Widespread deployment of wheat hybrids has been limited by high seed production costs in a commercial environment. This is due to poor outcrossing characteristics of wheat which can, in part, be attributed to poor female organ receptivity to airborne pollen. Here we underpin a detailed characterization of cross-pollination seed set progression in both emasculated wild-type, and a genetically male-sterile wheat line with a comprehensive RNA-Seq and co-expression analysis. We identify three clear phases in the fertilization window: stigma development and onset of receptivity, effective pollination period, and senescence onset and subsequent tissue deterioration. By profiling female-specific marker genes, we determined that physical emasculation of wild-type 'cv. Chris' (Ms1) advances female development 2 to 3 days relative to genic male sterility (ms1d). Gene networks linked to gibberellic acid homeostasis were found associated with styloid and stigma hair elongation, and increased expression of peroxidases associated with peak receptivity (3 days after floret gaping). Further, changes in the expression of exocyst complex components coincided with the onset of stigma hair senescence. Together the applied clustering and differential expression strategy identified biologically meaningful expression signatures, particularly in stigma hairs, that correlate with the effective pollination period and the observed cross-pollination seed set. Overall, the datasets represent a valuable resource to help identify and/or engineer improved cross-pollination seed set, and ultimately leading to greater insights into this complex biological process and a more cost-effective hybrid seed production system.

OzBarley is a comprehensive genotype-to-phenotype resource to support research and enhance barley breeding by integrating genotypic and phenotypic data for gene discovery. This publicly available dataset comprises genotypic data from historical and modern elite barley cultivars of significance to Australian barley breeding. The phenotypic component includes high-throughput imaging and X-ray CT-based spike analysis, enabling trait measurements such as plant growth dynamics and seed morphology. Users can leverage genome-wide association studies (GWAS) and genomic selection to identify genetic variants associated with agronomically important traits in the OzBarley datasets, thereby accelerating targeted breeding strategies. The dataset is accessible for download under CC-BY 4.0 license and users are invited to contribute new data when using OzBarley plant material in their research. Through its FAIR-compliant design (Findable, Accessible, Interoperable, Reusable), OzBarley represents a resource to protect genotypes of historical relevance, explore the genetic architecture of adaptation to dryland environments, and to enhance knowledge of the resilience, yield, and quality of barley cultivars under diverse environmental conditions, contributing to global food security and agricultural sustainability.

Soil salinity is a significant constraint to global wheat production, and breeding for salinity tolerance offers a sustainable solution. MW#293 is a recently developed bread wheat line, notable for both its high salinity tolerance and unusually high leaf sodium (Na+) accumulation. However, the association between high Na+ accumulation and salinity tolerance in this line was unknown. Using genetic, genomic, physiological, and agronomic approaches, we identified and delineated a terminal deletion on chromosome 4D encompassing the major Na+ transporter gene TaHKT1;5D and determined this as the cause of the elevated leaf Na+ in MW#293. In a Mace×MW#293 segregating population, leaf Na+ and shoot growth measured under salinity were shown to be under separate genetic control. Field trials were conducted in three environments ranging from slightly to moderately saline. Despite the deletion encompassing at least 286 genes, we observed neither a positive nor a negative influence on grain yield. These results suggest that TaHKT1;5D is not a critical determinant of salinity tolerance in MW#293 and related bread wheat germplasm, but that other mechanisms are responsible.

KEY MESSAGE:The dwarfing allele Rht14 of durum wheat associates with greater stigma length, an important trait for hybrid breeding, whilst major dwarfing alleles Rht-B1b and Rht-D1b showed little to no effect. Although much understudied in wheat, the stigma is a crucial component for attaining grain set, the fundamental basis for yield, particularly in hybrid production systems where successful grain set relies on wind-driven pollen dispersal by the male parent and effective pollen capture by the female parent. Females with long stigma that exsert early are thought to be advantageous. Using glasshouse-grown lines, we examined variation in Total Stigma Length (TSL) across diverse panels comprising 27 durum and 116 bread wheat genotypes. Contrasting genotypes were selected for population development and genetic analysis. Quantitative trait loci (QTL) analysis was performed on a durum F2 population and a bread wheat recombinant inbred line (RIL) population. Contrasting with studies of anther length, we found no large effect on TSL of the GA-insensitive semi-dwarfing genes Rht-B1 and Rht-D1 in either durum or bread wheat. However, in durum cultivar Italo, we identified a region on chromosome 6A which is robustly associated with larger TSL and contains the Rht14 allele for reduced plant height, a trait that is favourable for female line development in hybrid systems. This dual effect locus explained 25.2 and 19.2% of TSL phenotypic variation in experiments across two growing seasons, with preliminary results suggesting this locus may increase TSL when transferred to bread wheat. In a bread wheat, RIL population minor QTL on 1A and 2A was indicated, but the strongest association was with Ppd-B1. Methods developed here, and the identification of a TSL-enhancing locus provides advances and further opportunities in the study of wheat stigma.

