BMC Plant Biology

Abstract/SummaryGlandular trichomes are specialized epidermal structures on Cannabis sativa L. inflorescences that synthesize and store cannabinoids and terpenoids, making them central to the species economic and medicinal value. Although trichome development is a multistage genetic process, its regulatory basis in C. sativa remains poorly understood, particularly with respect to sexual dimorphism and sex plasticity. Here, we combined orthology-based gene discovery with transcriptomic profiling to investigate trichome development across four floral phenotypes: female flowers (FF), male flowers (MF), induced male flowers on XX plants (IMF), and induced female flowers on XY plants (IFF). Using trichome development-related genes from Arabidopsis thaliana, a model for unicellular non-glandular trichome development, and Solanum lycopersicum, a model for multicellular glandular trichomes, we identified and mapped 53 candidate C. sativa trichome development regulator genes (CsTDRGs). The CsTDRG set did not support a simple Arabidopsis- or tomato-like model, but instead included Arabidopsis-like epidermal fate components, including MBW-related regulators and GL2, alongside tomato-like multicellular trichome regulators, including MIXTA-like, HD-ZIP IV, WOX, MTR, GRAS, and hormone-associated candidates. RNA-seq analysis showed that CsTDRG expression was more strongly associated with floral phenotype than chromosomal sex. Genes with preferential expression in pistillate tissues were CsTT8, CsMYC1/GL3, CsGL2, CsYABBY4 and CsMIXTA-like1/MYB106, whereas CsMTR1, CsGRAS9, and CsCKX3 were upregulated in male (MF and IMF) flower. These findings suggest that sexually dimorphic trichome development in C. sativa reflects differential regulation of a shared developmental toolkit that combines conserved epidermal fate components with multicellular and glandular trichome regulatory modules.

The transformation of the free nuclear syncytium into cellular endosperm tissue with starch and protein accumulation is a well-established phenomenon, at least in the fruits of cereals of the Triticeae tribe. The present article demonstrates that there is considerable diversity inherent in this type of caryopsis morphogenesis. By examining various taxa (species, varieties, and cultivars) of wheat, oats, and some wild grasses, this research reveals significant deviations in endosperm morphogenesis from the typical state. A new developmental pattern of endosperm was identified, characterized by several distinctive features such as incomplete cellularization of the syncytium and starch accumulation within the acellular endosperm domains and the endosperm cavity. A large number of plastids were observed in the syncytium stage, which served as the basis for the later amyloplast stage. The acellular endosperm domains and the cavity domain exhibited connections at specific discontinuities in the modified aleurone layer surrounding the cavity. The peripheral parts of the caryopsis received fewer assimilates necessary for starch synthesis, which was attributed to their increased distance from the transfer system and a likely reduction in the efficiency of assimilate transport through the apoplast in these areas. The starch cavity volume constituted a few percent of the overall caryopsis volume, which could serve as a foundation for potential breeding improvements to enhance starch yields across different varieties.

Seed quality is a complex trait shaped by morphological, biochemical and microbiological properties that are rarely characterised simultaneously, limiting our ability to identify robust predictive indicators of germination speed and seedling emergence across varieties. Here, we performed a multi-factor characterisation of eight common bean (Phaseolus vulgaris L.) varieties, combining seed morphometrics, untargeted GC-MS metabolomics on three seed organs, and amplicon sequencing of bacterial and fungal communities, to identify indicators of germination speed and emergence percentage. The eight varieties showed substantial variation in both traits, used as physiological seed quality proxies. Seed weight and size variation between varieties were correlated with germination speed. The intravariety variance of seed weight was independently correlated with emergence performance. Metabolome composition differed strongly across seed organs, with variety as the dominant driver. Individual-seed metabolomic profiles in the plumule and cotyledon were associated with germination speed but not emergence, yielding 16 plumule and three cotyledon candidate metabolite markers. Fungal community composition was associated with both germination speed and emergence, while bacterial communities were associated with emergence only. Nine fungal and four bacterial taxa were identified as candidate indicators. Inter-kingdom co-occurrence network analysis revealed that fungi with similar germination speed associations tend to cluster in the same modules, suggesting that community-level modules rather than individual taxa may constitute more robust microbial indicators. These results demonstrate that germination speed and emergence capacity are governed by distinct seed properties, and provide morphological, metabolic and microbial candidate indicators for integration into targeted seed quality assessment frameworks for common bean.

