Shifting the limits in wheat research and breeding using a fully annotated reference genome

TaWUS-like-5D affects grain weight and filling by inhibiting the expression of sucrose and trehalose metabolism-related genes in wheat grain endosperm

Plant-specific WUSCHEL-related homeobox (Wox) transcription factors (TFs) are crucial for plant growth and development. However, the molecular mechanism of Wox-mediated regulation of thousand kernel weight (TKW) in crops remains elusive. In this research, we identified a major TKW-associated quantitative trait locus (QTL) on wheat chromosome 5DS by performing a genome-wide association study (GWAS) of a Chinese wheat mini-core collection (MCC) in four environments combined by bulked segregant analysis (BSA) and bulked segregant RNA-sequencing (BSR-seq) of wheat grains exhibiting a wide range of TKWs. The candidate TaWUS-like-5D was highly expressed in developing grains and was found to strongly negative influence grain TKW and wheat yield. Meanwhile, the RNAi lines, CRISPR/Cas9-edited single and double knockout mutants (AABBdd and AAbbdd), as well as the stop-gained aaBB Kronos mutants, exhibited a significant increase in grain size and TKW (P < 0.05 or P < 0.01) and a 10.0% increase in yield (P < 0.01). Further analyses indicated that TaWUS-like-5D regulates TKW by inhibiting the transcription of sucrose, hormone and trehalose metabolism-related genes, subsequently sharply decreasing starch synthesis in wheat grains. The results of this study provide a fundamental molecular basis for further elucidating the mechanism of Wox-mediated regulation of grain development in crops.

Fine mapping of PmL270, a new powdery mildew resistance gene on chromosome 7AL in wheat

Wheat (Triticum aestivum) is one of the most important cereal crops, providing essential food and nutrition for humans. Wheat powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt), seriously threatens wheat production by reducing yield and quality. Utilizing effective powdery mildew resistance (Pm) genes to develop resistant cultivars is a powerful means for controlling this disease. In this study, we identified a new resistance gene, PmL270, from the wheat line L270. By means of bulked segregant RNA‑Seq (BSR‑Seq) and molecular marker analysis, we fine-mapped PmL270 to a 0.1-cM interval on chromosome 7AL, flanked by the markers X7AL07 and X7AL09. This interval corresponds to a 630-kb region in the reference genome of Chinese Spring. Comparative analysis showed that PmL270 is distinct from other Pm genes previously reported on the same chromosome arm. A co-dominant marker, X7AL08, developed from a candidate NLR gene, co-segregated with PmL270 in the mapping population and showed high specificity for this gene. The mapping and development of co-segregation marker will facilitate the cloning of PmL270 and contribute to its rapid utilization in wheat resistance breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01574-0.

Epigenetics in the modern era of crop improvements

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

TaFT-D1 positively regulates grain weight by acting as a coactivator of TaFDL2 in wheat

FLOWERING LOCUS T (FT), a multifunctional regulator in crops, modulates multiple key agronomic traits such as flowering time or heading date and plant height; however, its role in grain development regulation is unclear. Herein, through genome-wide association studies (GWAS), we identified TaFT-D1, which encodes a phosphatidylethanolamine-binding protein (PEBP), as a candidate gene for grain weight in wheat. A one-bp insertion/deletion (InDel) (G/-) in the third exon of TaFT-D1, resulting in different protein lengths, was significantly associated with grain weight. TaFT-D1 knockout via the CRISPR-Cas9 system reduced grain size and weight, and TaFT-D1 increased grain size by promoting cell proliferation and starch synthesis. Transcriptome analysis revealed a significant decrease in the expression of cell cycle- and starch synthesis-related genes, including TaNAC019-3A, TaSWEET15-like-7B, TaCYCD4;1 and TaCYCD3;2, in the taft-d1 knockout line. TaFT-D1 interacted with the bZIP transcription factor TaFDL2, and the tafdl2 mutant presented relatively small grains, suggesting that TaFDL2 is a positive regulator of grain size. Moreover, TaFDL2 bound to the promoters of downstream cell cycle- and starch synthesis-related genes, activating their expression, whereas TaFT-D1 increased this activation via TaFDL2. Interaction assays demonstrated that TaFT-D1, Ta14-3-3A and TaFDL2 formed a regulatory complex. Furthermore, the TaFT-D1(G) allele was significantly correlated with greater thousand-grain weight and earlier heading. This favourable allele has undergone strong positive selection during wheat breeding in China. Our findings provide novel insights into how TaFT-D1 regulates grain weight and highlight its potential application for yield improvement in wheat.

TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation

Cis-regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce transposase-accessible chromosome conformation capture (TAC-C), a method integrating ATAC-seq and Hi-C to capture fine-scale chromatin interactions in four major crops: rice, sorghum, maize, and wheat. TAC-C reveals a strong association between chromatin interaction frequency and gene expression, particularly emphasizing the conserved roles of chromatin interaction hub anchors and hub genes across crop species. Integrating chromatin structure with population genetics data highlights that chromatin loops connect distal regulatory elements to phenotypic variation. In addition, asymmetrical open chromatin interactions among subgenomes, driven by transposon insertions and sequence variations, contribute to biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through chromatin interactions, with enhanced photosynthetic efficiency and starch content in Taspl7&15 mutant. TAC-C provides insights into the spatial organization of regulatory elements in crops, especially for SPL-mediated photosynthesis regulation in wheat.

Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations

BACKGROUND

Differences in the relative level of expression of homoeologs, known as homoeolog expression bias, are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridization has been characterized, on shorter timescales such as those found in crop breeding programs, the extent to which homoeolog expression bias is preserved or altered between generations remains elusive.

RESULTS

Here we use biparental mapping populations of hexaploid wheat (Triticum aestivum) with a common "Paragon" parent to explore the inheritance of homoeolog expression bias in the F5 generation. We found that homoeolog expression bias is inherited for 26-27% of triads in both populations. Most triads conserved a similar homoeolog expression bias pattern as one or both parents. Inherited patterns were largely driven by changes in the expression of one homoeolog, allowing homoeolog expression bias in subsequent generations to match parental expression. Novel patterns of homoeolog expression bias occurred more frequently in the biparental population from a landrace × elite cross, than in the population with two elite parents.

CONCLUSIONS

These results demonstrate that there is significant reprogramming and stabilization of homoeolog expression bias within a small number of generations that differs significantly based on the parental lines used in the crossing.

Divergent molecular pathways govern temperature-dependent wheat stem rust resistance genes

The wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt) causes severe crop losses worldwide. Several stem rust resistance (Sr) genes exhibit temperature-dependent immune responses. Sr6-mediated resistance is enhanced at lower temperatures, whereas Sr13 and Sr21 resistances are enhanced at higher temperatures. Here, we clone Sr6 using mutagenesis and resistance gene enrichment and sequencing (MutRenSeq), identifying it to encode a nucleotide-binding leucine-rich repeat (NLR) protein with an integrated BED domain. Sr6 temperature sensitivity is also transferred to wheat plants transformed with the Sr6 gene. Differential gene expression analysis of near-isogenic lines inoculated with Pgt at varying temperatures reveals that genes upregulated in the low-temperature-effective Sr6 response differ from those upregulated in the high-temperature-effective responses associated with Sr13 and Sr21. These findings highlight divergent molecular pathways involved in temperature-sensitive immunity and inform future strategies for deployment and engineering of genetic resistance in response to a changing climate.

Gene-based model to predict heading date in wheat based on allelic characterization and environmental drivers

While numerous wheat phenology prediction models are available, most of them are constrained to using variety-dependent coefficients. The overarching objective of this study was to calibrate a gene-based model to predict wheat heading date that allows breeders to select specific gene combinations that would head within the optimal window for a given environment independently of varietal genetic background. A dataset with a total of 49 Argentine wheat cultivars and two recombinant inbred lines was chosen to cover a wide range of allelic combinations for major vernalization, photoperiod, and earliness per se genes. The model was validated using independent data from an Argentine wheat trial network that includes sites from a wide latitudinal range. Ultimately, using this gene-based model, simulations were made to identify optimal gene combinations (ideotypes) × site combinations in contrasting locations. The selected model accurately predicted heading date with an overall median error of 4.6 d. This gene-based crop model for wheat phenology allowed the identification of groups of gene combinations predicted to produce heads within a low-risk window and can be adapted to predict other phenological stages based on accessible climatic information and publicly available molecular markers, facilitating its adoption in wheat-growing regions worldwide.