Phytophthora root rot (PRR), caused by Phytophthora medicaginis, is a major soil-borne disease of chickpea in Australia. Breeding for PRR resistance is an effective approach to avoid significant yield loss. Genetic resistance has been identified in cultivated chickpea (Cicer arietinum) and in the wild relative C. echinospermum, with previous studies identifying independent genetic loci associated with each of these sources. However, the molecular mechanisms associated with PRR resistance are not known. RNA sequencing analysis employed in this study identified changes in gene expression in roots of three chickpea genotypes grown hydroponically, early post-infection with P. medicaginis zoospores. Analyses of differentially expressed genes (DEG) identified the activation of a higher number of non-specific R-genes in a PRR-susceptible variety than in the resistant genotypes, suggesting a whole plant resistance response occurring in chickpea against the pathogen. Contrasting molecular changes in signaling profiles, proteolysis and transcription factor pathways were observed in the cultivated and wild Cicer-derived resistant genotypes. DEG patterns supported a hypothesis that increased root elongation and reduced adventitious root formation limit the pathogen entry points in the genotype containing the wild Cicer source of PRR resistance. Candidate resistance genes, including an aquaporin and a maltose transporter in the wild Cicer source and GDSL esterases/lipases in the cultivated source of resistance, were oppositely regulated. Increased knowledge of these genes and pathways will improve our understanding of molecular mechanisms controlling PRR resistance in chickpea, and support the development of elite chickpea varieties through molecular breeding approaches.

The volatile-mediated interplay between stressed and non-stressed plants has been described in many studies involving both biotic and abiotic stresses as a one-way channel. However, very little is known about the molecular basis and mechanisms by which volatile organic compounds (VOCs) mediate plant communication between drought-stressed ‘emitter’ plants and non-stressed ‘receiver’ neighbours for the defence against impending stress challenges. Aiming to address this in grapevine, this study investigated the effect of two-way VOC exchange between stressed and non-stressed Vitis vinifera L. cv. Shiraz during drought and recovery using four treatments: isolated well-watered (WW) vines, isolated drought-stressed (DS) vines, and co-located DS ‘emitter’ and WW ‘receiver’ vines in a growth room. The results obtained from solid-phase microextraction (SPME) gas chromatography mass spectrometry (GC-MS) analysis showed a synchronised decline in α-pinene concentration in the co-located treatment vines and higher isoprene levels in the DS emitters compared to the isolated DS vines. Targeted gene expression analysis further identified the over-expression of a key gene, allene oxide synthase (AOS), in the jasmonic acid (JA) biosynthesis pathway during peak drought in the DS emitter. Transcript expression of chorismate synthase (CHORS) and α-pinene synthase (VvPNaPin1) showed similar trends in the DS emitter. The results suggest that isoprene and α-pinene may be interplant signalling molecules used by grapevine during drought. To the best of our knowledge, this is the first report of a bi-directional interaction in grapevine between the emitters and receivers under drought stress mediated by the JA and terpenoid biosynthesis pathways.