Post-harvest physiological deterioration (PPD) represents a significant challenge of cassava production and commercialization. This multifaceted biological process involves a series of mechanisms, including enzymatic stress responses, alterations in gene expression, protein synthesis, accumulation of secondary metabolites, and ultimately, programmed cell death. These changes render the storage roots unpalatable and unmarketable. Therefore, unraveling the genetic architecture of PPD and exploring the interactions of associated genes during its early and late stages is essential for the crop production. We used modern genetic resources to unravel the genetic basis of PPD, based on a genome-wide association study (GWAS), utilizing a combination of different models, including BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway), SUPER (Settlement of MLM Under Progressively Exclusive Relationship), and MLMM (Multi-locus mixed models). The phenotyping dataset spanned five years and included evaluations from 42 different trials, evaluating the Embrapa (Brazilian Agricultural Research Corporation) germplasm along with a population derivative from a genomic selection cycle. We utilized a genotype dataset comprising 26,000 high-quality SNPs (single nucleotide polymorphisms). Our findings indicated four significant genetic variants located on chromosomes 2, 5, and 13, which together explain 35.83 % of the phenotypic variation. These variants are associated with genes that are closely linked to the pathways activated during the early and late symptoms of PPD. The identification of these three key genes provides valuable insights into the genetic architecture of PPD and lays a strong foundation for molecular breeding, supporting the efforts to identify cassava genotypes with enhanced PPD tolerance, the identified genomic regions may be incorporated into genomic selection models, thereby enhancing marker-assisted selection (MAS) and improving breeding strategies for long shelf life and high-quality agronomic cassava cultivars for the cassava community.

Horseweed (Erigeron canadensis) is a widely distributed annual weed that can cause significant yield losses if not properly controlled. Its phenotypic plasticity allows it to rapidly acclimate to new environmental conditions, such as drought and herbicides, such as glyphosate, with the potential for cross stress acclimatization. The objectives of this research were to uncover the physiological and genetic effects at the intersection of drought stress and glyphosate resistance. To this end, we performed greenhouse dose response experiments, RNAseq, 14C glyphosate absorption and translocation, and cuticular lipid profiling via GC/MS. Greenhouse dose-response experiments revealed that, after drought stress, there was a 2.5-3.7 fold reduction in glyphosate sensitivity via a significant reduction in glyphosate absorption, regardless if the starting population was resistant or susceptible to the field use rate already. Cuticular waxes were collected from each population with and without drought stress and were analyzed via GC/MS. When comparing total wax loads of plants grown under WW and DS conditions, we found that drought stress significantly increased total wax loads for all three populations. Additionally drought stress substantial increases the proportion of triterpenoids in the cuticle. By RNAseq, we found serval triterpenoid biosynthesis genes upregulated after drought, which likely drive the changes in cuticle composition and ultimately increased glyphosate resistance following drought. Ultimately, understanding how drought impacts glyphosate resistance is critical for maintaining optimal weed control in the changing climate. HighlightDrought stress induces changes to cuticle composition and gene expression that reduce glyphosate absorption, thereby increasing horseweeds ability to survive glyphosate application.

