Pre-harvest sprouting (PHS) can severely compromise yield and quality in wheat (Triticum aestivum L.). In this study, we performed quantitative trait locus (QTL) mapping to identify PHS resistance loci in two recombinant inbred line (RIL) populations genotyped using the Wheat 55 K SNP array and assessed for sprouting rate (SR) across multiple environments. We identified seven QTL in the P82/Luomai 21 and Cunmai 1/Jimai 22 RIL populations. Notably, QPhs.zknu-2D was mapped to a 5.02-Mb interval (627.96–632.97 Mb) in both populations and identified as a stable, background-independent major locus that explained 8.4%–21.3% of the phenotypic variance. Another QTL, QPhs.zknu-5D, exhibited the strongest effect, explaining up to 28.9% of the phenotypic variance. We developed KASP markers for these loci and validated them in a natural panel of 329 accessions across six environments. The favorable alleles significantly lowered the SR, and the combination of both favorable alleles demonstrated a strong additive effect, with the mean SR falling to 44.8%, compared to 82.0% with the two alternative alleles. We identified ten elite accessions with stable PHS resistance (SR < 10%), and performed transcriptomic profiling to help identify potential candidate genes for QPhs.zknu-2D, QPhs.zknu-5D, and QPhs.zknu-7A. This work provides robust markers, elite germplasm, and mechanistic insights to accelerate the breeding of PHS-resistant wheat.

Pre-harvest sprouting (PHS) significantly reduces yield and quality in wheat (Triticum aestivum). One effective way to address this issue is to identify and deploy quantitative trait loci (QTL) for PHS resistance. In this study, we developed a recombinant inbred line (RIL) population derived from a cross between the PHS-resistant red wheat line ‘Shannong0316’ (SN0316), which has strong seed dormancy, and the PHS-susceptible white wheat line ‘Gaoyou9409’ (GY9409), which has weak seed dormancy, to map QTL for PHS resistance. We also mapped grain color, an important quality trait that is related to PHS. In five experiments, we identified thirteen QTL for PHS resistance, nine of which were detected in at least two experiments. QTL mapping identified seven QTL for grain color, three of which were also associated with PHS resistance. A comparison with previously reported QTL suggested that QPhs.sdau-1A, QPhs.sdau-5A, QPhs.sdau-6D, QPhs.sdau-7A, and QPhs.sdau-7B.1 are newly discovered QTL for PHS resistance, and that QGc.sdau-5A.1, QGc.sdau-5A.2, QGc.sdau-7A, and QGc.sdau-7B are newly discovered QTL for grain color. The three major QTL (QPhs.sdau-3A.1, QPhs.sdau-3D.1, and QPhs.sdau-1A) showed additive effects on PHS. We identified six elite lines with high PHS resistance, with three white wheat lines. We converted the single-nucleotide polymorphisms linked to the nine QTL into Kompetitive Allele-Specific PCR (KASP) markers and used them to genotype the RIL population and 192 elite breeding lines. QPhs.sdau-1A was associated with PHS resistance in the breeding lines, whereas the other QTL require further validation due to the low frequency of one genotype. Therefore, we dissected the genetic basis of the strong seed dormancy and PHS resistance of wheat line SN0316, identified QTL, obtained germplasm lines, and developed molecular markers for marker-assisted selection of PHS resistance, which should be valuable for breeding.

Wheat is a major staple crop for over one-third of the world's population, crucial for global food security, economic stability and cultural traditions. Recently, single-cell and spatial omics approaches have transformed biological discovery, primarily in medical and animal sciences, and they are now beginning to be applied in plant research. Here we summarize the technical innovations and feasibility of spatial omics applications in wheat research, particularly for understanding developmental and environmental responses, thereby potentially enhancing wheat breeding. We highlight how these tools can reveal spatial and temporal patterns in gene expression, cellular heterogeneity and tissue organization in wheat. Furthermore, we propose developing a spatially resolved single-cell atlas of wheat across its life cycle to facilitate breakthroughs in basic research and potential applications in breeding. To achieve these goals, we advocate for a Wheat Spatial Omics Consortium to foster worldwide collaboration for overcoming barriers and developing sustainable and climate-resilient wheat.