Correct floral development is the result of a sophisticated balance of molecular cues. Floral mutants provide insight into the main genetic determinants that integrate these cues, as well as providing opportunities to assess functional variation across species. In this study, we characterize the barley (Hordeum vulgare) multiovary mutants mov2.g and mov1, and propose causative gene sequences: a C2H2 zinc-finger gene HvSL1 and a B-class gene HvMADS16, respectively. In the absence of HvSL1, florets lack stamens but exhibit functional supernumerary carpels, resulting in multiple grains per floret. Deletion of HvMADS16 in mov1 causes homeotic conversion of lodicules and stamens into bract-like organs and carpels that contain non-functional ovules. Based on developmental, genetic, and molecular data, we propose a model by which stamen specification in barley is defined by HvSL1 acting upstream of HvMADS16. The present work identifies strong conservation of stamen formation pathways with other cereals, but also reveals intriguing species-specific differences. The findings lay the foundation for a better understanding of floral architecture in Triticeae, a key target for crop improvement.

Despite frequent co-occurrence of drought and heat stress, the molecular mechanisms governing plant responses to these stresses in combination have not often been studied. This is particularly evident in non-model, perennial plants. We conducted large scale physiological and transcriptome analyses to identify genes and pathways associated with grapevine response to drought and/or heat stress during stress progression and recovery. We identified gene clusters with expression correlated to leaf temperature and water stress and five hub genes for the combined stress co-expression network. Several differentially expressed genes were common to the individual and combined stresses, but the majority were unique to the individual or combined stress treatments. These included heat-shock proteins, mitogen-activated kinases, sugar metabolizing enzymes, and transcription factors, while phenylpropanoid biosynthesis and histone modifying genes were unique to the combined stress treatment. Following physiological recovery, differentially expressed genes were found only in plants under heat stress, both alone and combined with drought. Taken collectively, our results suggest that the effect of the combined stress on physiology and gene expression is more severe than that of individual stresses, but not simply additive, and that epigenetic chromatin modifications may play an important role in grapevine responses to combined drought and heat stress.

Salinity is a major abiotic stress that causes substantial agricultural losses worldwide. Chickpea (Cicer arietinum L.) is an important legume crop but is salt-sensitive. Previous physiological and genetic studies revealed the contrasting response of two desi chickpea varieties, salt-sensitive Rupali and salt-tolerant Genesis836, to salt stress. To understand the complex molecular regulation of salt tolerance mechanisms in these two chickpea genotypes, we examined the leaf transcriptome repertoire of Rupali and Genesis836 in control and salt-stressed conditions. Using linear models, we identified categories of differentially expressed genes (DEGs) describing the genotypic differences: salt-responsive DEGs in Rupali (1,604) and Genesis836 (1,751) with 907 and 1,054 DEGs unique to Rupali and Genesis836, respectively, salt responsive DEGs (3,376), genotype-dependent DEGs (4,170), and genotype-dependent salt-responsive DEGs (122). Functional DEG annotation revealed that the salt treatment affected genes involved in ion transport, osmotic adjustment, photosynthesis, energy generation, stress and hormone signalling, and regulatory pathways. Our results showed that while Genesis836 and Rupali have similar primary salt response mechanisms (common salt-responsive DEGs), their contrasting salt response is attributed to the differential expression of genes primarily involved in ion transport and photosynthesis. Interestingly, variant calling between the two genotypes identified SNPs/InDels in 768 Genesis836 and 701 Rupali salt-responsive DEGs with 1,741 variants identified in Genesis836 and 1,449 variants identified in Rupali. In addition, the presence of premature stop codons was detected in 35 genes in Rupali. This study provides valuable insights into the molecular regulation underpinning the physiological basis of salt tolerance in two chickpea genotypes and offers potential candidate genes for the improvement of salt tolerance in chickpeas.