Flowering time and monocarpic senescence are tightly environmentally and genetically controlled. Typically, early flowering and staygreen traits are associated with opposing life-history strategies; stress avoidance versus adaptation; with flowering time an overarching regulator of crop cycle length. We developed RIL populations segregating for Ppd-1 and NAM-1 variation, which are otherwise isogenic. Multi-year field experiments enabled exploration and uncoupling of the relationship between heading and staygreen traits. Heading date manipulation enabled introduction of staygreen traits to their target breeding environments, characterised by a hot-finish. Under moderate stress, we report a 2.9% and 1.9% increase in grain width (P<0.0001), and 5.8% and 3.7% increase in TGW (P<0.0001), plus significantly greater yield (P<0.1) for late heading staygreen RILs homozygous for NAM-A1, and NAM-D1 missense variants, respectively. Grain yield increases were proportionate to the delay in senescence, being greater for the NAM-A1 than the NAM-D1 variant. For RIL populations segregating for both traits, senescence variation was observed relative to heading-date. Regarding grain yield, the staygreen trait-associated increase in source size could not compensate for the Ppd-1a associated pleiotropic reduction in sink size, even under hypothesised continental target breeding environments, with trait competition identified. Therefore, to maximise the benefits associated with staygreen traits, especially in early-heading favouring environments required targeted manipulation of source-sink dynamics, and we propose multiple strategies. HighlightStaygreen traits were associated with extending grain fill duration, increasing grain width, TGW and grain yield. There appears an antagonist relationship between earlier heading and staygreen traits.

Cassava is a major staple crop in tropical regions, and improving its root nutritional quality, particularly carotenoid and dry matter content (DMC), remains a central breeding goal. To elucidate the genetic basis of these traits by locating genomic regions associated with them, we analyzed 3,043 cassava clones from the Brazilian Agricultural Research Corporation (Embrapa) breeding program, phenotyped across 188 multi-environment trials conducted from 2011 to 2022 in Brazil. All clones were genotyped using Genotyping-by-Sequencing (27,045 Single Nucleotide Polymorphism - SNPs) and Diversity Arrays Technology - DArTseq (25,923 SNPs). Trait values were estimated using a two-stage mixed model to obtain deregressed BLUPs (Best Linear Unbiased Predictions), and genome-wide association analyses were performed using both the Mixed Linear Model (MLM) and Multi-Locus Mixed Model (MLMM). We detected six significant SNPs consistently associated with carotenoid content and DMC after Bonferroni correction. These SNPs mapped to six candidate genes involved in pathways relevant to root physiology, including Abscisic Acid ABA-related signaling, hydrolase activity affecting carotenoid conversion, fatty-acid biosynthesis within plastids, cell-wall remodeling, and glycolytic energy metabolism. The loci jointly explained 75.56 % of the phenotypic variance for carotenoids and 76.23 % for DMC, with individual SNP effects ranging from [~]17 % to [~]42 % PVE (Proportion of Variance Explained). Broad-sense heritability was H2 = 0.78 for carotenoids and H{superscript 2} = 0.34 for DMC, confirming substantial genetic control and suitability for molecular breeding. Haplotype analyses revealed four superior haplotypes for carotenoids and one key haplotype for DMC, each showing significantly higher trait values compared with other allelic combinations. These haplotypes represent promising targets for marker-assisted selection and genomic selection, with direct applicability for accelerating genetic gain in elite breeding populations. The results provide actionable genomic resources for breeding programs aiming to develop biofortified and high-root quality cultivars and establish a foundation for future multi-omics and functional validation studies.

Most extant plants show evidence of past polyploidization events in their genomes. Allopolyploids arise from hybridisation, resulting in the polyploid genome comprising subgenomes from different ancestors. Subsequent adaptation to their environment or selection pressure for specific traits has led to several allopolyploids exhibiting an unequal contribution from their subgenomes to their phenotype. Given the diversity of cultivars grown for different environments, it is possible that the associated regulatory changes may have given rise to different subgenome expression biases. Likewise, different tissues and developmental stages have distinct expression profiles that may correspond more strongly to one subgenome over the other(s). Here, we investigate different metrics for quantifying the contribution of each subgenome in space (tissue) and time (development) in cultivars of Brassica napus. Brassica napus has two subgenomes, A and C, from its ancestors Brassica rapa (A) and Brassica oleracea (C). We find that the C genome has higher overall expression than the A genome, whereas the average expression per gene is higher for the A genome. Direct comparison of homoeologous pairs reveals higher expression of genes on the C genome. We find that the degree of expression bias can change between cultivars, tissues and across time with bias quantification being strongly dependent on the metric. These findings help explain contradictory reports on expression bias and genome dominance. Significance statementWe demonstrate how different metrics of expression bias between subgenomes in polyploids can lead to conflicting inferences. We show that expression can be viewed as either A or C-biased, yet the differences are small, calling into question the relevance of subgenome dominance and expression bias in B. napus.

