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Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, “Cardos” (registered in 1998) which was the first among the panel to contain this translocation. A “selective sweep” for this important translocation region on chromosome 2AS was found, putatively linked to plant response to biotic stress factors. Our approach helps in overcoming the drawbacks of incorrectly anchored markers on the wheat reference assembly and facilitates detection of selective sweeps for important agronomic traits.

Eight advanced durum-breeding lines were treated with 5-methyl-azacytidine to test the feasibility of generating sources of Fusarium head blight (FHB) resistance. Of the 800 treated seeds, 415 germinated and were advanced up to four (M4) generations by selfing. Thirty-two of the resulting 415 M4 lines were selected following preliminary screening and were further tested for FHB resistance for three years at two field locations, and in the greenhouse. Five of the 32 M4 lines showed less than 30% disease severity, as compared to the parental lines and susceptible checks. Fusarium-damaged kernels and deoxynivalenol analyses supported the findings of the field and greenhouse disease assessments. Two of the most resistant M4 lines were crossed to a susceptible parent, advanced to third generation (BC 1 :F 3 ) and were tested for stability and inheritance of the resistance. About, one third of the BC 1 :F 3 lines showed FHB resistance similar to their M4 parents. The overall methylation levels (%) were compared using FASTmC method, which did not show a significant difference between M4 and parental lines. However, transcriptome analysis of one M4 line revealed significant number of differentially expressed genes related to biosynthesis of secondary metabolites, MAPK signaling, photosynthesis, starch and sucrose metabolism, plant hormone signal transduction and plant-pathogen interaction pathways, which may have helped in improved FHB resistance.

Crop improvements can help us to meet the challenge of feeding a population of 10 billion, but can we breed better varieties fast enough? Technologies such as genotyping, marker-assisted selection, high-throughput phenotyping, genome editing, genomic selection and de novo domestication could be galvanized by using speed breeding to enable plant breeders to keep pace with a changing environment and ever-increasing human population.

Drought tolerant germplasm is needed to increase crop production, since water scarcity is a critical bottleneck in crop productivity worldwide. Auxin Regulated Gene involved in Organ Size ( ARGOS ) is a large protein family of transcription factors that plays a vital role in organ size, plant growth, development, and abiotic stress responses in plants. Although, the ARGOS gene family has been discovered and functionalized in a variety of crop plants, but a comprehensive and systematic investigation of ARGOS genes in locally used commercial wheat cultivars is still yet to be reported. The relative expression of three highly conserved TaARGOS homoeologous genes ( TaARGOS-A, TaARGOS-B, TaARGOS-D) was studied in three drought-tolerant (Pakistan-2013, NARC-2009 and NR-499) and three sensitive (Borlaug-2016, NR-514 and NR-516) wheat genotypes under osmotic stress, induced by PEG-6000 at 0 (exogenous control), 2, 4, 6, and 12 h. The normalization of target genes was done using β-actin as endogenous control, whereas DREB3 , as a marker gene was also transcribed, reinforcing the prevalence of dehydration in all stress treatments. Real-time quantitative PCR revealed that osmotic stress induced expression of the three TaARGOS transcripts in different wheat seedlings at distinct timepoints. Overall, all genes exhibited significantly higher expression in the drought-tolerant genotypes as compared to the sensitive ones. For instance, the expression profile of TaARGOS-A and TaARGOS-D showed more than threefold increase at 2 h and six to sevenfold increase after 4 h of osmotic stress. However, after 6 h of osmotic stress these genes started to downregulate, and the lowest gene expression was noticed after 12 h of osmotic stress. Among all the homoeologous genes, TaARGOS-D , in particular, had a more significant influence on controlling plant growth and drought tolerance as it showed the highest expression. Altogether, TaARGOSs are involved in seedling establishment and overall plant growth. In addition, the tolerant group of genotypes had a much greater relative fold expression than the sensitive genotypes. Ultimately, Pakistan-2013 showed the highest relative expression of the studied genes than other genotypes which shows its proficiency to mitigate osmotic stress. Therefore, it could be cultivated in arid and semi-arid regions under moisture-deficient regimes. These findings advocated the molecular mechanism and regulatory roles of TaARGOS genes in plant growth and osmotic stress tolerance in contrasting groups of wheat genotypes, accompanied by the genetic nature of identified genotypes in terms of their potential for drought tolerance.