Utilising a nested association mapping (NAM) population-based GWAS, 98 stable marker-trait associations with 127 alleles unique to the exotic parents were detected for grain yield and related traits in wheat. Grain yield, thousand-grain weight, screenings and hectolitre weight are important wheat yield traits. An understanding of their genetic basis is crucial for improving grain yield in breeding programmes. Nested association mapping (NAM) populations are useful resources for the dissection of the genetic basis of complex traits such as grain yield and related traits in wheat. Coupled with phenotypic data collected from multiple environments, NAM populations have the power to detect quantitative trait loci and their multiple alleles, providing germplasm that can be incorporated into breeding programmes. In this study, we evaluated a large-scale wheat NAM population with two recurrent parents in unbalanced trials in nine diverse Australian field environments over three years. By applying a single-stage factor analytical linear mixed model (FALMM) to the NAM multi-environment trials (MET) data and conducting a genome-wide association study (GWAS), we detected 98 stable marker-trait associations (MTAs) with their multiple alleles. 74 MTAs had 127 alleles that were derived from the exotic parents and were absent in either of the two recurrent parents. The exotic alleles had favourable effects on 46 MTAs of the 74 MTAs, for grain yield, thousand-grain weight, screenings and hectolitre weight. Two NAM RILs with consistently high yield in multiple environments were also identified, highlighting the potential of the NAM population in supporting plant breeding through provision of germplasm that can be readily incorporated into breeding programmes. The identified beneficial exotic alleles introgressed into the NAM population provide potential target alleles for the genetic improvement of wheat and further studies aimed at pinpointing the underlying genes.

In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data

The sessile plant has developed mechanisms to survive the “rough and tumble” of its natural surroundings, aided by its evolved innate immune system. Precise perception and rapid response to stress stimuli confer a fitness edge to the plant against its competitors, guaranteeing greater chances of survival and productivity. Plants can “eavesdrop” on volatile chemical cues from their stressed neighbours and have adapted to use these airborne signals to prepare for impending danger without having to experience the actual stress themselves. The role of volatile organic compounds (VOCs) in plant–plant communication has gained significant attention over the past decade, particularly with regard to the potential of VOCs to prime non-stressed plants for more robust defence responses to future stress challenges. The ecological relevance of such interactions under various environmental stresses has been much debated, and there is a nascent understanding of the mechanisms involved. This review discusses the significance of VOC-mediated inter-plant interactions under both biotic and abiotic stresses and highlights the potential to manipulate outcomes in agricultural systems for sustainable crop protection via enhanced defence. The need to integrate physiological, biochemical, and molecular approaches in understanding the underlying mechanisms and signalling pathways involved in volatile signalling is emphasised.

Summary In the recent years, the agricultural world has been progressing towards integrated crop protection, in the context of sustainable and reasoned agriculture to improve food security and quality, and to preserve the environment through reduced uses of water, pesticides, fungicides or fertilisers. For this purpose, one possible issue is to cross‐elite varieties widely used in fields for crop productions with exotic or wild genetic resources in order to introduce new diversity for genes or alleles of agronomical interest to accelerate the development of new improved cultivars. However, crossing ability (or crossability) often depends on genetic background of the recipient varieties or of the donor, which hampers a larger use of wild resources in breeding programmes of many crops. In this review, we tried to provide a comprehensive summary of genetic factors controlling crossing ability between Triticeae species with a special focus on the crossability between wheat ( Triticum aestivum L.) and rye ( Secale cereale ), which lead to the creation of Triticale ( x Triticosecale Wittm.). We also discussed potential applications of newly identified genes or markers associated with crossability for accelerating wheat and Triticale improvement by application of modern genomics technologies in breeding programmes.

Abstract Objectives High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. Bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its performance under low irrigation conditions, which further improves upon irrigation. In order to explore and exploit the genomic potential of this elite variety, in 2015, we sequenced the modern elite cultivar Sonmez genome which represents a diverse genetic background. Data description Here, we provide a reference-guided whole genome sequence of Sonmez-2001, assembled into 21 chromosomes of the A, B and D genomes and totaling to 13.3 gigabase-pairs in length. Additionally, a de novo assembly, of an additional 1.05 gigabase-pairs, was generated that represents either Sonmez-specific sequences or sequences that considerably diverged between Sonmez and Chinese Spring. We identified up to 24 million sequence variants, of which up to 2.4% reside in coding sequences, that can be used to develop molecular markers that should be of immediate use to the cereal community.

High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. The bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its performance under low-irrigation conditions, which further improves upon irrigation. Additionally, Sonmez-2001 is resilient against certain biotic stressors, particularly soil-borne pathogens. Here, we provide a reference-guided whole genome sequence of Sonmez-2001, assembled into 21 chromosomes of the A, B and D genomes and totaling 13.3 gigabase-pairs in length. Additionally, a de novo assembly of an additional 1.05 gigabase-pairs was generated that represents either Sonmez-specific sequences or sequences that considerably diverged between Sonmez and Chinese Spring. Within this de novo assembly, we identified 35 gene models, of which 11 were high-confidence, that may contribute to the favorable traits of this high-performing variety. We identified up to 24 million sequence variants, of which up to 2.4% reside in coding sequences, that can be used to develop molecular markers that should be of immediate use to the cereal community.