Hybrid wheat breeding offers a promising route to enhance grain yield and yield stability through heterosis, yet hybrid grain production remains constrained by limited cross-pollination efficiency due to high rates of autogamy. To achieve cross-pollination in an autogamous species like wheat, pollen must shed outside the floret. This is typically assessed by scoring visual anther extrusion (VAEX), a key floral trait that sets the foundation for cross-pollination. However, VAEX explains only part of the variation in hybrid grain set. To address this, we analyzed floral structures and reproductive processes underlying cross-pollination efficiency in wheat. From 24 elite winter wheat genotypes, we developed traits describing anther extrusion kinetics, pollen release, and floral bract architecture. These traits showed substantial genotypic variation and high heritability. While VAEX alone explained approximately 49% of the variation in hybrid grain set, combined trait analyses explained up to 77%, demonstrating that hybrid grain production is governed by coordinated floral and reproductive trait interactions. Together, our analyses define a hierarchical trait architecture linking floral bract mechanics, anther extrusion dynamics, and pollen shedding to cross-fertilization success. This establishes a systems-level phenotyping framework for improving male parent selection in hybrid wheat breeding. HighlightHigh cross-pollination efficiency in wheat is a multi-factorial process that requires lighter floral bract architecture combined with adequate anther extrusion and pollen release for improving hybrid grain production.

The current understanding of Crassulacean Acid Metabolism (CAM), including semi-controlled studies in pineapple, does not fully explain outcomes observed under commercial field conditions. Although empirical agronomy confirms a strong climatic influence on growth and development, mechanistic explanations at the metabolic level--particularly for photosynthate allocation--remain scarce. This study evaluated how environmental variation affects diel CAM outputs and how such effects can be agronomically interpreted. MD-2 pineapple plants were cultivated in contrasting natural environments across Costa Rica. Leaf samples were collected at defined phenological stages and at the end of CAM Phases I and IV. Field data revealed distinct metabolic balances between soluble sugar accumulation and nocturnal malic acid content. Under high radiation and temperature, sucrose concentrations increased markedly, reflecting shifts toward leaf growth over stem reserve storage. These shifts were associated with differences in harvest index, highlighting the role of sucrose dynamics in phenotypic plasticity. From a seed selection perspective, integrating CAM diel profiling into research protocols--together with physiological age (thermal units)--could provide a stronger basis for classifying planting material beyond current fresh-weight standards. Such integration would improve the prediction of photosynthetic performance, early establishment success, and ultimately, crop uniformity at harvest. Approximately 38% of diel metabolic patterns deviated from the classical CAM model, indicating dynamic regulatory mechanisms under field conditions. Understanding these patterns could improve the interpretation of yield variability, natural flowering incidence, and harvest index across agroecosystems. Recognizing these CAM particularities offers a path to bridge the gap between fundamental CAM biochemistry and agronomic application, enabling the development of precise management strategies that respond to metabolic plasticity under real-world conditions. Closing this gap is essential to enhance productivity, uniformity, and sustainability in pineapple agroecosystems.

In sunflower (Helianthus annuus L.), the composition of fatty acids in the seeds, primarily oleic, linoleic, stearic and palmitic acid, is of utmost importance for oil quality. Despite this, the genetic basis of this trait and its interaction with the environment is poorly understood. Understanding this interaction is critical to improvement of sunflower within the context of climate change. In this work, we incorporated fatty acid composition measurements from the sunflower SAM population and eight environments across an extensive geographic cline into GWAS. The SAM panel consists of 287 varieties representing approximately 90% of sunflower diversity, for which 2.2 million high-quality SNPs with a MAF > 5% are available. For increased power, multivariate GWAS was performed with four different inputs: (i) mean fatty acid composition within each environment, (ii) mean fatty acid composition within each environment omitting high oleic varieties, (iii) trait stability within environments quantified by standard errors among replicate samples ( stability) and (iv) Eberhart and Russells {beta} which quantifies trait stabilities across environments ({beta} stability). All four analyses yielded highly significantly associated SNPs. We found that high oleic varieties exhibited high {beta} trait stability, resulting in substantial overlap in markers between analyses (i) and (iv), with signals being fairly consistent between environments in analysis (i). For analyses (ii) and (iii), significant markers tended to vary between trials. For significant SNPs across all analyses, 147 candidate genes were identified, including promising candidates such as 15 fatty acid metabolism genes, 6 heat shock proteins and 22 transcription factors. Lastly, a large introgression consisting of two flanking inverted sequences on Chromosome 5 was found to coincide with stability in the Georgia trial, suggesting a role in FA composition stability under high heat conditions.