The selection and application of tiller number QTLs in modern wheat breeding

Tiller number is a key factor influencing wheat plant architecture and yield potential. This study analyzed the variation in tiller number among 323 wheat accessions across nine environmental conditions. The results revealed a significant decrease in tiller number in modern cultivars compared to traditional landraces, indicating a trend in selective breeding for fewer tillers. Genome-wide association studies (GWASs) identified four quantitative trait loci (QTLs) associated with tiller number on chromosomes 2D, 5A, and 6A. Haplotypes linked to reduced tiller number at three of these QTLs have been significantly selected and are predominantly found in various Chinese agroecological zones, positively affecting grain number and/or weight. These findings suggest that contemporary Chinese wheat breeding strategies have prioritized reducing tiller number while improving spike yield. Identifying selected haplotype combinations can further enhance breeding efforts aimed at optimizing the tiller number trait. This study provides insights into the genetic basis of tiller number QTLs and their relevance to wheat breeding practices.

Survey of tocopherol and the associated genetic loci in wheat grain

KEY MESSAGE

Survey of tocopherol and identification of genetic loci in wheat grain: toward a better understanding for breeding tocopherol cultivars. Tocopherol is essential in maintaining human sex hormone as well as antioxidation and immune functions. In this study, the contents of α-, γ- and δ-tocopherol in a Chinese wheat mini-core collection were measured with high-performance liquid chromatography. The effects of various factors such as accession types, winter/spring types and grain colors on tocopherol content were analyzed, and the genetic loci for tocopherol were identified with genome-wide association analysis and linkage analysis. There was no significant difference in total tocopherol in grain of wheat grown in three environments. Seven high-tocopherol (≥ 110 μg/g) germplasms were selected. The genotypic and environmental effects on total tocopherol and its three components ranked G > G × E > E and the tocopherol content were not correlated with accession types, spring/winter variety, red/white grain and release years. Among the eleven agronomic and four grain traits, α-tocopherol was positively correlated with grain thickness, γ-tocopherol was positively correlated with heading date, maturity date and flag leaf length, and γ-, δ- and total tocopherol were negatively correlated with the number of kernels in the middle of the spike. The total tocopherol showed positive correlation with lycopene and lutein. A total of twenty-seven QTL associated with tocopherol were identified with genome-wide association analysis, with obvious additive effects. The fine mapping of Qδ.toc.6 A narrowed functional region down to a 5.26-Mb region via analyzing the tocopherol content among genotypes in secondary mapping population. We proposed five candidate genes with known pathways for tocopherol synthesis in wheat, potentially useful in breeding high-tocopherol wheat varieties.

Scaffolded and annotated nuclear and organelle genomes of the North American brown alga Saccharina latissima

Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica. While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.

Epigenetic perspectives on wheat speciation, adaptation, and development

Bread wheat (Triticum aestivum) has undergone a complex evolutionary history shaped by polyploidization, domestication, and adaptation. Recent advances in multiomics approaches have shed light on the role of epigenetic mechanisms, including DNA methylation, histone modification, chromatin accessibility, and noncoding RNAs, in regulating gene expression throughout these processes. Epigenomic reprogramming contributes to genome stability and subgenome differentiation and modulates key agronomic traits by influencing flowering time, environmental responses, and developmental programs. This review synthesizes current insights into epigenetic regulation of wheat speciation, adaptation, and development, highlighting their potential applications in crop improvement. A deeper understanding of these mechanisms will facilitate targeted breeding strategies leveraging epigenetic variations to enhance wheat resilience and productivity in the face of changing environments.

Identification and validation of a novel tiller inhibition locus (tin7) on chromosome 2BL in wheat

Tiller number is a key determinant of the number of spikes per plant, significantly influencing yield. Here, we identify and characterize a novel tiller inhibition line, N2496. Using an F2 segregating population derived from crossing N2496 and CN16, we mapped this locus. The F1 line demonstrated a high number of tillers, while the F2 population exhibited segregated ratios of 3:1 in tiller number. BSR-Seq analysis indicated that only one locus controls tiller number, located on chromosome 2B (Chr. 2B). This genetic analysis confirmed the presence of a single recessive locus controlling the tiller inhibition trait within this population. Subsequently, we constructed a genetic map on Chr. 2B using a wheat 55 K single nucleotide polymorphism array. By combining recombinant analysis with the genotype and phenotype of the F2-3 family, we identified and named a major and novel locus, tiller inhibition gene (tin7), mapped within a 2.43 cM interval. The influence of tin7 was verified across six different background populations all sharing N2496 as a common parent. Using new recombinant lines from these six populations, we further narrowed down the interval of tin7 to a genetic interval of 2.08 cM. Analysis of thousand grain weight and grain-related traits suggests that by regulating tiller number, tin7 holds the potential to increase yield in wheat. Our research provides access to a novel tiller number locus and available markers for regulating tiller number, which could be used in developing new cultivars with an optimal number of tillers.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01567-z.

A system genetics analysis uncovers the regulatory variants controlling drought response in wheat

Plants activate a variable response to drought stress by modulating transcription of key genes. However, our knowledge of genetic variations governing gene expression in response to drought stress remains limited in natural germplasm. Here, we performed a comprehensive analysis of the transcriptional variability of 200 wheat accessions in response to drought stress by using a systems genetics approach integrating pan-transcriptome, co-expression networks, transcriptome-wide association study (TWAS), and expression quantitative trait loci (eQTLs) mapping. We identified 1621 genes and eight co-expression modules significantly correlated with wheat drought tolerance. We also defined 620 664 and 654 798 independent eQTLs associated with the expression of 17 429 and 18 080 eGenes under normal and drought stress conditions. Focusing on dynamic regulatory variants, we further identified 572 eQTL hotspots and constructed transcription factors governed drought-responsive network by the XGBoost model. Subsequently, by combining with genome-wide association study (GWAS), we uncovered a 369-bp insertion variant in the TaKCS3 promoter containing multiple cis-regulatory elements recognized by eQTL hotspot-associated transcription factors that enhance its transcription. Further functional analysis indicated that elevating TaKCS3 expression affects cuticular wax composition to reduce water loss during drought stress, and thereby increase drought tolerance. This study sheds light on the genome-wide genetic variants that influence dynamic transcriptional changes during drought stress and provides a valuable resource for the mining of drought-tolerant genes in the future.

Comparative transcriptomes reveal insights into different host responses associated with Fusarium head blight resistance in wheat

Fusarium head blight (FHB) has become a major challenge in global wheat production, causing severe yield losses and exacerbating food safety concerns. In recent years, FHB-related research has focused on understanding resistance mechanisms, identifying genetic markers, and breeding resistant varieties to mitigate the disease's impact on yield and quality. This study comparatively analyzed transcriptome data from six wheat materials with differing levels of resistance following infection by Fusarium graminearum (F. graminearum). The results displayed that a total of 26,767 protein-coding genes and 2,463 long non-coding RNAs (lncRNAs) showed differential expression levels between normal and FHB treatment in at least one material. Among them, 14,130 FHB-responsive protein-coding genes and 913 lncRNAs were identified as material-specific, with functions related to the unique disease resistance mechanisms of the respective materials. Some of these genes have previously been reported to participate in physiological processes related to wheat FHB resistance, including Pm3-like resistance proteins, lactoylglutathione lyase, serine/threonine protein phosphatases, NBS-LRR resistance proteins, glutathione S-transferase (GST), and RPM1 resistance proteins. Additionally, we integrated FHB-responsive genes and lncRNAs with previously reported FHB QTLs, and constructed an interaction regulatory network between pathogen and host through a co-expression network. Based on this network, we identified five genes (one gene encoding glutathione synthetase and four genes encoding glutathione transferase) in the glutathione metabolism pathway, which overlapped with Fhb2 QTLs regions and exhibited material-specific expression patterns. These results will provide new insights into further dissecting of the functional genes and lncRNAs involved in wheat FHB resistance.

Differential brainstem connectivity according to sex and menopausal status in healthy male and female individuals

BACKGROUND

Brainstem nuclei play a critical role in both ascending monoaminergic modulation of cortical function and arousal, and in descending bulbospinal pain modulation. Even though sex-related differences in the function of both systems have been reported in animal models, a complete understanding of sex differences, as well as menopausal effects, in brainstem connectivity in humans is lacking. This study evaluated resting-state connectivity of the dorsal raphe nucleus, right and left locus coeruleus complex (LCC), and periaqueductal gray (PAG) according to sex and menopausal status in healthy individuals. In addition, relationships between systemic estrogen levels and brainstem-network connectivity were examined in a subset of participants.