Grain number and size are important agronomic traits determining grain yield, and yield improvement depends on exploring functional variations of key regulatory genes. Mitogen-activated protein kinase 6 (MAPK6) plays a key role in crop development; however, its function and variation in wheat remain largely unclear. In this study, we aimed to characterize the function and haplotype variations of TaMAPK6-7A in wheat and develop functional molecular markers for marker assisted breeding. We identified three TaMAPK6 homoeologs on 7A, 7B, and 7D in wheat through bioinformatics analysis and revealed their evolutionary trajectory by phylogenetic analysis, with clear monocot-dicot lineage divergence and TaMAPK6 homoeolog clustering matching with hexaploid wheat’s allopolyploid origin. Spatiotemporal expression analysis showed that the TaMAPK6 homoeologs constitutively expressed in wheat tissues and were highly abundant in endosperm, spike, grain, and anther, with TaMAPK6-7A showing slightly higher transcript levels. In an ethyl methanesulfonate (EMS)-induced Jing411 mutant library, we identified a loss-of-function mutant of TaMAPK6-7A (J7633452), which exhibited severely reduced grain number per spike, impaired anther fertility, and increased grain size. Natural variation analysis of a large set of wheat accessions identified two major haplotypes of TaMAPK6-7A, with Type I was identical to the reference genome cultivar ‘Chinese Spring’, and Type II was consistent with the elite wheat cultivar ‘AK58’. We developed a PCR marker to accurately distinguish the two haplotypes and genotyped 192 wheat cultivars and elite breeding lines. Phenotypic evaluation indicated that Type II was an elite haplotype significantly associated with higher grain number per spike. This study characterizes TaMAPK6-7A as a key regulator of grain number per spike, providing a gene and molecular marker for marker-assisted breeding to improve grain yield.

Spike length (SL) is an important factor affecting yield in wheat (Triticum aestivum L.). Here, a recombinant inbred line (RIL) population derived from a cross between Shannong 4155 (SN4155) and Shimai 12 (SM12) was used to map quantitative trait loci (QTL) controlling SL. A QTL, qSL2B, on chromosome 2B was identified in all experiments and explained 9.92%-12.71% of the phenotypic variation. Through transcriptome and gene expression analysis, we identified a gene encoding Elongation Factor 1-alpha (TaeEF1A) as the candidate gene for qSL2B. Genome editing of TaeEF1A demonstrated that TaeEF1A positively regulates SL, spikelet number per spike (SNS), and grain number per spike (GN). Transcriptome analysis showed that TaeEF1A may affect the protein translation process and photosynthesis to regulate spike development. We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in TaeEF1A, with Type I, Type II, and Type III being the major haplotypes. Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as Type I and Type II haplotypes, respectively, with Type III not detected. Comparison of SL, SNS, and GN between the Type I and Type II haplotypes revealed that the Type I allele can increase SL, SNS, and GN simultaneously, and is thus preferred for use in wheat molecular breeding efforts to increase SL, SNS, and GN. (c) 2025 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Wheat grains contain various bioactive substances, of which, condensed tannins (CT) are polymeric flavan-3-ols that accumulate in wheat seed coat influencing the end-use quality and nutritional value. However, the genetic architecture underlying CT biosynthesis in wheat grain remains unclear. Here, we studied the deposition and genetic regulation of CT in wheat grains, and found that CT deposited specifically in the testa layer of red-grained wheat as catechin- and epicatechin-formed polymers. Genome-wide association study identified 22 genetic loci affecting CT content, one of which, TaTAN, a single dominant gene controlling CT presence, was mapped to chromosome 3A in a segregation population. Further pan-genome analysis, transcriptome profiling and ethyl methanesulfonate induced mutants sequencing revealed a R2R3-MYB transcription factor, TaMYB10-3A, as the causal gene. Three loss-of-function alleles in TaMYB10-3A caused by large fragment inversion-deletion and insertion were identified which abolish both CT deposition and red pigmentation, demonstrating the pleiotropic effect of TaMYB10-3A on CT presence and grain color. TaMYB10-3A directly trans-activates core flavonoid genes such as chalcone synthase and dihydroflavonol 4-reductase to initiate CT biosynthesis. Our investigation provides a comprehensive understanding of CT presence in wheat grains and lays a solid foundation for manipulating CT metabolites to improve wheat grain end-use quality and nutrition values in wheat.