Thionins are cysteine-rich peptides involved in plant defense. However, their genomic organization, evolutionary expansion, and potential function in barley remain unclear. Here, we integrated reference genome, pan-genome, and pan-transcriptome resources to systematically characterize the thionin gene family in barley. Fifty-six thionin genes were identified in the reference genome Morex V3, displaying pronounced chromosomal clustering and high sequence conservation consistent with extensive tandem duplication. Promoter analysis of these genes revealed enrichment of cis-acting elements associated with stress- and hormone-related signaling pathways, suggesting a potential role for thionins in biotic stress responses, including aphid defense, as suggested by previous studies. Analysis of 20 barley genotypes revealed substantial copy number variation, particularly on chromosomes 6H and 7H, indicating dynamic population-level expansion. Sequence-based clustering grouped thionins into ten clusters and five singletons, with major clusters corresponding to specific chromosomes. Integration of pan-transcriptome data showed that transcriptional activity was largely confined to four major clusters. Aphid infestation of four genotypes featuring copy number variation in chr 6H thionin genes resulted in a strong induction of thionin gene expression, with more pronounced responses during poor-host interactions. Aphid-induced expression tended to increase with thionin gene number, however, this no correlation was observed regarding basal gene expression levels. Together, these findings indicate that the thionin gene family in barley has undergone species-specific expansion driven by tandem duplication and contributes to genotype-dependent aphid defense responses.

Abstract/SummarySex expression in Cannabis sativa is determined by XX/XY sex chromosomes but remains plastic, with ethylene inhibition inducing male flowers on XX plants and ethylene release inducing female flowers on XY plants. Although ethylene is a central regulator of this process, the contribution of gibberellin signaling to cannabis sex reversal remains poorly defined. Here, we reconstructed the GA biosynthesis, regulation, and signaling pathway in C. sativa and profiled GA-related gene expression during chemically induced sex reversal. Orthology-based searches identified 50 putative C. sativa GA-related genes, widely distributed across the genome, with the X chromosome harboring 11 genes, including six within the non-recombining region. Transcriptomic analyses across vegetative baseline, early post-treatment leaves, and developing flowers showed that expression profiles were broadly similar between XX and XY plants at day 0, weakly perturbed at day 1, and strongly structured by floral phenotype at day 14. Early responses were limited to downregulation of CsGA3ox1 in ethephon-treated XY plants and CsGASA1 in STS-treated XX plants. By day 14, sex reversal was associated with differential expression of key genes, including CsGA1, multiple GA20ox orthologs, CsGID1B, CsSLY2, and several GASA genes, indicating broad remodeling of GA regulation. Our findings position the GA pathway as a downstream module of ethylene-driven sex reversal in C. sativa, with GA activity tracking floral sexual identity, extending the framework of sexual plasticity beyond ethylene, and identifying candidate genes for functional validation and the development of sex-stable cultivars.