Winter wheat is a vital grain crop in Xinjiang and severe water scarcity in this arid region necessitates efficient irrigation strategies for sustainable production. A two-year field experiment (2022–2023) in northern Xinjiang was conducted to evaluate the effects of sowing patterns and drip irrigation levels on winter wheat growth and yield. Two sowing patterns were tested: uniform row spacing (CK1, 15 cm) and wide–narrow row spacing, comprising 13.3 cm + 13.3 cm + 13.3 cm + 20 cm (M1), 10 cm + 10 cm + 10 cm + 30 cm (M2), and 10 cm + 10 cm + 10 cm + 20 cm (M3). Four drip irrigation levels were applied: 4500 mm 2 /hm 2 CK), 3600 m³/hm² (D1), 2700 m³/hm² (D2), and 0 m 2 /hm 2 (D3). The results indicate that wide–narrow row spacing increased the single-plant dry matter weight, with the stem + sheath and spike allocation ratios at maturity increasing by 15.31% and 6.59%, respectively. Wide–narrow rows improved spike traits, particularly in the outer rows, increasing spike length and grain number per spike by 0.46% and 0.68%, respectively, and reducing sterile spikelets by 1.35%. Compared with the CK1D1 treatment, the M2D1 treatment significantly increased the number of spikes per unit area, number of grains per spike, and yield by 19.15%, 5.92%, and 19.10%, respectively, with no significant difference in thousand-kernel weight. These findings demonstrated that M2D1 treatment optimized yield and water-saving efficiency, providing critical guidance for winter wheat production in arid regions.

Seed coat color, a trait exhibiting significant phenotypic variation, has been reported in previous studies to influence key germination parameters, including germination percentage, germination rate, and mean germination time. Looking into these relationships can help us identify plant varieties that better withstand both living threats and environmental challenges, which would make breeding programs more effective and focused. The objectives of this study were to evaluate the drought tolerance of 20 flax varieties at the germination stage, investigate the effects of gamma-aminobutyric acid (GABA) on seed germination performance under drought stress conditions, and explore potential associations between seed coat color and germination parameters under both stressed and non-stressed conditions using digital image processing. The final germination percentage, germination speed, and span of germination were assessed for seeds germinated under various germination conditions, including 23% PEG (− 0.169 MPa), 10 mM GABA, 23% PEG + 10 mM GABA, and a control treatment at 25 ± 0.5 °C. The results demonstrated substantial genetic variation across all germination parameters measured in the seeds of 20 distinct flax varieties. Genotype-specific responses to drought stress were observed, with 10 mM GABA alleviating the effects of drought. Among the varieties tested, Hermes exhibited the highest drought tolerance, while Lisette and Bonny-Doon were identified as drought-sensitive. Digital image processing analysis revealed significant differences ( p  < 0.05) in drought tolerance levels among flax varieties based on variations in RGB values of their seed coats. Although no statistically significant correlations were found in direct pairwise correlations between the color parameters converted from RGB (Red, Green, and Blue) to L*a*b* and germination parameters, multivariate PCA-biplot analysis indicated that L* and b* values had a positive influence on germination performance. In contrast, seeds with higher a* values exhibited reduced germination performance. Furthermore, the biplot analysis suggested that varieties with lighter seed coats tended to show better germination compared to those with darker seed coats. These findings highlight the potential of incorporating seed coat color parameters into flax breeding programs, suggesting their role in enhancing seed germination and overall seed quality under various stress conditions.

Brassinolide (BR) is a sterol compound, which can regulate plant seed germination, flowering, senescence, tropism, photosynthesis, stress resistance, and is closely related to other signaling molecules. This study aimed to evaluate the ability of soaking with BR to regulate growth quality at rice seedling stage under salt stress. Results demonstrated that salt stress increases the contents of ROS, MDA, Na + and ABA, reduces the the SPAD value, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), maximum fluorescence (Fm), variable fluorescence (Fv), the effective photochemical efficiency of PSII (Fv/Fo) and the maximum photochemical efficiency of PSII (Fv/Fm), reduces the biomass production and inhabits plant growth. All of these responses were effectively alleviated by BR soaking treatment. Soaking with BR could increase the activities of superoxide dismutase, peroxidase, catalase, ascorbate peroxidase, and the contents of ascorbic acid, glutathione as well as soluble protein and proline, while BR soaking treatment inhibited the accumulation of ROS and reduced the content of MDA. BR soaking significantly reduced the contents of Na + and increased the contents of K + and Ca 2+ , indicating that soaking with BR is beneficial to the excretion of Na + , the absorption of K + and Ca 2+ and the maintenance of ion balance in rice seedlings under salt stress. BR also maintained endogenous hormone balance by increasing the contents of indoleacetic acid (IAA), zeatin (ZT), salicylic acid (SA), and decreasing the ABA content. Soaking with BR significantly increased the SPAD value, Pn and Tr and enhanced the Fm, Fv/Fm and Fv/Fo of rice seedlings under NaCl stress, protected the photosythetic system of plants, and improved their biomass. It is suggested that BR was beneficial to protect membrane lipid peroxidation, the modulation of antioxidant defense systems, ion balance and endogenous hormonal balance with imposition to salt stress.

