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• Rht-B1b and Rht-D1b, the ‘Green Revolution’ (GR) genes, greatly improved yield potential of wheat under nitrogen fertilizer application, but reduced coleoptile length, seedling vigor and grain weight. Thus, mining alternative reduced plant height genes without adverse effects is urgently needed. • We isolated the causal gene of Rht24 through map-based cloning and characterized its function using transgenic, physiobiochemical and transcriptome assays. We confirmed genetic effects of the dwarfing allele Rht24b with an association analysis and also traced its origin and distribution. • Rht24 encodes a gibberellin (GA) 2-oxidase, TaGA2ox-A9. Rht24b conferred higher expression of TaGA2ox-A9 in stems, leading to a reduction of bioactive GA in stems but an elevation in leaves at the jointing stage. Strikingly, Rht24b reduced plant height, but had no yield penalty; it significantly increased nitrogen use efficiency, photosynthetic rate and the expression of related genes. Evolutionary analysis demonstrated that Rht24b first appeared in wild emmer and was detected in more than half of wild emmer and wheat accessions, suggesting that it underwent both natural and artificial selection. • These findings uncover an important genetic resource for wheat breeding and also provide clues for dissecting the regulatory mechanisms underlying GA-mediated morphogenesis and yield formation.

Seed germination is one of the most important biological processes in the life cycle of plants, and temperature and water are the two most critical environmental factors that influence seed germination. In the present study, we investigated the roles of the plant hormone abscisic acid (ABA) and reactive oxygen species (ROS) in high temperature (HT) and drought-induced inhibition of rice seed germination. HT and drought stress caused ABA accumulation in seeds and inhibited seed germination and seedling establishment. Quantitative real-time polymerase chain reaction analysis revealed that HT and drought stress induced the expression of OsNCED3, a key gene in ABA synthesis in rice seeds. In addition, ROS (O2•- and H2O2) and malondialdehyde contents were increased in germinating seeds under HT and drought stress. Moreover, we adopted the non-invasive micro-test technique to detect H2O2 and Ca2+ fluxes at the site of coleoptile emergence. HT and drought stress resulted in a H2O2 efflux, but only drought stress significantly induced Ca2+ influx. Antioxidant enzyme assays revealed that superoxide dismutase (SOD), peroxidase, catalase (CAT), and ascorbate peroxidase (APX) activity were reduced by HT and drought stress, consistent with the expression of OsCu/ZnSOD, OsCATc, and OsAPX2 during seed germination. Altogether, these results suggest that ABA and ROS accumulation under HT and drought conditions can inhibit rice seed germination and growth.

1. Seeding native plants is a key management practice to counter land degradation across the globe, yet the majority of seeding efforts fail, limiting our ability to accelerate ecosystem recovery. 2. Recruitment requires transitions through several seed and seedling stages, some of which may have overriding influences on restoration outcomes. We lack, however, a general framework to understand and predict differences in these critical demographic processes across species. Functional traits influence fitness, and consequently, trait variation could provide the basis for a framework to explain and predict variation in life stage transition probabilities. 3. We used seed and seedling traits, and field probabilities of germination, emergence, seedling establishment, and survival for 47 varieties of drylands grasses under two watering treatments to identify critical life stage transitions and quantify the effect of traits on cumulative survival through the first growing season. 4. Variation in germination and emergence probabilities explained over 90% of the variation in cumulative survival regardless of seedling survival probabilities or watering treatment, with emergence probability being the strongest predictor of cumulative survival. 5. Coleoptile tissue density and seed mass had significant effects on emergence and germination, respectively, explaining 10-23% of the variation in transition probabilities. 6. Synthesis and applications. While the majority of functional trait work has centred on linking leaf and root traits to resource acquisition and utilization, our study demonstrates that traits associated with germination and emergence may have prevailing influences on restoration outcomes. A portion of these traits have been examined, but there is substantial opportunity to identify other key traits driving these demographic processes. These advancements will underpin our ability to develop trait-based frameworks for overcoming recruitment barriers and facilitating recovery of degraded systems across the globe.

Lysinibacillus is a bacterial genus that has generated recent interest for its biotechnological potential in agriculture. Strains belonging to this group are recognized for their mosquitocidal and bioremediation activity. However, in recent years some reports indicate its importance as plant growth promoting rhizobacteria (PGPR). This research sought to provide evidence of the PGP activity of Lysinibacillus spp. and the role of the indole-3-acetic acid (IAA) production associated with this activity. Twelve Lysinibacillus spp. strains were evaluated under greenhouse conditions, six of which increased the biomass and root architecture of corn plants. In most cases, growth stimulation was evident at 108 CFU/mL inoculum concentration. All strains produced IAA with high variation between them (20–70 µg/mL). The bioinformatic identification of predicted genes associated with IAA production allowed the detection of the indole pyruvic acid pathway to synthesize IAA in all strains; additionally, genes for a tryptamine pathway were detected in two strains. Extracellular filtrates from all strain’s cultures increased the corn coleoptile length in an IAA-similar concentration pattern, which demonstrates the filtrates had an auxin-like effect on plant tissue. Five of the six strains that previously showed PGPR activity in corn also promoted the growth of Arabidopsis thaliana (col 0). These strains induced changes in root architecture of Arabidopsis mutant plants (aux1-7/axr4-2), the partial reversion of mutant phenotype indicated the role of IAA on plant growth. This work provided solid evidence of the association of Lysinibacillus spp. IAA production with their PGP activity, which constitutes a new approach for this genus. These elements contribute to the biotechnological exploration of this bacterial genus for agricultural biotechnology.