Increasing the diversity of biofuel crops can help meet energy demands while also stabilizing the domestic biofuel market. Sorghum bicolor is a promising feedstock for bioethanol production due to its sugar accumulation and storage in the stem in addition to its cellulosic biomass. Sorghum also exhibits high tolerance to abiotic stresses like extreme temperatures and drought. However, sorghums sugar production falls short when compared to current bioethanol feedstocks like maize and sugarcane. Therefore, to improve sorghum for the bioethanol market, an autotetraploid sorghum line was induced using colchicine treatments to increase cell size for greater sugar production and storage. Induced autotetraploid sorghum lines were validated with flow cytometry and screened using stomatal prints to detect larger stomatal cells. Two separate autotetraploid sorghum lines that were derived from the same M1 plant were characterized and evaluated for sugar production in a two-year field trial. The two autotetraploid lines displayed equal or improved performance when compared to their diploid equivalents for multiple juicing traits. Altogether, the data illustrate sorghums tolerance for autopolyploidy induction in an inbred background and suggest an opportunity for further improvements through progressive heterosis. SIGNIFICANCE STATEMENTPolyploidy has played a significant role in the improvement of some crop species. The characterization of a novel autotetraploid sweet sorghum line demonstrates the potential of increased sugar production in polyploids for biofuel applications.

IntroductionMany plant species secrete nectar to attract beneficial animals. The chemical composition of floral nectar influences pollinator nutrition and behavior, as well as microbial growth in flowers. Yet factors that predict nectar composition across plant species, as well as chemical compounds determining microbial growth in nectar, remain poorly understood. MethodsWe used both targeted and untargeted metabolomics to compare the nectar chemical profiles across 31 phylogenetically diverse plant species that span a range of floral morphologies. We examined the common classes of compounds detected in nectar and patterns of co-occurrence among them. We combined newly collected chemical data with previously published data on microbial growth in nectar of the same plant species to examine how nectar chemistry is associated with microbial growth. ResultsPlant species and clades varied in amino acid, minor sugar, and secondary metabolite composition and concentration. Sampled rosids and lilioids generally contained higher amino acids while asterids contained greater concentrations of oligosaccharides and sugar alcohols. Across plant species, proteinogenic amino acids frequently co-occurred in nectar but many were negatively associated with sucrose concentration. Plant species with greater concentrations of amino acids and other nitrogen-containing compounds hosted greater microbial density in nectar, while some other compound groups were negatively associated with microbial diversity. ConclusionsNegative correlations between nectar amino acid and sucrose concentration across species suggest ecological tradeoffs or physiological constraints in nectar composition. Given that the growth of common nectar microbes is limited by amino acid concentration, these findings suggest an ecological cost to amino acid production in nectar. Finally, we document variation among species in nectar vitamins, non proteinogenic amino acids and secondary metabolites with hypothesized yet currently untested ecological roles.

Background. DNA-based molecular markers underpin plant genetic diversity assessment, germplasm characterisation, and conservation prioritisation. Four marker systems dominate the field: Amplified Fragment Length polymorphisms (AFLPs), simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and random amplified polymorphic DNA (RAPDs). No quantitative meta-analysis had pooled their performance on the canonical diversity metrics: polymorphism information content (PIC), expected heterozygosity (He), and resolution power, across plants. Existing reviews are narrative, marker-restricted, or qualitatively conclusive of infeasibility. Methods. A PRISMA 2020-compliant systematic review (registered at the Open Science Framework) was executed. Eligible studies were within-study paired comparisons genotyping the same accession panel with at least two of {SNP, SSR, AFLP, RAPD} and reporting at least one diversity metric. Effect sizes were paired standardised mean differences (Hedges' g) computed under the Bernoulli-variance approximation. Random-effects REML meta-analysis used metafor 5.0.1 with Knapp-Hartung adjustment, leave-one-out, and r-sensitivity. Results. Fifteen within-study paired contrasts were eligible, distributed across three pools. Pool 2 (SSR vs SNP, He, k = 5) yielded a pooled Hedges' g of 0.494 (95% CI: -0.078 to 1.066, p = 0.075; I-squared = 90.2%; 95% PI [-0.82, 1.81]). SSRs exceeded SNPs on He in 4 of 5 studies; leave-one-out removal of the panel-size-asymmetric outlier raised the estimate to g = 0.644 (p = 0.025). Pool 3a (dominant-marker stratum, k = 6) yielded g = 0.419 (95% CI: -0.121 to 0.960, p = 0.103; I-squared = 56.5%); five of six contrasts showed SSR or AFLP exceeding RAPD on per-locus PIC. Pool 1 (PIC, k = 3, exploratory) gave a consistent direction (g = 0.453). All three pools point in the same direction: codominant or AFLP markers carry more per-locus information than the alternative being compared. Conclusions. SSR markers reported higher per-locus diversity than SNP and RAPD markers in plant within-study paired comparisons, mechanistically grounded in the SNP biallelic ceiling and the multi-allelic richness of SSRs. The effect attenuated or reversed in selfing/low-diversity panels and at the per-panel level when SNP panels exceeded approximately 1000 loci. RAPDs show the lowest per-locus information content of the four classes.