Melatonin (MT) and methyl jasmonate (MeJA) play important roles in the adaptation of plants to different stress factors by modulating stress tolerance mechanisms. The present study reports the involvement of MT (100 µM) in MeJA (10 µM)-induced photosynthetic performance and heat stress acclimation through regulation of the antioxidant metabolism and ethylene production in wheat ( Triticum aestivum L.) plants. Plants exposed to 40 °C for 6 h per day for 15 days and allowed to retrieve at 28 °C showed enhanced oxidative stress and antioxidant metabolism, increased 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) activity and ethylene production, and decreased photosynthetic performance. In contrast, the exogenously applied MT and MeJA reduced oxidative stress through improved S-assimilation (+ 73.6% S content), antioxidant defense system (+ 70.9% SOD, + 115.8% APX and + 104.2% GR, and + 49.5% GSH), optimized ethylene level to 58.4% resulting in improved photosynthesis by 75%. The use of p -chlorophenyl alanine, a MT biosynthesis inhibitor along with MeJA in the presence of heat stress reduced the photosynthetic performance, ATP-S activity and GSH content, substantiated the requirement of MT in the MeJA-induced photosynthetic response of plants under heat stress. These findings suggest that MeJA evoked the plant’s ability to withstand heat stress by regulating the S-assimilation, antioxidant defense system, and ethylene production, and improving photosynthetic performance was dependent on MT.

Wood, a type of xylem tissue, originates from cell proliferation of the vascular cambium. Xylem is produced inside, and phloem outside, of the cambium 1 . Morphogenesis in plants is typically coordinated by organizer cells that direct the adjacent stem cells to undergo programmed cell division and differentiation. The location of the vascular cambium stem cells and whether the organizer concept applies to the cambium are currently unknown 2 . Here, using lineage-tracing and molecular genetic studies in the roots of Arabidopsis thaliana , we show that cells with a xylem identity direct adjacent vascular cambial cells to divide and function as stem cells. Thus, these xylem-identity cells constitute an organizer. A local maximum of the phytohormone auxin, and consequent expression of CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, promotes xylem identity and cellular quiescence of the organizer cells. Additionally, the organizer maintains phloem identity in a non-cell-autonomous fashion. Consistent with this dual function of the organizer cells, xylem and phloem originate from a single, bifacial stem cell in each radial cell file, which confirms the classical theory of a uniseriate vascular cambium 3 . Clones that display high levels of ectopically activated auxin signalling differentiate as xylem vessels; these clones induce cell divisions and the expression of cambial and phloem markers in the adjacent cells, which suggests that a local auxin-signalling maximum is sufficient to specify a stem-cell organizer. Although vascular cambium has a unique function among plant meristems, the stem-cell organizer of this tissue shares features with the organizers of root and shoot meristems. In the roots of Arabidopsis thaliana , cells with xylem identity and high levels of auxin signalling function as organizer cells that direct neighbouring vascular cambial cells to act as stem cells.

Soil salinity is a major environmental stressor impacting global food production. Staple crops like wheat experience significant yield losses in saline environments. Bioprospecting for beneficial microbes associated with stress-resistant plants offers a promising strategy for sustainable agriculture. We isolated two novel endophytic bacteria, Bacillus cereus (ADJ1) and Priestia aryabhattai (ADJ6), from Agave desmettiana Jacobi. Both strains displayed potent plant growth-promoting (PGP) traits, such as producing high amounts of indole-3-acetic acid (9.46, 10.00 µgml −1 ), ammonia (64.67, 108.97 µmol ml −1 ), zinc solubilization (Index of 3.33, 4.22, respectively), ACC deaminase production and biofilm formation. ADJ6 additionally showed inorganic phosphate solubilization (PSI of 2.77), atmospheric nitrogen fixation, and hydrogen cyanide production. Wheat seeds primed with these endophytes exhibited enhanced germination, improved growth profiles, and significantly increased yields in field trials. Notably, both ADJ1 and ADJ6 tolerated high salinity (up to 1.03 M) and significantly improved wheat germination and seedling growth under saline stress, acting both independently and synergistically. This study reveals promising stress-tolerance traits within endophytic bacteria from A. desmettiana . Exploiting such under-explored plant microbiomes offers a sustainable approach to developing salt-tolerant crops, mitigating the impact of climate change-induced salinization on global food security.