Nitrogen (N) is an essential nutrient for plant growth, and most plants absorb it as nitrate. AtNRG2 has been reported to play an important role in nitrate regulation. In this study, we investigated the functions of AtNRG2 family members of Arabidopsis thaliana and maize in nitrate signalling and metabolism. Our results showed that both AtNRG2.10 and AtNRG2.15 regulated nitrate signalling and metabolism. Overexpression of AtNRG2.11 (AtNRG2) could promote plant growth and improve nitrogen use efficiency (NUE). In addition, the maize genome harbors 23 ZmNRG2 members. We detected the expression of these genes treated with nitrate and the expression of four genes was strongly induced with ZmNRG2.7 having the highest levels. Overexpression of ZmNRG2.7 in the atnrg2 mutant could restore the defects of atnrg2, suggesting that ZmNRG2.7 is involved in nitrate signalling and metabolism. Moreover, the overexpression lines of ZmNRG2.7 showed increased biomass and NUE. These findings demonstrate that at least a part of NRG2 family genes in Arabidopsis and maize regulate nitrate signalling and provide a molecular basis for improving the NUE of crops.

Wheat is one of the most important staple foods in the world. Genetic characterization of wheat agronomically important traits is crucial for yield improvement through molecular breeding. In this study, a recombinant inbred line (RIL) population was developed by crossing a local adapted high yield variety Jimai 22 (JM22) with an external variety Cunmai no.1 (CM1). A high-density genetic map containing 7,359 single nucleotide polymorphism (SNP) markers was constructed. Quantitative trait loci (QTL) mapping identified 61 QTL for eight yield-related traits under six environments (years). Among them, 17 QTL affecting spike number per plant, grain number per spike and thousand grain weight showed high predictability for theoretical yield per plant (TYP), of which, 12 QTL alleles positively contributed to TYP. Nine promising candidate genes for seven of the 12 QTL were identified including three known wheat genes and six rice orthologs. Four elite lines with TYP increased by 5.6

An allelic variation of TaCRTISO is valuable in adjusting spike number per plant and plant height in wheat breeding.

Sorghum is an important food crop commonly used for brewing, feed, and bioenergy. Certain genotypes of sorghum contain high concentrations of condensed tannins in seeds, which are beneficial, such as protecting grains from herbivore bird pests, but also impair grain quality and digestibility. Previously, we identified Tannin1 and Tannin2, each with three recessive causal alleles, regulate tannin absence in sorghum. In this study, via characterizing 421 sorghum accessions, we further identified three novel recessive alleles from these two genes. The tan1-d allele contains a 12-bp deletion at position 659 nt and the tan1-e allele contains a 10-bp deletion at position 771 nt in Tannin1. The tan2-d allele contains a C-to-T transition, which results in a premature stop codon before the bHLH domain in Tannin2, and was predominantly selected in China. We further developed KASP assays targeting these identified recessive alleles to efficiently genotype large populations. These studies provide new insights in sorghum domestication and convenient tools for breeding programs.

