustering near subtelomeres in the A subgenome and more evenly spread across the C subgenome. Models trained on A subgenome data outperformed those based on the C subgenome, although combining both subgenomes improved overall accuracy.

Plant carnivory evolved through gene co-option and whole genome duplications (WGDs) over millions of years in at least 13 independent flowering plant lineages, but its genetic mechanisms remain largely unknown. To elucidate these mechanisms in Sarraceniaceae, we sequenced and assembled the Sarracenia purpurea genome and conducted a comparative analysis with both carnivorous and non-carnivorous species within a phylogenetic framework. Our chromosome-scale assembly is the first carnivorous genome from the order Ericales and the largest carnivorous genome sequenced (3.41 Gbp). This assembly has an N₅₀ > 220 Mbp, L₅₀ = 7, and N_max > 281.4 Mbp and contains 52,067 gene models, 96% of which are supported by direct mRNA evidence. The genome shows evidence of an ancient paleopolyploidization event about 81-84 Mya, which may have facilitated the evolution of different carnivory flavors within Sarraceniaceae. The WGD event resulted in the expansion of ∼33 gene families enriched in seven metabolic and regulatory pathways. The network of these seven pathways regulates plant defense and stress responses and appears to underpin carnivory in this species. Our comparative genomic analysis revealed that gene gain, rather than loss, was the primary driver of functional innovation and adaptation in Sarracenia and identified key orthogroups that may have contributed to the evolution of plant carnivory across different lineages. This genome is key to uncovering the genetic basis of plant carnivory, with broad relevance to evolution, ecology, and functional genomics.

The mandarin (Citrus reticulata) variety Premier (11C017) is a gamma-irradiated mutant hybrid derived from a cross between Murcott and Ellendale. The variety Premier exhibits favorable traits, including good fruit size and productivity similar to its progenitor variety (01C011), along with a reduced seed count compared to the progenitor. Here, we developed haplotype-resolved genomes for both Premier and its parental line Ellendale using PacBio HiFi and Hi-C sequencing, followed by a combination of de novo and reference-guided assembly approaches. The size of the assemblies ranged from 320 to 337 Mb, with N50s more than 31 Mb, and more than 98% BUSCO for the assembly and annotation. Comparative analysis revealed multiple structural rearrangements including inversions, translocations, and duplications in the Premier haplotypes relative to the parental genomes. Notably, we identified heterozygous reciprocal translocations (between Chr2 and Chr4 in haplotype 1, and Chr5 and Chr7 in haplotype 2) and a large heterozygous inversion (∼22 Mb on Chr2 of haplotype 1) as prominent rearrangements unique to Premier. These complex structural variants may disrupt normal meiotic pairing and gamete formation, potentially contributing to the observed reduction in seed number. These findings suggest that structural rearrangements may play a significant role in the reduction of the seed content of gamma-irradiated plants.

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass species in the family Poaceae. This species is a popular choice for lawns in the Southern United States, due to its higher tolerance to shade, heat and humidity. However, there is little genomic information available to researchers and breeders, limiting knowledge on the genetic basis for favorable traits. We present a reference-grade chromosome-scale genome assembly for the popular freeze-tolerant diploid cultivar Raleigh. The reference genome has been resolved into two haplotype assemblies (465.41 and 401.52 Mb), accounting for 95.2% and 82.1% of the expected haplotype genome size respectively, each anchored on the nine chromosomes and a total of 62,454 genes. Analysis of the assembly revealed 50.70% of the genome contained repeats. Analysis of the diversity within the species was investigated across 79 genotypes including commercial cultivars, breeding lines, and plant introductions by low-coverage sequencing identifying 605,038 single nucleotide polymorphisms (SNPs). The SNPs were used to investigate genetic diversity across the panel and the effectiveness of low-coverage sequencing on the high GC content species. SNPs classified genotypes into groups matching their phylogenetic and breeding history, with the plant introductions clustering into two groups on either side of the plot. Breeding lines for those whose parents existed in the panel clustered in between the two parents. These results showed that the cheaper, low-coverage option can be used for this type of analysis. Together, all of the resources produced in this study allow the start of the genomics-enabled genetic improvement for St. Augustinegrass.

Target of rapamycin (TOR) is an evolutionarily conserved serine/threonine kinase that plays a central role in regulating biological growth, development, and stress responses in eukaryotes. However, the TOR signaling pathway has not been thoroughly studied in apple (Malus domestica). Here, through sequence alignment with homologous genes in Arabidopsis thaliana, 14 conserved members of the TOR signaling pathway, encoded by 28 sequences, were identified in the apple genome. A comprehensive analysis of these members was subsequently performed by integrating their structural features, phylogenetic relationships, and expression profiles under low-nitrogen stress conditions. The results showed that the functional motifs of these members are highly conserved across species, while there are significant differences in the physicochemical properties of each member in apple. Subcellular localization predictions indicated that most members are likely localized to the nucleus; a few may reside in the cytoplasm or chloroplast. Quantitative PCR analysis showed that TOR pathway members are differentially regulated under low-nitrogen stress, suggesting their potential involvement in nitrogen stress response. Furthermore, MdTORs were found to directly interact with several autophagy-related (ATG) proteins in apple plants, in addition to its canonical target ATG13. Collectively, this study systematically characterizes the components of the TOR pathway in the apple genome, examines their expression dynamics under low nitrogen stress, and identifies novel interactions between TOR and ATGs. These research findings broaden our understanding of TOR-regulated autophagic pathways, provide a valuable foundation for future studies into their regulatory mechanisms, and also provide data support for clarifying the responses of TOR signaling pathway members in apple to low-nitrogen stress.