METHODS

Resting-state fMRI was performed in 47 healthy male (age, 31.2 ± 8.0 years), 53 healthy premenopausal female (age, 24.7 ± 7.3 years; 22 in the follicular phase, 31 in the luteal phase), and 20 postmenopausal female participants (age, 54.6 ± 7.2 years). Permutation Analysis of Linear Models (5000 permutations) was used to evaluate differences in brainstem-network connectivity according to sex and menopausal status, controlling for age. In 10 males and 17 females (9 premenopausal; 8 postmenopausal), estrogen and estrogen metabolite levels in plasma and stool were determined by liquid chromatography-mass spectrometry/mass spectrometry. Relationships between estrogen levels and brainstem-network connectivity were evaluated by partial least squares analysis.

RESULTS

Left LCC-executive control network connectivity showed an overall sex difference (p = 0.02), with higher connectivity in females than in males; however, this was mainly due to differences between males and premenopausal females (p = 0.008). Additional sex differences were dependent on menopausal status: PAG-default mode network (DMN) connectivity was higher in postmenopausal females than in males (p = 0.04), and PAG-sensorimotor network (SMN) connectivity was higher in premenopausal females than in males (p = 0.03) and postmenopausal females (p = 0.007). Notably, higher free 2-hydroxyestrone levels in stool were reliably associated with higher PAG-SMN and PAG-DMN connectivity in premenopausal females (p < 0.01).

CONCLUSIONS

Healthy females show higher brainstem-network connectivity involved in cognitive control, sensorimotor function, and self-relevant processes than males, dependent on their menopausal status. Further, 2-hydroxyestrone, implicated in pain, may modulate PAG connectivity in premenopausal females. These findings may relate to differential vulnerabilities to chronic stress-sensitive disorders at different life stages.

Recombination and structural variation in a large 8-founder wheat MAGIC population

Identifying the genetic architecture of complex traits requires access to populations with sufficient genetic diversity and recombination. Multiparent Advanced Generation InterCross (MAGIC) populations are a powerful resource due to their balanced population structure, allelic diversity, and enhanced recombination. However, implementing a MAGIC population in complex polyploids such as wheat is challenging, as wheat harbors many introgressions, inversions, and other genetic factors that interfere with linkage mapping. By utilizing a comprehensive crossing strategy, additional rounds of mixing, and novel genotype calling approaches, we developed a bread wheat 8-parent MAGIC population of over 3,000 genotyped recombinant inbred lines derived from 2,151 distinct crosses. This effort resulted in a dense genetic map covering the complete genome. Further rounds of intercrossing led to increased recombination in inbred lines, as expected. We identified structural variation highlighted by segregation distortion, along with epistatic allelic interactions between specific founders. We report on a novel and effective resource for genomic and trait exploration in hexaploid wheat, capable of detecting small genetic effects and epistatic interactions due to the high level of recombination and large number of lines. The interactions and genetic effects identified provide a basis for ongoing research to understand the basis of allelic frequencies across the genome, particularly where economically important loci are involved.

Ancient diversity of Triticum aestivum subspecies as source of novel loci for bread wheat improvement

Ancient subspecies of hexaploid wheat, not yet subjected to intensive selection, harbor potentially valuable alternative genetic variability for the genetic improvement of modern cultivated bread wheat. To investigate these hitherto unexplored resources, we established a panel, currently unique, consisting of 190 accessions of Triticum aestivum belonging to five different neglected subspecies, compactum, sphaerococcum, macha, spelta, and vavilovii, with few aestivum references. The panel was genotyped through the iSelect Illumina arrays (20K and 25K) and phenotyped for 25 traits related to phenology, morphology, yield, and physiology for 4 years under field conditions. We found wide variability for all traits analyzed, both within and among subspecies, demonstrating the richness contained therein. Through a genome-wide association study (GWAS), we identified a total of 126 marker-trait associations (MTAs), including 4 for years, 58 for morphological traits, 39 related to yield, and 25 for physiological traits, some of them confirming loci previously published and others being novel. Fourteen MTAs were associated with multiple traits. Among them, one on chromosome 2D at 360.2 Mb was associated with spike density, length, and shape, and thus is of particular interest because it may underlie the compactum (C) gene, until now considered difficult to clone because of its centromeric position. The physical distance defined by this MTA is considerably smaller (1.7 Mb) than what is reported so far in the literature, paving the way toward physical mapping of the C gene. A potential candidate gene has been identified for the trait grain number per spike. This is TraesCS6A03G0476500, coding for a monosaccharide-sensing protein 2, located on chromosome 6A at 233 Mb and identified through an MTA that segregates exclusively in compactum accessions. The results obtained confirm the remarkable potential present in the panel of wheat subspecies analyzed in this study, which, being characterized by a very short linkage disequilibrium (LD) decay, allowed the definition of rather narrow ranges around key traits, such as those related to yield, providing new perspectives on transferring genes across subspecies for wheat improvement.

REPrise: de novo interspersed repeat detection using inexact seeding

BACKGROUND

Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-free de novo repeat detection approaches are powerful for annotating genomes that lack well-curated repeat databases. However, existing tools do not yet have sufficient repeat detection performance.

RESULTS

In this study, we developed REPrise, a de novo interspersed repeat detection software program based on a seed-and-extension method. Although the algorithm of REPrise is similar to that of RepeatScout, which is currently the de facto standard tool, we incorporated three unique techniques into REPrise: inexact seeding, affine gap scoring and loose masking. Analyses of rice and simulation genome datasets showed that REPrise outperformed RepeatScout in terms of sensitivity, especially when the repeat sequences contained many mutations. Furthermore, when applied to the complete human genome dataset T2T-CHM13, REPrise demonstrated the potential to detect novel repeat sequence families.

CONCLUSION

REPrise can detect interspersed repeats with high sensitivity even in long genomes. Our software enhances repeat annotation in diverse genomic studies, contributing to a deeper understanding of genomic structures.

Omic characterisation of multi-component defences against the necrotrophic pathogen Pyrenophora tritici-repentis in wheat

Tan Spot disease is caused by the necrotrophic pathogen Pyrenophora tritici-repentis (Ptr) and poses a significant threat to global wheat production. Therefore, novel sources of resistance need to be identified, coupled with a fuller mechanistic understanding of host responses to Ptr. Herein, we characterise the interaction between a ToxA-positive Ptr strain and parental wheat lines from a multiparent advanced generation intercross (MAGIC) population. Genotypes displaying moderate resistance ('Robigus') or susceptibility ('Hereward') to Ptr challenge were identified and characterised through histological, metabolomic, and transcriptomic approaches. Histological investigations indicated the prominence of papilla-based defences in Robigus. Transcriptomic analyses could link this to the expression of barrier-related genes i.e. actin polymerisation, callose deposition, vesicle trafficking, and cellulose synthesis. Inhibiting actin polymerisation with cytochalasin E increased lesion numbers but did not augment lesion growth, suggesting the deployment of other defence mechanisms. These may be influenced by auxin, as its exogenous application exacerbated symptom development. Transcriptomic and metabolomic analyses in Hereward following challenge with Ptr suggested shifts in primary metabolism, affecting glycolysis, the TCA cycle, and the γ-aminobutyric acid (GABA) shunt. Activation of salicylic acid (SA)-associated genes, including NPR1 and WRKY33, was specific to Hereward, and exogenous SA increased susceptibility to Ptr in both genotypes. This study suggests barrier defences could be effective against Ptr as well as a lack of susceptibility factors like SA or the appropriate processing of IAA. These findings offer potential avenues for enhancing wheat resistance to Ptr.