In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats,

Diversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.

QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in diverse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.), genomic data from a bi-parental population and multiple diversity panels were used to identify QTL, sequence-level haplotypes and genetic markers associated with vigour-related traits in Australian environments. Using 182 Recombinant Inbred Lines (RILs) derived from a cross between two desi varieties, Rupali and Genesis836, vigour QTL independent of flowering time were identified on chromosomes (Ca) 1, 3 and 4 with genotypic variance explained (GVE) ranging from 7.1 to 28.8%. Haplotype analysis, association analysis and graphical genotyping of whole-genome re-sequencing data of two diversity panels consisting of Australian and Indian genotypes and an ICRISAT Chickpea Reference Set revealed a deletion in the FTa1–FTa2–FTc gene cluster of Ca3 significantly associated with vigour and flowering time. Across the RIL population and diversity panels, the impact of the deletion was consistent for vigour but not flowering time. Vigour-related QTL on Ca4 co-located with a QTL for seed size in Rupali/Genesis836 (GVE = 61.3%). Using SNPs from this region, we developed and validated gene-based KASP markers across different panels. Two markers were developed for a gene on Ca1, myo -inositol monophosphatase (CaIMP), previously proposed to control seed size, seed germination and seedling growth in chickpea. While associated with vigour in the diversity panels, neither the markers nor broader haplotype linked to CaIMP was polymorphic in Rupali/Genesis836. Importantly, vigour appears to be controlled by different sets of QTL across time and with components which are independent from phenology.

Wheat productivity is severely reduced by high temperatures. Breeding of heat tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits with high temperature and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We completed the positional cloning of qYDH.3BL , a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene - seven in absentia, TaSINA . This was associated with the QTL’s effects on early vigour, plant biomass and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL under-expressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia. Significance statement Wheat is the world’s most widely grown crop and a staple of human diet. Even brief episodes of high temperature in the growing season cause severe yield reductions. Finding and deploying genes for heat stress tolerance in new varieties is a priority for food security with climate change. We narrowed a genetic locus to a small genomic region where genetic variation was present only in one gene that showed clear differences of expression and improved yield and physiology under stress in the populations. Using diagnostic markers to track the positive haplotype in nearly 750 accessions, we found many regions where the allele could be used in breeding programmes to increase wheat’s heat tolerance.

Nitrogen is an essential nutrient for plants, but crop plants are inefficient in the acquisition and utilization of applied nitrogen. This often results in producers over applying nitrogen fertilizers, which can negatively impact the environment. The development of crop plants with more efficient nitrogen usage is, therefore, an important research goal in achieving greater agricultural sustainability. We utilized genetically modified rice lines over-expressing a barley alanine aminotransferase ( HvAlaAT ) to help characterize pathways which lead to more efficient use of nitrogen. Under the control of a stress-inducible promoter OsAnt1 , OsAnt1:HvAlaAT lines have increased above-ground biomass with little change to both nitrate and ammonium uptake rates. Based on metabolic profiles, carbon metabolites, particularly those involved in glycolysis and the tricarboxylic acid (TCA) cycle, were significantly altered in roots of OsAnt1:HvAlaAT lines, suggesting higher metabolic turnover. Moreover, transcriptomic data revealed that genes involved in glycolysis and TCA cycle were upregulated. These observations suggest that higher activity of these two processes could result in higher energy production, driving higher nitrogen assimilation, consequently increasing biomass production. Other potential mechanisms contributing to a nitrogen-use efficient phenotype include involvements of phytohormonal responses and an alteration in secondary metabolism. We also conducted basic growth studies to evaluate the effect of the OsAnt1:HvAlaAT transgene in barley and wheat, which the transgenic crop plants increased seed production under controlled environmental conditions. This study provides comprehensive profiling of genetic and metabolic responses to the over-expression of AlaAT and unravels several components and pathways which contribute to its nitrogen-use efficient phenotype.