Wheat (Triticum aestivum L.) is one of the most important food crops worldwide and provides the staple food for 40% of the world’s population. Increasing wheat production has become an important goal to ensure global food security. The grain yield of wheat is a complex trait that is usually influenced by multiple agronomically important traits. Thus, the genetic dissection and discovery of quantitative trait loci (QTL) of wheat-yield-related traits are very important to develop high-yield cultivars to improve wheat production. To analyze the genetic basis and discover genes controlling important agronomic traits in wheat, a recombinant inbred lines (RILs) population consisting of 180 RILs derived from a cross between Xinong822 (XN822) and Yannong999 (YN999), two well-adapted cultivars, was used to map QTL for plant height (PH), spike number per spike (SNS), spike length (SL), grain number per spike (GNS), spike number per plant (SN), 1000- grain weight (TGW), grain length (GL), grain width (GW), length/width of grain (GL/GW), perimeter of grain (Peri), and surface area of grains (Sur) in three environments. A total of 64 QTL were detected and distributed on all wheat chromosomes except 3A and 5A. The identified QTL individually explained 2.24–38.24% of the phenotypic variation, with LOD scores ranging from 2.5 to 29. Nine of these QTL were detected in multiple environments, and seven QTL were associated with more than one trait. Additionally, Kompetitive Allele Specific PCR (KASP) assays for five major QTL QSns-1A.2 (PVE = 6.82), QPh-2D.1 (PVE = 37.81), QSl-2D (PVE = 38.24), QTgw-4B (PVE = 8.78), and QGns-4D (PVE = 13.54) were developed and validated in the population. The identified QTL and linked markers are highly valuable in improving wheat yield through marker-assisted breeding, and the large-effect QTL can be fine-mapped for further QTL cloning of yield-related traits in wheat.

Ellisembia appendiculata is described and illustrated as a new species from a specimen collected on dead branches of an unidentified broadleaf tree in Hainan Province. The fungus is characterized by distinct, unbranched conidiophores with monoblastic conidiogenous cells that produce distoseptate, obclavate or ellipsoidal conidia with 1 – 2 filiform, hyaline, aseptate, simple or branched appendages.

Waterlogging occurs when field soil is saturated with water induced by extensive rainfall or improper irrigation, which is a severe abiotic stress influencing wheat plant growth and yield production. At the germination stage, waterlogging usually induces rot of seeds and reduced germination rate and seedling survival. Development of tolerant wheat varieties is the most efficient approach to improve seed germination and mitigate the damages caused by waterlogging. In this study, we screened 432 wheat accessions at germination stage by waterlogging treatment, and identified 27 tolerant accessions with a germination rate of over 80% after treatment. To identify quantitative trait loci (QTL) for waterlogging tolerance, two segregation populations were developed by crossing waterlogging-tolerant cultivars Shannong 135 and Huaimai 18 with sensitive cultivars Siyang 936 and CD1840, respectively. Three QTL qWlg5A, qWlg7B and qWlg2D for waterlogging tolerance were detected on chromosomes 5A, 7B and 2D through bulked segregation analysis genotyped by wheat 55K SNP array. Two, one, and two kompetitive allele specific PCR (KASP) assays linked with qWlg5A, qWlg7B and qWlg2D were developed and validated in the two populations, respectively. The identified waterlogging tolerant germplasm lines, the QTL for waterlogging tolerance and the high-throughput KASP markers, were highly valuable in improving waterlogging tolerance in wheat-marker-assisted breeding.