Background and AimsPaspalum notatum reproduces through either sexuality or apomixis, two pathways that may coexist within the same individual and are regulated by interconnected molecular networks responsive to environmental cues. Here, we characterized the transcript structure and expression of BUD SITE SELECTION PROTEIN 13 (BUD13), a component of the RES spliceosomal complex previously reported as differentially expressed in florets of sexual and apomictic plants, as a first step toward testing its involvement in the molecular regulation of the apomixis-sexuality switch. MethodsPreviously generated floral and leaf transcriptomes from sexual and apomictic Paspalum notatum plants, including Oxford Nanopore long-read data, were mined to characterize BUD13 transcript structure and expression. Phylogenetic analyses and in silico mapping were conducted to infer evolutionary relationships and determine the origin of the transcripts. Differential expression was validated by RT-qPCR, while in situ hybridization was used to reveal cell-specific ovule expression patterns. Key resultsBUD13 is expressed in Paspalum notatum florets as a truncated isoform (SHORT) encoding a small protein lacking part of the herpes simplex virus regulatory protein (ICP4) domain. Two SHORT transcripts, SHORT1 and SHORT2, with different 5' untranslated region (UTR) regions, were identified in flowers. SHORT1 was consistently upregulated in apomictic ovules from premeiosis to anthesis. Both transcripts originated from a single genomic locus located in the subtelomeric region of the short arm of chromosome 6. SHORT isoforms with variable structures were detected in other monocots. In situ hybridization showed that, whereas BUD13 was expressed throughout sexual ovules, expression was absent from the female germline of apomictic ovules. A consistent expression was observed in somatic proembryos of aposporous embryo sacs. ConclusionsOur findings reveal structural, spatial and temporal divergence in BUD13 expression between sexual and apomictic reproductive programs, providing new insights into the molecular regulation of asexual seed formation.

Strigolactones (SLs) are known to regulate shoot architecture and to be involved in plant responses to environmental stress, whereas their specific contributions to drought adaptation in barley remain incompletely defined. In this study, we analysed transcriptional, hormonal, and physiological responses to water deficit in barley SL mutants affected in early biosynthesis (Hvd10 and Hvd17), late biosynthesis (Hvmax1a), or signalling (Hvd14). The Hvd10, Hvd17, and Hvd14 mutants exhibited the typical high-tillering phenotype of SL deficiency, whereas Hvmax1a displayed characteristics similar to the wild type (WT), indicating functional differences within the SL biosynthetic pathway. Transcriptome analysis showed a clear overlap in gene expression among the high-tillering SL mutants under both control and drought conditions. We also used computational methods to identify potential transcription factors that might regulate SL-dependent gene expression. A drought experiment showed that SL mutants exhibited reduced biomass, relative water content, and photosynthetic efficiency, with the most pronounced effects observed in the high-tillering lines. Drought also activated the abscisic acid (ABA) pathway in all genotypes, with particularly high accumulation of ABA metabolites in the high-tillering SL mutants. Notably, Hvmax1a resembled the mutant-like metabolic profile, despite maintaining a wild-type-like architecture. Taken together, these results provide new insights into the roles of SL pathway components in drought responses and highlight functional differences among individual genes influencing both plant architecture and stress-related transcriptional programmes. Furthermore, the mutants generated in this study using Cas9-mediated genome editing represent a valuable genetic collection for future research into SL-mediated development and stress responses in barley.