Transcriptomic and metabolomic analyses unveil TaASMT3-mediated wheat resistance against stripe rust by promoting melatonin biosynthesis

Plants have evolved a series of complicated defense mechanisms to counteract pathogen invasions. Although many studies have provided molecular evidence of resistance proteins and downstream signal transduction networks, the mechanisms by which plants resist pathogens remain poorly understood at the metabolite level. Here, we performed transcriptomic analyses of wheat leaves infected with Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust. Functional enrichment analysis of identified differentially expressed genes (DEGs) revealed the strongest resistance responses at 24 h post-inoculation (hpi) in the incompatible wheat-Pst interaction system. Integrated with the metabolomics data at 24 hpi, we found that the amino acid metabolic pathways appeared to be directly involved in stripe rust resistance. Among these, five differentially abundant metabolites (DAMs) indole, tryptophan, tryptamine, N-Methylserotonin, and 5-Methoxyindoleacetate were enriched to the biosynthesis pathway of melatonin, a branch of tryptophan metabolism. Subsequent UPLC-MS/MS analysis confirmed that melatonin was highly accumulated in the incompatible wheat-Pst system, but not in the compatible interaction system. Exogenous melatonin treatment induced wheat resistance to Pst. The most significantly upregulated melatonin biosynthesis-related gene in the incompatible wheat-Pst system was TaASMT3, which encodes an acetylserotonin O-methyltransferase. Virus-induced gene silencing analysis revealed that knocking down TaASMT3 reduced wheat resistance to stripe rust, further suggesting a positive role of melatonin in wheat resistance to Pst. Taken together, these data suggest that melatonin was accumulated during Pst infection to activate wheat defense responses, offering a new perspective for elucidation of wheat stripe rust resistance based on metabolic dynamics.

A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat

The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 rDNA units. Genome-wide rearrangements, centromeric elements, transposable element expansion and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, transposable element insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence protein-coding genes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity and provides insights for future wheat research and breeding.

TTLOC: A Tn5 transposase-based approach to localize T-DNA integration sites

Thermal asymmetric interlaced-polymerase chain reaction-based and whole-genome sequencing-based T-DNA localization approaches have been developed for the recovery of T-DNA integration sites (TISs). Nevertheless, a low-cost and high-throughput technique for the detection of TISs, which would facilitate the identification of genetically engineered plants, is in high demand for rapid crop breeding and plant synthetic biology. Here, we present Tn5 transposase-based T-DNA integration site localization (TTLOC), a Tn5-based approach for TIS localization. TTLOC employs specialized adaptor-assembled Tn5 transposases for genomic DNA tagmentation. TTLOC library construction is straightforward, involving only six steps that requires two and a half hours to complete. The resulting pooled library is compatible with next-generation sequencing, which enables high-throughput determination. We demonstrate the ability of TTLOC to recover 95 non-redundant TISs from 65 transgenic Arabidopsis (Arabidopsis thaliana) lines, and 37 non-redundant TISs from the genomes of transgenic rice (Oryza sativa), soybean (Glycine max), tomato (Solanum lycopersicum), potato (Solanum tuberosum), and from the large hexaploid wheat (Triticum aestivum) genome. TTLOC is a cost-effective method, as 1 to 2 Gb of raw data for each multiplexing library are sufficient for efficient TIS calling, independent of the genome size. Our results establish TTLOC as a promising strategy for evaluation of genome engineered plants and for selecting genome safe harbors for trait stacking in crop breeding and plant synthetic biology.

Deciphering the regulatory network of lignocellulose biosynthesis in bread wheat through genome-wide association studies

KEY MESSAGE

This study identified 46 key QTL and 17 candidate genes and developed a KASP marker, providing valuable molecular tools for enhancing lignocellulose traits, lodging resistance, and bioenergy potential in wheat. Wheat lignocellulose, composed of lignin, cellulose, and hemicellulose, plays a crucial role in strengthening plant cell walls, enhancing lodging resistance, and contributing to bioenergy production. However, the genetic basis underlying the variation in lignocellulose content in wheat remains poorly understood. The stem lignin, cellulose, and hemicellulos contents in the second stem internode of a panel of 166 wheat accessions grown in three environments were measured, combined with the genotyping data with 660 K wheat SNP chip; a genome-wide association studies (GWAS) were conducted to identify loci associated with the lignocellulose content in wheat. Significant variations in lignin, cellulose, and hemicellulose contents were observed among the wheat accessions. GWAS identified 1146 significant SNPs associated with lignin, cellulose, and hemicellulose contents, distributed across the A, B, and D sub-genomes of wheat. Joint analysis of haplotype blocks refined these associations, identifying 46 significant quantitative trait loci (QTL) regions and 17 candidate genes, primarily linked to vascular development, hemicellulose synthesis, internode elongation regulation, and lignin biosynthesis. A KASP marker (NW_CC5951) for lignocellulose was developed. These findings provide valuable molecular markers for marker-assisted selection, supporting wheat breeding for improved stem quality and lodging resistance, and offer insights into balancing grain yield with lodging resistance and lignocellulosic energy production.

A special short-wing petal faba genome and genetic dissection of floral and yield-related traits accelerate breeding and improvement of faba bean

BACKGROUND

A comprehensive study of the genome and genetics of superior germplasms is fundamental for crop improvement. As a widely adapted protein crop with high yield potential, the improvement in breeding and development of the seeds industry of faba bean have been greatly hindered by its giant genome size and high outcrossing rate.

RESULTS

To fully explore the genomic diversity and genetic basis of important agronomic traits, we first generate a de novo genome assembly and perform annotation of a special short-wing petal faba bean germplasm (VF8137) exhibiting a low outcrossing rate. Comparative genome and pan-genome analyses reveal the genome evolution characteristics and unique pan-genes among the three different faba bean genomes. In addition, the genome diversity of 558 accessions of faba bean germplasm reveals three distinct genetic groups and remarkable genetic differences between the southern and northern germplasms. Genome-wide association analysis identifies several candidate genes associated with adaptation- and yield-related traits. We also identify one candidate gene related to short-wing petals by combining quantitative trait locus mapping and bulked segregant analysis. We further elucidate its function through multiple lines of evidence from functional annotation, sequence variation, expression differences, and protein structure variation.

CONCLUSIONS

Our study provides new insights into the genome evolution of Leguminosae and the genomic diversity of faba bean. It offers valuable genomic and genetic resources for breeding and improvement of faba bean.

Enhancing wheat resilience: biotechnological advances in combating heat stress and environmental challenges

Climate change, with its increasing temperatures, is significantly disrupting global agricultural systems, and wheat, a key cereal crop faces severe challenges. Heat stress has emerged as a critical threat, accelerating wheat growth, leading to premature maturation, reduced grain filling, and ultimately lower yields. The situation is exacerbated by more frequent and intense heat waves, particularly in regions already struggling with water scarcity. Maintaining the delicate balance of temperature and water necessary for optimal wheat production is becoming challenging, posing a serious risk to global food security. Therefore, there is an urgent need to develop adaptive strategies with innovations in breeding and transgenic technologies crucial to improving wheat resilience to environmental stresses, especially to combat the growing impacts of heat stress. Modern tools like CRISPR/Cas9, Transcription Activator-Like Effector Nucleases, and Zinc Finger Nucleases have been instrumental in developing wheat varieties with improved traits. However, the future of wheat cultivation requires more than just resistance to a single stressor. As climate change intensifies, there is an urgent need for wheat varieties that can withstand multiple stresses, including heat, drought, and pests. Developing these multi-stress-tolerant cultivars is crucial for ensuring food security in a rapidly changing climate.

Hordeum I genome unlocks adaptive evolution and genetic potential for crop improvement

Crop wild relatives (CWRs) are invaluable for crop improvement. Among these, Hordeum I-genome species exhibit exceptional tolerance to alkali and salt stresses. Here we present a chromosome-scale genome assembly of Hordeum brevisubulatum (II, 2n = 2x =14) and genome resequencing of 38 diploid germplasms spanning 7 I-genome species. We reveal that the adaptive evolution of the H. brevisubulatum genome is shaped by structural variations, some of which may contribute to its adaptation to high alkali and salt environments. Evolutionary duplication of the stress sensor-responder module CaBP-NRT2 and the horizontally transferred fungal gene Fhb7 were identified as novel alkaline-saline tolerance mechanisms. We also demonstrate the potential of the Hordeum I genome in crop breeding through the newly synthesized hexaploid Tritordeum (AABBII) with enhanced alkaline-saline tolerance. Our study fills critical gaps in Hordeum genomics and CWR research, advancing introgression of CWR resources into current crops for sustainable agriculture.