Wheat stripe (yellow) rust is a worldwide disease that seriously reduces wheat grain yield and quality. Adult-plant resistance (APR) to stripe rust is generally more durable but usually controlled by multiple genes with partial resistance. In this study, a recombinant inbred line population was developed from a cross between a Chinese wheat landrace, Tutoumai, with APR to stripe rust, and a highly susceptible wheat cultivar, Siyang 936. The population was genotyped by genotyping-by-sequencing and phenotyped for APR to stripe rust in four consecutive field experiments. Three QTLs, QYr.sdau-1BL, QYr.sdau-5BL, and QYr.sdau-6BL, were identified for APR to stripe rust, and explained 8.0–21.2%, 10.1–22.7%, and 11.6–18.0% of the phenotypic variation, respectively. QYr.sdau-1BL was further mapped to a 21.6 Mb region using KASP markers derived from SNPs identified by RNA-seq of the two parents. In the QYr.sdau-1BL region, 13 disease-resistance-related genes were differently expressed between the two parents, and therefore were considered as the putative candidates of QYr.sdau-1BL. This study provides favorable gene/QTL and high-throughput markers to breeding programs for marker-assisted selection of the wheat stripe rust APR genes.

在从农业大国向农业强国迈进的历程中,我国的农业科技工作者一直在默默努力着.近年来,随着测序技术的迅速发展,通过测序鉴定高密度单核苷酸多态性(SNP),进行全基因组关联分析已经成为水稻、玉米等重要农作物中对产量等复杂性状进行遗传解析的一种十分有效的方法.在这些作物中,由于连锁不平衡(LD)衰减距离较短,能够将一些鉴定到的数量性状位点(QTL)界定到较小的基因组区域, 同时进行候选基因的鉴定与克隆.但在小麦中,由于其庞大的基因组构成及多倍体特性,基因组学研究难度较大,尤其是在关联分析中,由于使用的标记密度低,小麦中的连锁不平衡一般认为较大,从而限制了通过关联分析在小麦中进行基因发掘、精细作图、克隆及分子设计育种等研究的实施.

High-resolution genome-wide association study (GWAS) facilitated QTL fine mapping and candidate gene identification, and the GWAS based genomic prediction models were highly predictive and valuable in wheat genomic breeding. Wheat is a major staple food crop and provides more than one-fifth of the daily calories and dietary proteins for humans. Genome-wide association study (GWAS) and genomic selection (GS) for wheat stress resistance and tolerance related traits are critical to understanding their genetic architecture for improvement of breeding selection efficiency. However, the insufficient marker density in previous studies limited the utility of GWAS and GS in wheat genomic breeding. Here, we conducted a high-resolution GWAS for wheat leaf rust (LR), yellow rust (YR), powdery mildew (PM), and cold tolerance (CT) by genotyping a panel of 768 wheat cultivars using genotyping-by-sequencing. Among 153 quantitative trait loci (QTLs) identified, 81 QTLs were delimited to ≤ 1.0 Mb intervals with three validated using bi-parental populations. Furthermore, 837 stress resistance-related genes were identified in the QTL regions with 12 showing induced expression by YR and PM pathogens. Genomic prediction using 2608, 4064, 3907, and 2136 pre-selected SNPs based on GWAS and genotypic correlations between the SNPs showed high prediction accuracies of 0.76, 0.73, and 0.78 for resistance to LR, YR, and PM, respectively, and 0.83 for resistance to cold damage. Our study laid a solid foundation for large-scale QTL fine mapping, candidate gene validation and GS in wheat.

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to ≤1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.

Pre-harvest sprouting (PHS) influences yield and end-use quality of bread wheat. Developing varieties with PHS resistance is the most effective way to reduce this problem. In this study, a panel of 725 Chinese wheat accessions were evaluated for PHS resistance in three environments. There was abundant variation in PHS resistance and 63 accessions showing high resistance had germination rates of less than 10% across three experiments. The distribution of three causal single nucleotide polymorphisms in TaPHS1 at bases −222, +646, and +666 were assessed and frequencies were determined. Favorable alleles conferring PHS resistance were identified for each locus. Haplotype analysis showed that bases C, G, and A at each of the three loci comprised the best haplotype for PHS resistance, whereas TAT showed the highest sprouting rate. Accessions with the superior TaPHS1 haplotypes proved to be resistant to PHS providing a basis to develop varieties with PHS resistance through marker assisted breeding.