Key messageThis study identified Rht25, a new plant height locus on wheat chromosome arm 6AS, and characterized its pleiotropic effects on important agronomic traits.Understanding genes regulating wheat plant height is important to optimize harvest index and maximize grain yield. In modern wheat varieties grown under high-input conditions, the gibberellin-insensitive semi-dwarfing alleles Rht-B1b and Rht-D1b have been used extensively to confer lodging tolerance and improve harvest index. However, negative pleiotropic effects of these alleles (e.g., poor seedling emergence and reduced biomass) can cause yield losses in hot and dry environments. As part of current efforts to diversify the dwarfing alleles used in wheat breeding, we identified a quantitative trait locus (QHt.ucw-6AS) affecting plant height in the proximal region of chromosome arm 6AS (< 0.4 cM from the centromere). Using a large segregating population (~ 2800 gametes) and extensive progeny tests (70–93 plants per recombinant family), we mapped QHt.ucw-6AS as a Mendelian locus to a 0.2 cM interval (144.0–148.3 Mb, IWGSC Ref Seq v1.0) and show that it is different from Rht18. QHt.ucw-6AS is officially designated as Rht25, with Rht25a representing the height-increasing allele and Rht25b the dwarfing allele. The average dwarfing effect of Rht25b was found to be approximately half of the effect observed for Rht-B1b and Rht-D1b, and the effect is greater in the presence of the height-increasing Rht-B1a and Rht-D1a alleles than in the presence of the dwarfing alleles. Rht25b is gibberellin-sensitive and shows significant pleiotropic effects on coleoptile length, heading date, spike length, spikelet number, spikelet density, and grain weight. Rht25 represents a new alternative dwarfing locus that should be evaluated for its potential to improve wheat yield in different environments.

Hypoxia is a key limiting factor for seedling emergence and establishment of direct-seeded rice (DSR) under submergence. The anaerobic germination (AG) tolerance, therefore, is one of the most critical traits in DSR breeding programs. However, the genetic basis of AG is still unclear. In this study, 229 single segment substitution lines (SSSLs) were arranged in an augmented design in field planting. We evaluated the anaerobic germinability by measuring the SSSLs’ coleoptile length (CL) under submergence, and then identified AG QTLs. AG was a typical quantitative trait based on the results of five cropping seasons. We repeatedly detected 19 SSSLs with putative AG QTLs in at least two cropping seasons. Moreover, substitution mapping identified 11 integrated AG QTLs on nine chromosomes, including six positive and five negative QTLs with additive effect contributions ranging from 6.8 to 18.5%. Among the 11 QTLs, qAG4 and qAG11 were novel ones, qAG9 was cloned in a previous study, and the remaining eight QTLs overlapped with reported AG QTLs. Overall, we identified some genetic loci controlling AG in multiple environments, which may be useful for developing varieties suitable for DSR.

Increasing numbers of rice farmers are adopting methods of direct seeding in flooded paddy fields to save costs associated with labor and transplanting. Successful seedling establishment under anoxic conditions requires rapid coleoptile growth to access oxygen near the water surface. It is important to identify relevant genetic loci for coleoptile growth in rice. In this study, the coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of a germplasm collection consisting of 200 cultivars growing in a low-oxygen environment for 6 days varied extensively. A genome-wide association study (GWAS) was performed using 161,657 high-quality single nucleotide polymorphisms (SNPs), which were obtained via genotyping by sequencing (GBS). A total of 96 target trait-associated loci were detected, of which 14 were detected repeatedly in both the wet and dry seasons. For these 14 loci, 384 genes were located within a 200-kb genomic region (± 100 kb from the peak SNP). In addition, 12,084 differentially expressed genes (DEGs) were identified using transcriptome expression profiling. Based on the GWAS and expression profiling, we further narrowed the candidate genes down to 111. Among the 111 candidate DEGs, Os02g0285300, Os02g0639300, Os04g0671300, Os06g0702600, Os06g0707300, and Os12g0145700 were the most promising candidates associated with anaerobic germination. In addition, we performed a detailed analysis of OsTPP7 sequences from 29 samples in our panel containing 200 diverse germplasms. A total of 11 mutation sites were identified, and four haplotypes were obtained. We found that 7 varieties with the OsTPP7-1 haplotype had higher phenotypic values. This work broadens our understanding of the genetic control of germination tolerance of anaerobic conditions. This study also provides a material basis for breeding superior direct-seeded rice varieties.