Amand P, Rupp J, Pumphrey M, Fritz A, Zhang G, Jordan KW, Bai G. A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger

Barley yellow dwarf (BYD) is one of the most serious viral diseases in cereal crops worldwide. Identification of quantitative trait loci (QTLs) underlining wheat resistance to barley yellow dwarf virus (BYDV) is essential for breeding BYDV-tolerant wheat cultivars. In this study, a recombinant inbred line (RIL) population was developed from the cross between Jagger (PI 593688) and a Jagger mutant (JagMut1095). A linkage map of 3106 cM consisting of 21 wheat chromosomes was developed using 1003 unique single nucleotide polymorphisms (SNPs) from the RIL population and was used to identify QTLs for BYDV resistance and yield-related traits, including 1000-kernel weight (TKW), kernel area (KA), kernel width (KW), and kernel length (KL). QByd.hwwg-2DL, a QTL on chromosome arm 2DL for BYDV resistance, was consistently identified in three field experiments and explained 11.6%-44.5% of the phenotypic variation. For yield-related traits, six major and repeatable QTLs were identified on 1AS (QKa.hwwg-1AS), 2DL (QTkw.hwwg-2DL, QKa.hwwg-2DL, QKw.hwwg-2DL, and QKl.hwwg-2DL), and 5AL (QKw.hwwg-5AL). The major QTLs on chromosome 2DL for TKW, KA, KW, and KL were mapped between 621 and 643 Mb, overlapping with QByd.hwwg-2DL with all the favorable alleles from Jagger. This study reports the first native BYDV resistance QTL (QByd.hwwg-2DL) originating from common wheat and tightly linked markers to the QTL for improvement of wheat BYDV resistance in wheat breeding.

Multi-Omics and Physiological Analysis Reveal Crosstalk Between Aphid Resistance and Nitrogen Fertilization in Wheat

The availability of nitrogen (N) can dramatically influence crops resistance to herbivorous insects. However, the interaction between N fertilization and crop resistance to insects is not well understood. In this study, the effects of N fertilization on the grain aphid (Sitobion miscanthi) were investigated using three wheat (Triticum aestivum) cultivars with different aphid resistances. We measured aphid life cycle parameters, fecundity, survival rate, weight and feeding behavior, in conjunction with wheat metabolomics, transcriptomics and alien introgression analysis. Our results demonstrated that higher N application benefits aphid feeding across all three wheat cultivars. We also reveal that the highly resistant cultivar (ZM9) can only exert its resistance-advantage under low N fertilization, losing its advantage compared to moderately resistant cultivar YN19 and susceptible cultivar YN23 under higher N fertilization. The effects of N fertilization on wheat-aphid interactions were due to changes in the regulation of carbon and nitrogen metabolism. Integration of multi-omics highlighted specific aphid-induced differentially expressed genes (DEGs, e.g., TUB6, Tubulin 6; ENODL20, Early nodulin-like protein 20; ACT7 Actin 7; Prx47, Peroxidase 47) and significantly different metabolites (SDMs, e.g., crotonoside, guanine, 2'-O-methyladenosine, ferulic acid) in ZM9. Additionally, we report the unique SDMs-DEGs interactions, associated with introgression during wheat domestication, may help infer aphid resistance. In summary, this study provides new insights into the relationships between N fertilization practices, defense responses and integrated pest management for sustainable wheat production.

A Genome-Wide Association Study Identifies Markers and Candidate Genes Affecting Tolerance to the Wheat Pathogen Zymoseptoria tritici

Plants defend themselves against pathogens using either resistance, measured as the host's ability to limit pathogen multiplication, or tolerance, measured as the host's ability to reduce the negative effects of infection. Tolerance is a promising trait for crop breeding, but its genetic basis has rarely been studied and remains poorly understood. Here, we reveal the genetic basis of leaf tolerance to the fungal pathogen Zymoseptoria tritici that causes the globally important septoria tritici blotch (STB) disease on wheat. Leaf tolerance to Z. tritici is a quantitative trait that was recently discovered in wheat by using automated image analyses that quantified the symptomatic leaf area and counted the number of pycnidia found on the same leaf. A genome-wide association study identified four chromosome intervals associated with tolerance and a separate chromosome interval associated with resistance. Within these intervals, we identified candidate genes, including wall-associated kinases similar to Stb6, the first cloned STB resistance gene. Our analysis revealed a strong negative genetic correlation between tolerance and resistance to STB, indicative of a trade-off. Such a trade-off between tolerance and resistance would hinder breeding simultaneously for both traits, but our findings suggest a way forward using marker-assisted breeding. We expect that the methods described here can be used to characterize tolerance to other fungal diseases that produce visible fruiting bodies, such as speckled leaf blotch on barley, potentially unveiling conserved tolerance mechanisms shared among plant species. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

A node-localized transporter TaSPDT is responsible for the distribution of phosphorus to grains in wheat

Wheat (Triticum aestivum L.) is one of the world's main food crops and the largest phosphorus (P) fertilizer consumer globally. However, the molecular mechanism of P distribution in wheat remains largely unknown. This study investigated the TaSULTR gene family and functionally characterized TaSPDT (TaSULTR3;4). Thirty-three TaSULTR genes were identified and divided into four groups. These genes contained three tandem duplications and 28 segmental duplications. TaSPDT was localized on the plasma membrane and demonstrated P transport activity. TaSPDT was mainly expressed at nodes, and its expression was elevated under low P conditions. TaSPDT was distributed on the xylem and phloem of enlarged and diffuse vascular bundles at nodes, as well as on the parenchyma cell bridge between vascular bundles. TaSPDT knockout reduced P distribution to young leaves but increased it in older leaves during the vegetative stage under low P availability. P uptake by roots, transfer to above-ground tissues, and redistribution within aerial organs were unaffected. At the reproductive stage, TaSPDT knockout notably diminished P allocation to grains, resulting in a significant decrease in grain yield, particularly under P-deficient conditions. These results suggest that TaSPDT mediates the transmembrane transport of P from the xylem to the phloem at the nodes, resulting in the preferential distribution of P to grains. This study enables a better understanding of the TaSULTR gene family and P distribution in wheat.

Future of durum wheat research and breeding: Insights from early career researchers

Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.

Genome-wide association studies on resistance to powdery mildew in cultivated emmer wheat

Powdery mildew, caused by the fungal pathogen Blumeria graminis (DC.) E. O. Speer f. sp. tritici Em. Marchal (Bgt), is a constant threat to global wheat (Triticum aestivum L.) production. Although ∼100 powdery mildew (Pm) resistance genes and alleles have been identified in wheat and its relatives, more is needed to minimize Bgt's fast evolving virulence. In tetraploid wheat (Triticum turgidum L.), wild emmer wheat [T. turgidum ssp. dicoccoides (Körn. ex Asch. & Graebn.) Thell.] accessions from Israel have contributed many Pm resistance genes. However, the diverse genetic reservoirs of cultivated emmer wheat [T. turgidum ssp. dicoccum (Schrank ex Schübl.) Thell.] have not been fully exploited. In the present study, we evaluated a diverse panel of 174 cultivated emmer accessions for their reaction to Bgt isolate OKS(14)-B-3-1 and found that 66% of accessions, particularly those of Ethiopian (30.5%) and Indian (6.3%) origins, exhibited high resistance. To determine the genetic basis of Bgt resistance in the panel, genome-wide association studies were performed using 46,383 single nucleotide polymorphisms (SNPs) from genotype-by-sequencing and 4331 SNPs from the 9K SNP Infinium array. Twenty-five significant SNP markers were identified to be associated with Bgt resistance, of which 21 SNPs are likely novel loci, whereas four possibly represent emmer derived Pm4a, Pm5a, PmG16, and Pm64. Most novel loci exhibited minor effects, whereas three novel loci on chromosome arms 2AS, 3BS, and 5AL had major effect on the phenotypic variance. This study demonstrates cultivated emmer as a rich source of powdery mildew resistance, and the resistant accessions and novel loci found herein can be utilized in wheat breeding programs to enhance Bgt resistance in wheat.

Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111

Leaf rust, caused by Puccinia triticina (Pt), poses a constant threat to global wheat production, and novel leaf rust resistance genes are needed to combat the disease. A previous genome-wide association study (GWAS) identified a single nucleotide polymorphism (SNP) marker associated with leaf rust resistance in the terminal region of chromosome arm 5BS in the Iranian landrace PI 622111. An F2 population and 175 F2:3 families from cross PI 622111 × Yuanyu 3 were evaluated for response to Pt isolate Pt52-2 (MMPSD). Genotyping-by-sequencing analysis and genotyping of a subset of the F2 plants identified 32 SNPs closely associated with leaf rust resistance in the target region. Some of these SNPs were converted into kompetitive allele-specific polymorphic (KASP) markers and used to genotype the F2 population together with a set of simple sequence repeat (SSR) markers also located in the target genomic region. Linkage analysis delimited the leaf rust resistance gene in PI 622111, designated Lr622111, to a 0.4 Mb interval flanked by Xstars700 (7.22 Mb) and Xstars678 (7.62 Mb) in IWGSC RefSeq v.2.1. An allelism test involving 811 F2 plants indicated that Lr622111 was allelic to Lr52. Since PI 622111 reacted differently from the Lr52 donor to Pt races in the GWAS, Lr622111 is considered a new Lr52 allele conferring a wide spectrum of resistance to current US Pt races. KASP marker Xstars-KASP239, which is 0.9 cM distal to Lr622111, can be widely used to tag Lr622111 in breeding populations.