The TETRATRICOPEPTIDE THIOREDOXIN-LIKE (TTL) proteins are a plant-specific family proposed to function as peripheral membrane proteins that contribute to abiotic stress tolerance in Arabidopsis, likely by maintaining cell wall integrity through brassinosteroid signaling. Previously, we identified a TTL gene that was differentially regulated at the translational level in nitrogen-fixing soybean plants under water deficit (WD) conditions. This finding prompted the characterization of the soybean TTL gene family. Using the Glycine max v4.0 proteome, we identified ten TTL homologs (GmTTL1-GmTTL10), which are unevenly distributed across five chromosomes. Phylogenetic and structural analyses grouped these genes into three clades and revealed a highly conserved exon-intron organization. Likewise, GmTTL proteins display a conserved number and arrangement of TPR and TRXL motifs. To gain insights into their potential biological functions, we integrated co-expression and differential expression analyses. This approach identified a co-expression module enriched for translationally downregulated genes related to the Gene Ontology terms "cellular anatomical entity", "membrane", "cell periphery", "cell wall modification", "nitrate assimilation", and "cell wall organization or biogenesis". Protein-protein interaction network analysis of this specific subset of genes uncovered a novel GmTTL connection with two nitrate reductase enzymes in nitrogen-fixing plants subjected to WD, potentially linking the TTL gene family to new functions or roles. This study provides a framework for future functional studies of GmTTL proteins and their contribution to abiotic stress adaptation in soybean. Key MessageThis work presents the first functional characterization of TTLs proteins in legume species and highlights key processes that may link the TTL gene family to new functions or roles.

Structured AbstractO_ST_ABSContext and ObjectiveC_ST_ABSDelayed sowing can expose chickpea crops to stress during the critical period for yield determination, but the effect of yield components and phenology to grain yield variation is not well characterised in diverse germplasm under rainfed conditions. Identifying genetic resources for grain yield improvement requires integration of multi-environment trial and genomic analyses to disentangle direct yield effects from indirect effects of phenology. This study aimed to (1) characterise genotype by environment interaction patterns for grain yield, yield components and phenology across times of sowing and seasons, and (2) identify genomic regions associated with improved grain yield that are present in genebank accessions but absent from current Australian commercial cultivars. MethodsA diversity panel of 141 kabuli chickpea genotypes, including six commercial Australian cultivars and 135 genebank accessions, was evaluated across six rainfed trials at Narrabri, New South Wales over three seasons (2018 to 2020) under typical (MAIN) and delayed (LATE) sowing. Multi-environment trial analyses with factor analytic models partitioned genotype by environment interactions for grain yield, 100-seed weight, seed number, and thermal time to flowering, podding, and maturity. Haplotype block analysis identified high variance blocks associated with seed number, classified by their overlap with high variance thermal time to flowering blocks, to distinguish from effects mediated by phenology. Results and ConclusionsDelayed sowing reduced grain yield by up to 1.04 t ha-{superscript 1}, driven primarily by reductions in seed number rather than 100-seed weight. Accelerated phenology was a key component of adaptation among commercial cultivars. Four haploblocks with high block variance for seed number were identified across all six trials. SignificanceSeed number was the dominant driver of grain yield variation in this diverse kabuli chickpea panel. Targeted introgression of rare superior haplotypes from genebank accessions provides an opportunity to broaden the genetic base of Australian kabuli chickpea and improve yield through higher seed number, with relevance to chickpea production systems facing similar climate variability. HighlightsDelayed sowing reduced grain yield in diverse kabuli chickpea germplasm by up to 1.04 t ha-1 across three years and six trials in northern New South Wales. Seed number, not seed weight, was the dominant driver of grain yield variation, and a shorter phenological duration was associated with higher seed number. Across all six trials, haplotype block analysis identified four genomic regions in high linkage disequilibrium with high variance for seed number and low variance for flowering time. The accession FLIP 94 62C uniquely carried rare superior haplotypes at two chromosome 4 blocks, the haplotype at the 17.0 Mb block was the most superior haplotype in all trials while the haplotype at the 8.5Mb block was most superior only in the most heat stressed environment.