Coleoptile length, in wheat, is a significant agronomic trait impacting yield by facilitating the successful establishment of seedlings. In arid regions, varieties possessing longer coleoptile can evade harsh conditions by deep sowing, paving the way for improved yield. However, the study of genes involved in coleoptile development is insufficient. In this study, a high-density 660 K SNP array was used for genome-wide association study (GWAS) on coleoptile length in 150 wheat varieties. The findings revealed the detection of 353 significantly associated SNPs across all environments. The integration of linkage disequilibrium analysis and haplotype analysis mined 23 core QTLs capable responsible for the stable regulating coleoptile length in wheat. In wheat varieties characterized by extended coleoptile length, 6,600, 11,524, and 6,059 genes were found to be differentially expressed at three distinct developmental stages within the coleoptile, respectively. Through GWAS, gene expression levels, and functional annotation, we concluded the identification of two candidate genes ( TraesCS2B02G423500 , TraesCS2B02G449200 ) regulating wheat coleoptile length. By employing WGCNA and protein interactions prediction, discovered that the 19 genes were found to interact with candidate genes and participate in plant hormone metabolism and signaling, cell elongation or proliferation, which collectively contributing to coleoptile elongation. Additionally, two KASP markers were developed which can be used in breeding. These results offer a basis for understanding the genetic regulatory network responsible for wheat coleoptile length formation. The QTLs and candidate genes identified in this study can be further utilized for genetic improvement of wheat coleoptile length.

The objective of this investigation was to evaluate the impact of seed priming with seaweed liquid extracts (SLEs) prepared from three Egyptian seaweeds (Ulva fasciata, Cystoseira compressa, and Laurencia obtusa) in a concentration of 20 g L-1 on seed germination and seedling growth of Vigna sinensis and Zea mays as well as the effectiveness of these extracts in ameliorating salinity stress. Laurancia extract (LLE) induced the maximum positive response in germination as well as producing the maximum increases in all seedling morphological parameters with percent of response 87.14% for hypocotyl growth of V. sinensis and 85.71% coleoptile elongation of Z. mays. The maximum amylase and protease activities were recorded with LLE priming. Ulva, Cystoseira, Laurencia liquid extract consortium (UCLLE) induced the highest promotion effect for both V. sinensis and Z. mays giving significant increments for all growth criteria, dry biomass 0.301 and 0.438 g seedling-1, Chl a 18.98 and 13.79 mg g-1 FW, total carbohydrates 460.88 and 518.14 g seedling-1, protein 219.72 and 207.49 g seedling-1 respectively. Seeds primed with UCLLE consortium exhibited remarkable tolerance for salinity stress, meanwhile the highest ameliorating effect was pronounced with 10% SW supplementation. Priming with SLEs enhances the growth of either V. sinensis or Z. mays under salinity stress, whereas UCLLE consortium induced significant increases in biomass 0.231 and 0.379 g seedling-1, respectively. Seed priming with SLEs enhanced guaiacol peroxidase activity giving the highest value with UCLLE consortium conjugated with 25% SW (12.47 and 13.05 μmol min-1 g-1 FW), respectively. Application of Canonical Corresponding analysis (bi-plot) demonstrates a significant correlation between variables of SLEs components and germination indices of the two plants concluding total nitrogen, total phosphorous, potassium, ascorbic acid, and amino acids besides carbohydrate content. Therefore, results maintain the concept of SLEs as agricultural biocatalyst which could be practiced as prospective biostimulants for being feasible, sustainable, eco-friendly, and effective in improving salinity tolerance for some plants.

In the context of climate change, drought is a critical challenge that drastically limits the growth and productivity of crops. Seminal roots and coleoptile play an important role in crop establishment and growth. This study assessed the adaptive changes at an early stage of development using a resurrection approach on 40 populations of wild barley [Hordeum vulgare subsp. spontaneum (C. Koch)] that were collected in 1991 and recollected from the same sites in 2014. Significant genetic variability (P < 0.001) was detected for seminal shoot and root traits assessed based on collection sites and with collection-time interactions. All traits except root length showed an increase in broad-sense heritability (h2) and diversity in the population collected in 2014, with root number and first leaf length showing the highest values (68% and 57%, respectively). The two populations diverged into two distinctive structure categories: a conserved structure and an evolved structure. Moreover, the study revealed a trend in adaptative changes of the populations by grouping them according to their eco-geographical pattern, such as a better shoot and seminal roots traits expression that allows the plant to respond to increases in drought from the north to the south over time. These results provide useful information on the responses of crop wild relatives to environmental pressures and highlight the importance of in-situ conservation in the context of climate change adaptation and sustainability of crop improvement.