Association mapping and genomic prediction for processing and end-use quality traits in wheat (Triticum aestivum L.)

End-use and processing traits in wheat (Triticum aestivum L.) are crucial for varietal development but are often evaluated only in the advanced stages of the breeding program due to the amount of grain needed and the labor-intensive phenotyping assays. Advances in genomic resources have provided new tools to address the selection for these complex traits earlier in the breeding process. We used association mapping to identify key variants underlying various end-use quality traits and evaluate the usefulness of genomic prediction for these traits in hard red spring wheat from the Northern United States. A panel of 383 advanced breeding lines and cultivars representing the diversity of the University of Minnesota wheat breeding program was genotyped using the Illumina 90K single nucleotide polymorphism array and evaluated in multilocation trials using standard assessments of end-use quality. Sixty-three associations for grain or flour characteristics, mixograph, farinograph, and baking traits were identified. The majority of these associations were mapped in the vicinity of glutenin/gliadin or other known loci. In addition, a putative novel multi-trait association was identified on chromosome 6AL, and candidate gene analysis revealed eight genes of interest. Further, genomic prediction had a high predictive ability (PA) for mixograph and farinograph traits, with PA up to 0.62 and 0.50 in cross-validation and forward prediction, respectively. The deployment of 46 markers from GWAS to predict dough-rheology traits yielded low to moderate PA for various traits. The results of this study suggest that genomic prediction for end-use traits in early generations can be effective for mixograph and farinograph assays but not baking assays.

Integrated transcriptome and metabolome analyses reveals the mechanisms of function loss of Lr29 leaf rust resistance gene at high temperatures in wheat

Leaf rust (LR) is one of the most common diseases of wheat. The resistance gene Lr29 provides wide resistance to LR, but loses its function under high temperatures. Despite the importance of this gene, the mechanism of resistance is unclear. In this study we investigated the resistance mechanism of the Lr29 gene to LR at the seedling stage, as well as the reasons behind the loss of gene function at high temperatures by using integrated transcriptome and metabolome analyses. Results suggests that the pathways of reactive oxygen species (ROS), which could be due to expression of genes including LOX (lipoxygenase), APX (ascorbate peroxidase) and GST (glutathione S-transferase), play a key role in the resistance of Lr29 to LR, furthermore flavonoids, such as epicatechin, cosmosiin, apiin, vitexin and rutin, were identified as the key metabolites linked to Lr29 resistance. We also found that, at high temperatures, Lr29 downregulated the genes and metabolites associated with glycolysis and the tricarboxylic acid (TCA) cycle, while genes and metabolites related to the shikimic acid pathway were upregulated. This study might provide a valuable theoretical foundation for the cloning of the Lr29 gene, the analysis of its disease resistance mechanism, and the understanding of how temperature affects gene function.

Transcriptomic analysis reveals cloquintocet-mexyl-inducible genes in hexaploid wheat (Triticum aestivum L.)

Identification and characterization of genes encoding herbicide-detoxifying enzymes is lacking in allohexaploid wheat (Triticum aestivum L.). Gene expression is frequently induced by herbicide safeners and implies the encoded enzymes serve a role in herbicide metabolism and detoxification. Cloquintocet-mexyl (CM) is a safener commonly utilized with halauxifen-methyl (HM), a synthetic auxin herbicide whose phytotoxic form is halauxifen acid (HA). Our first objective was to identify candidate HA-detoxifying genes via RNA-Seq by comparing untreated and CM-treated leaf tissue. On average, 81% of RNA-Seq library reads mapped uniquely to the reference genome and 76.4% of reads were mapped to a gene. Among the 103 significant differentially expressed genes (DEGs), functional annotations indicate the majority of DEGs encode proteins associated with herbicide or xenobiotic metabolism. This finding was further corroborated by gene ontology (GO) enrichment analysis, where several genes were assigned GO terms indicating oxidoreductase activity (34 genes) and transferase activity (45 genes). One of the significant DEGs is a member of the CYP81A subfamily of cytochrome P450s (CYPs; denoted as CYP81A-5A), which are of interest due to their ability to catalyze synthetic auxin detoxification. To investigate CYP expression induced by HM and/or CM, our second objective was to measure gene-specific expression of CYP81A-5A and its homoeologs (CYP81A-5B and CYP81A-5D) in untreated leaf tissue and leaf tissue treated with CM and HM over time using RT-qPCR. Relative to the reference gene (β-tubulin), basal CYP expression is high, expression among these CYPs varies over time, and expression for all CYPs is CM-inducible but not HM-inducible. Further analysis of CYP81A-5A, such as gene knock-out, overexpression experiments, or in vitro activity assays with purified enzyme are necessary to test the hypotheses that the encoded CYP detoxifies HA and that CM upregulates this reaction.

Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data

Curated resources at centralized repositories provide high-value service to users by enhancing data veracity. Curation, however, comes with a cost, as it requires dedicated time and effort from personnel with deep domain knowledge. In this paper, we investigate the performance of a large language model (LLM), specifically generative pre-trained transformer (GPT)-3.5 and GPT-4, in extracting and presenting data against a human curator. In order to accomplish this task, we used a small set of journal articles on wheat and barley genetics, focusing on traits, such as salinity tolerance and disease resistance, which are becoming more important. The 36 papers were then curated by a professional curator for the GrainGenes database (https://wheat.pw.usda.gov). In parallel, we developed a GPT-based retrieval-augmented generation question-answering system and compared how GPT performed in answering questions about traits and quantitative trait loci (QTLs). Our findings show that on average GPT-4 correctly categorized manuscripts 97% of the time, correctly extracted 80% of traits, and 61% of marker-trait associations. Furthermore, we assessed the ability of a GPT-based DataFrame agent to filter and summarize curated wheat genetics data, showing the potential of human and computational curators working side-by-side. In one case study, our findings show that GPT-4 was able to retrieve up to 91% of disease related, human-curated QTLs across the whole genome, and up to 96% across a specific genomic region through prompt engineering. Also, we observed that across most tasks, GPT-4 consistently outperformed GPT-3.5 while generating less hallucinations, suggesting that improvements in LLM models will make generative artificial intelligence a much more accurate companion for curators in extracting information from scientific literature. Despite their limitations, LLMs demonstrated a potential to extract and present information to curators and users of biological databases, as long as users are aware of potential inaccuracies and the possibility of incomplete information extraction.

Predicting Fitness-Related Traits Using Gene Expression and Machine Learning

Evolution by natural selection occurs at its most basic through the change in frequencies of alleles; connecting those genomic targets to phenotypic selection is an important goal for evolutionary biology in the genomics era. The relative abundance of gene products expressed in a tissue can be considered a phenotype intermediate to the genes and genomic regulatory elements themselves and more traditionally measured macroscopic phenotypic traits such as flowering time, size, or growth. The high dimensionality, low sample size nature of transcriptomic sequence data is a double-edged sword, however, as it provides abundant information but makes traditional statistics difficult. Machine learning (ML) has many features which handle high-dimensional data well and is thus useful in genetic sequence applications. Here, we examined the association of fitness components with gene expression data in Ipomoea hederacea (Ivyleaf morning glory) grown under field conditions. We combine the results of two different ML approaches and find evidence that expression of photosynthesis-related genes is likely under selection. We also find that genes related to stress and light responses were overall important in predicting fitness. With this study, we demonstrate the utility of ML models for smaller samples and their potential application for understanding natural selection.

TaDL interacts with TaB3 and TaNF-YB1 to synergistically regulate the starch synthesis and grain quality in bread wheat

Starch biosynthesis is a critical factor in wheat (Triticum aestivum L.) quality and yield. However, the full scope of its regulation is not fully understood. Here we report that TaDL interacts with TaB3 and TaNF-YB1 to synergistically regulate starch biosynthesis and quality in wheat. Genome-edited tadl mutant lines had smaller and lighter grains with lower total starch and amylose contents compared to wild type (WT). Correspondingly, the transcript levels of starch biosynthesis-related genes, including TaSUS1, TaSUS2, TaAGPL2, TaSBEIIa, TaGBSSII, and TaSWEET2a, were markedly lower at 15 d after flowering (DAF) in tadl mutants. TaDL physically interacted with TaB3 and TaNF-YB1 and activated the transcription of TaSUS2 and TaAGPL2 through direct binding to their promoter regions. A null mutant of TaB3 also affected grain filling, with phenotypes similar to those of tadl mutants, whereas overexpression of TaNF-YB1 promoted grain filling. Our study demonstrated that TaDL plays an essential role in starch biosynthesis and identified an elite allele (TaDL-BI) associated with starch content, providing insights into the underlying molecular mechanism of wheat grain filling, which may be useful in breeding of high-yielding wheat and quality improvement.

The location and genome origin of alien chromatin in wheat founder parent Xiaoyan 6

KEY MESSAGE

The location of alien chromatin in Xiaoyan 6 was identified using mc-GISH analysis, genetic mapping and whole genome re-sequencing, and its possible origin was discussed. As a founder parent, Xiaoyan 6 has played an important role in distant hybridization breeding in China. Although it came from the cross between common wheat and Thinopyrum ponticum (Podp.) Barkworth and D.R. Dewey, the location of its alien chromatin has not been determined using traditional genomic in situ hybridization (GISH). In the present study, chromosome variation in Xiaoyan 6 was discovered by multicolor GISH analysis. Four alien-specific markers were developed by specific-locus amplified fragment sequencing technique. Their amplified sequences were analyzed by basic local alignment search tool with the reference genome sequences of common wheat Chinese Spring (CS) and Th. elongatum, and the whole genome re-sequencing reads of Th. ponticum and CS. Furthermore, the four markers were mapped on three different chromosomes in two RIL populations. By dissecting the mapped reads depth of the whole genome re-sequencing of Xiaoyan 6, we found that the depth of nine chromosome regions was obviously lower than the average. Among these, three regions on 1A, 3A and 7B were demonstrated as the alien introgressions in Xiaoyan 6 by multiple methods. Finally, the genetic transmission of the alien chromatin was analyzed in a set of wheat-Th. ponticum introgression lines. Some stable QTLs for morphological and physiological traits have been mapped near the alien chromatin.

Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat

BACKGROUND

Grain number (GN) is one of the key yield contributing factors in modern wheat (Triticum aestivum) varieties. Fruiting efficiency (FE) is a key trait for increasing GN by making more spike assimilates available to reproductive structures. Thousand grain weight (TGW) is also an important component of grain yield. To understand the genetic architecture of FE and TGW, we performed a genome-wide association study (GWAS) in a panel of 236 US soft facultative wheats that were phenotyped in three experiments at two locations in Florida and genotyped with 20,706 single nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing (GBS).

RESULTS

FE showed significant positive associations with GN, grain yield (GY), and harvest index (HI). Likewise, TGW mostly had a positive correlation with GY and HI, but a negative correlation with GN. Eighteen marker-trait associations (MTAs) for FE and TGW were identified on 11 chromosomes, with nine MTAs within genes. Several MTAs associated with other traits were found within genes with different biological and metabolic functions including nuclear pore complex protein, F-box protein, oligopeptide transporter, and glycoside vacuolar protein. Two KASP markers showed significant mean differences for FE and TGW traits in a validation population.

CONCLUSIONS

KASP marker development and validation demonstrated the utility of these markers for improving FE and TGW in breeding programs. The results suggest that optimizing intra-spike partitioning and utilizing marker-assisted selection (MAS) can enhance GY and HI.

Transformation of Plant Breeding Using Data Analytics and Information Technology: Innovations, Applications, and Prospective Directions

Our study focused on plant breeding, from traditional methods to the present most advanced genetic and data-driven concepts. Conventional breeding techniques, such as mass selection and cross-breeding, have been instrumental in crop improvement, although they possess inherent limitations in precision and efficiency. Advanced molecular methods allow breeders to improve crops quicker by more accurately targeting specific traits. Data analytics and information technology (IT) are crucial in modern plant breeding, providing tools for data management, analysis, and interpretation of large volumes of data from genomic, phenotypic, and environmental sources. Meanwhile, emerging technologies in machine learning, high-throughput phenotyping, and the Internet of Things (IoT) provide real-time insights into the performance and responses of plants to environmental variables, enabling precision breeding. These tools will allow breeders to select complex traits related to yield, disease resistance, and abiotic stress tolerance more precisely and effectively. Moreover, this data-driven approach will enable breeders to use resources judiciously and make crops resilient, thus contributing to sustainable agriculture. Data analytics integrated into IT will enhance traditional breeding and other key applications in sustainable agriculture, such as crop yield improvement, biofortification, and climate change adaptation. This review aims to highlight the role of interdisciplinary collaboration among breeders, data scientists, and agronomists in absorbing these technologies. Further, this review discusses the future trends that will make plant breeding even more effective with this new wave of artificial intelligence (AI), blockchain, and collaborative platforms, bringing new data transparency, collaboration, and predictability levels. Data and IT-based breeding will greatly contribute to future global food security and sustainable food production. Thus, creating high-performing, resource-efficient crops will be the foundation of a future agricultural vision that balances environmental care. More technological integration in plant breeding is needed for resilient and sustainable food systems to handle the growing population and changing climate challenges.

Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Single-nucleotide polymorphisms (SNPs) are widely used as molecular markers for constructing genetic linkage maps in wheat. Compared with available SNP-based genotyping platforms, a genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology has become the favored genotyping technology because it is less demanding and more cost effective, flexible, and user-friendly. In this study, a new GenoBaits WheatSNP16K (GBW16K) GBTS array was designed using datasets generated by the wheat 660K SNP array and resequencing platforms in our previous studies. The GBW16K array contains 14 868 target SNP regions that are evenly distributed across the wheat genome, and 37 669 SNPs in these regions can be identified in a diversity panel consisting of 239 wheat accessions from around the world. Principal component and neighbor-joining analyses using the called SNPs are consistent with the pedigree information and geographic distributions or ecological environments of the accessions. For the GBW16K marker panel, the average genetic diversity among the 239 accessions is 0.270, which is sufficient for linkage map construction and preliminary mapping of targeted genes or quantitative trait loci (QTLs). A genetic linkage map, constructed using the GBW16K array-based genotyping of a recombinant inbred line population derived from a cross of the CIMMYT wheat line Yaco"S" and the Chinese landrace Mingxian169, enables the identification of Yr27, Yr30, and QYr.nwafu-2BL.4 for adult-plant resistance to stripe rust from Yaco"S" and of Yr18 from Mingxian169. QYr.nwafu-2BL.4 is different from any previously reported gene/QTL. Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 on the basis of haplotype analysis, micro-collinearity, gene annotation, RNA sequencing, and SNP data. This array provides a new tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.

Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement

The allotetraploid wild grass Aegilops ventricosa (2n = 4x = 28, genome DvDvNvNv) has been recognized as an important germplasm resource for wheat improvement owing to its ability to tolerate biotic stresses. In particular, the 2NvS segment from Ae. ventricosa, as a stable and effective resistance source, has contributed greatly to wheat improvement. The 2NvS/2AS translocation is a prevalent chromosomal translocation between common wheat and wild relatives, ranking just behind the 1B/1R translocation in importance for modern wheat breeding. Here, we assembled a high-quality chromosome-level reference genome of Ae. ventricosa RM271 with a total length of 8.67 Gb. Phylogenomic analyses revealed that the progenitor of the Dv subgenome of Ae. ventricosa is Ae. tauschii ssp. tauschii (genome DD); by contrast, the progenitor of the D subgenome of bread wheat (Triticum aestivum L.) is Ae. tauschii ssp. strangulata (genome DD). The oldest polyploidization time of Ae. ventricosa occurred ∼0.7 mya. The Dv subgenome of Ae. ventricosa is less conserved than the D subgenome of bread wheat. Construction of a graph-based pangenome of 2AS/6NvL (originally known as 2NvS) segments from Ae. ventricosa and other genomes in the Triticeae enabled us to identify candidate resistance genes sourced from Ae. ventricosa. We identified 12 nonredundant introgressed segments from the Dv and Nv subgenomes using a large winter wheat collection representing the full diversity of the European wheat genetic pool, and 29.40% of European wheat varieties inherit at least one of these segments. The high-quality RM271 reference genome will provide a basis for cloning key genes, including the Yr17-Lr37-Sr38-Cre5 resistance gene cluster in Ae. ventricosa, and facilitate the full use of elite wild genetic resources to accelerate wheat improvement.

Testing the potential of zebularine to induce heritable changes in crop growth and development

KEY MESSAGE

Zebularine-treated wheat uncovered a phenotype with characteristics of an epigenetically regulated trait, but major chromosomal aberrations, not DNA methylation changes, are the cause, making zebularine unsuitable for epigenetic breeding. Breeding to identify disease-resistant and climate-tolerant high-yielding wheats has led to yield increases over many years, but new hardy, higher yielding varieties are still needed to improve food security in the face of climate change. Traditional breeding to develop new cultivars of wheat is a lengthy process taking more than seven years from the initial cross to cultivar release. The speed of breeding can be enhanced by using modern technologies including high-throughput phenomics, genomic selection, and directed mutation via CRISPR. Here we test the concept of modifying gene regulation by transiently disrupting DNA methylation with the methyltransferase inhibitor, zebularine (Zeb), as a means to uncover novel phenotypes in an elite cultivar to facilitate breeding for epigenetically controlled traits. The development and architecture of the wheat inflorescence, including spikelet density, are an important component of yield, and both grain size and number have been extensively modified during domestication and breeding of wheat cultivars. We identified several Zeb-treated plants with a dominant mutation that increased spikelet density compared to the untreated controls. Our analysis showed that in addition to causing loss of DNA methylation, Zeb treatment resulted in major chromosomal abnormalities, including trisomy and the formation of a novel telocentric chromosome. We provide evidence that increased copy number of the domestication gene, Q, is the most likely cause of increased spikelet density in two Zeb-treated plants. Collateral damage to chromosomes in Zeb-treated plants suggests that this is not a viable approach to epigenetic breeding.

Impact of structural variations and genome partitioning on bread wheat hybrid performance

The agronomical interest of hybrid wheat has long been a matter of debate. Compared to maize where hybrids have been successfully grown for decades, the mixed results obtained in wheat have been attributed at least partially to the lack of heterotic groups. The wheat genome is known to be strongly partitioned and characterized by numerous presence/absence variations and alien introgressions which have not been thoroughly considered in hybrid breeding. The objective was to investigate the relationships between hybrid performance and genomic diversity. For this, we characterized a set of 124 hybrids as well as their 19 female and 16 male parents. Phenotyping for yield and yield components was conducted during two years in three locations. Parental lines were genotyped using a 410 K SNP array as well as through sequence capture of roughly 200,000 loci. This led to the identification of 180 structural variations including presence-absence variations and alien introgressions. Twenty-six of them were associated to hybrid performance through either additivity or dominance effects. While no correlation was observed at the whole genome level, the genetic distance for 25 genomic regions resulting from the structural and functional partitioning of the chromosomes shown positive or negative correlation with agronomic traits including yield. Large introgressions, like the Aegilops ventricosa 2NS-2AS translocation, can correspond to entire chromosomal regions, such as the R1 region, with an impact on yield. Our results suggest hybrid breeding should consider both structural variations and chromosome partitioning rather than maximizing whole-genome genetic distance, and according to genomic regions to combine homozygosity and heterozygosity.

Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa

Ancient whole-genome duplications are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent whole-genome duplications may contribute to evolvability within recent polyploids. Hybridization accompanying some whole-genome duplications may combine divergent gene content among diploid species. Some theory and evidence suggest that polyploids have a greater accumulation and tolerance of gene presence-absence and genomic structural variation, but it is unclear to what extent either is true. To test how recent polyploidy may influence pangenomic variation, we sequenced, assembled, and annotated 12 complete, chromosome-scale genomes of Camelina sativa, an allohexaploid biofuel crop with 3 distinct subgenomes. Using pangenomic comparative analyses, we characterized gene presence-absence and genomic structural variation both within and between the subgenomes. We found over 75% of ortholog gene clusters are core in C. sativa and <10% of sequence space was affected by genomic structural rearrangements. In contrast, 19% of gene clusters were unique to one subgenome, and the majority of these were Camelina specific (no ortholog in Arabidopsis). We identified an inversion that may contribute to vernalization requirements in winter-type Camelina and an enrichment of Camelina-specific genes with enzymatic processes related to seed oil quality and Camelina's unique glucosinolate profile. Genes related to these traits exhibited little presence-absence variation. Our results reveal minimal pangenomic variation in this species and instead show how hybridization accompanied by whole-genome duplication may benefit polyploids by merging diverged gene content of different species.

Mining genomic regions associated with stomatal traits and their candidate genes in bread wheat through genome-wide association study (GWAS)

KEY MESSAGE

112 candidate quantitative trait loci (QTLs) and 53 key candidate genes have been identified as associated with stomatal traits in wheat. These include bHLH, MADS-box transcription factors, and mitogen-activated protein kinases (MAPKs). Stomata is a common feature of the leaf surface of plants and serve as vital conduits for the exchange of gases (primarily CO₂ and water vapor) between plants and the external environment. In this study, a comprehensive genome analysis was conducted by integrating genome-wide association study (GWAS) and genome prediction to identify the genomic regions and candidate genes of stomatal traits associated with drought resistance and water-saving properties in a panel of 184 diverse bread wheat genotypes. There were significant variations on stomatal traits in the wheat panel across different environmental conditions. GWAS was conducted with the genotypic data from the wheat 660 K single-nucleotide polymorphism (SNP) chip, and the stomatal traits conducted across three environments during two growing seasons. The final GWAS identified 112 candidate QTLs that exhibited at least two significant marker-trait associations. Subsequent analysis identified 53 key candidate genes, including 13 bHLH transcription factor, 2 MADS-box transcription factors, and 4 mitogen-activated protein kinase genes, which may be strongly associated with stomatal traits. The application of Bayesian ridge regression for genomic prediction yielded an accuracy rate exceeding 60% for all four stomatal traits in both SNP matrices, with stomatal width achieving a rate in excess of 70%. Additionally, three Kompetitive allele-specific PCR markers were developed and validated, representing a significant advancement in marker-assisted prediction. Overall, these results will contribute to a more comprehensive understanding of wheat stomatal traits and provide a valuable reference for germplasm screening and innovation in wheat germplasm with novel stomatal traits.

Identification of 39 stripe rust resistance loci in a panel of 465 winter wheat entries presumed to have high-temperature adult-plant resistance through genome-wide association mapping and marker-assisted detection

Stripe rust of wheat is a serious disease caused by Puccinia striiformis f. sp. tritici (Pst). Growing resistant cultivars is the most preferred approach to control the disease. To identify wheat genotypes with quantitative trait loci (QTL) for durable resistance to stripe rust, 465 winter wheat entries that were presumed to have high-temperature adult-plant (HTAP) resistance were used in this study. In the greenhouse seedling tests with seven Pst races, 16 entries were resistant to all the tested races. The 465 entries were also phenotyped for stripe rust responses at the adult-plant stage under natural infection of Pst in multiple field locations from 2018 to 2021 in the Washington state, and 345 entries were found to have stable resistance. The contrast of the susceptibility in the greenhouse seedling tests and the resistance in the field adult-plant stage for most of the entries indicated predominantly HTAP resistance in this panel. The durability of the resistance was demonstrated by a subset of 175 entries that were tested in multiple locations from 2007 to 2021. The 465 entries were genotyped through genotyping by multiplexed sequencing of single-nucleotide polymorphism (SNP) markers. Combining the stripe rust response and SNP marker data, a genome-wide association study (GWAS) was conducted, resulting in 143 marker-trait associations, from which 28 QTL that were detected at least with two races or in two field environments were identified, including seven for all-stage resistance and 21 for HTAP resistance. These QTL each explained 6.0% to 40.0% of the phenotypic variation. Compared with previously reported Yr genes and QTL based on their genomic positions, five QTL including two for HTAP resistance were identified as new. A total of 10 user-friendly Kompetitive allele specific PCR (KASP) markers were developed for eight of the HTAP resistance loci. In addition, molecular markers were used to detect 13 previously reported HTAP resistance genes/QTL, including two also identified in the GWAS analyses, and their frequencies ranged from 0.86% to 88.17% in the panel. The durable resistant genotypes, the genes/QTL identified, and the KASP markers developed in this study should be useful to develop wheat cultivars with long-lasting resistance to stripe rust.