Fusarium crown rot (FCR) is a hard-to-control wheat disease prevalent in arid and semi-arid regions. However, the relationship between arid conditions and FCR disease remains unclear. Here, we confirm that drought stress exacerbates the severity of FCR, and that FCR intensifies drought-induced damage. Integrated transcriptome analysis indicates that TaMPK3 gene exhibits distinctly opposite expression patterns under these two stress conditions. Functional identification verifies that TaMPK3 positively regulate FCR resistance while negatively influencing drought tolerance. Upon TaMPK3 gene knockout, the mutually reinforcing effect between drought and FCR is eliminated. TaMPK3 is found to modulate TaWRKY26 activity to regulate the expression of sterol synthesis gene clusters, thereby influencing FCR resistance. Within this cluster, the key gene TaCYP51H37 significantly enhances FCR resistance. Combined with our findings that TaMPK3 decreases drought tolerance through ABA signaling pathway, this study proposes a molecular model in which TaMPK3 mediates the synergistic damage caused by drought and FCR.

This study evaluated salt tolerance across germination, seedling, and maturity stages in three Agropyron cultivars to identify rapid assessment indicators. Cultivars were stressed with seawater at varying concentrations. Salt tolerance was assessed using principal component analysis (PCA), fuzzy membership functions, and stepwise regression on agronomic and physiological traits (SOD, CAT, POD, K⁺, Na⁺, etc.). Optimal seawater concentrations were 30

Agropyron cristatum (2n=4x=28, PPPP), a wild perennial relative of wheat, is considered as an excellent donor for wheat improvement given its multiple florets and spikelets, broad-spectrum disease resistance, and extreme stress tolerance. In this study, we created the addition line II-24 of A. cristatum chromosome 4P, and telosomic addition lines of 4PS and 4PL by backcross of the addition line II-23 containing multiple A. cristatum chromosomes with common wheat Fukuho. Multi-year agronomic evaluations revealed that addition of 4PL in common wheat variety Fukuho resulted in a significant increase of grain number per spike (GNS) and effective tiller number (ETN) without compromising thousand-grain weight (TGW). Additionally, we developed a translocation line WAT41 (T4PL-3DS·3DL). Compared to the control, the line WAT41 simultaneously exhibited an increase of GNS (5.79%), spikelet number per spike (2.42%), kernel number per spikelet (3.52%), and spike length (4.93%) without compromising TGW. Resequencing analysis revealed that WAT41 carries a chromosomal segment from 505 to 585 Mb of 4P, harboring sixteen spike development-related genes. Furthermore, we developed two specific molecular markers from these genes to track the high-GNS chromatin segment for breeding selection. Collectively, this study provides novel germplasm resources, which is able to overcome the negative relationship between GNS and TGW and broadening the genetic base for wheat breeding.

A QTL, QSNS.caas-3D.1, was identified and found to increase spikelet number per spike and grain number per spike without compromising thousand-grain weight. This result was validated in various genetic populations. Increasing the grain number per spike (GNS) is crucial for increasing the yield potential of wheat. This goal depends on the optimization of its key components, namely, the spikelet number per spike (SNS) and kernel number per spikelet (KNS). Here, we constructed a recombinant inbred line (RIL) population comprising 1,220 lines derived from a cross between the high- spikelet-number line PB3504 and the elite cultivar Yecora Rojo (YKL), to dissect the genetic architecture of GNS-related traits. Using the Wheat 60 K SNP array, we constructed a high-density genetic map and conducted multienvironment QTL mapping. A total of 53 quantitative trait loci (QTLs) were identified, among which QSNS.caas-3D.1 was highlighted as a major and stable QTL for SNS, explaining 13.34–13.72

Wheat is a major staple crop worldwide, and with the ongoing changes in dietary patterns, the demand for improved nutritional quality in wheat has been increasing. Black-grained wheat is a promising germplasm rich in nutrients. Agropyron cristatum (2n = 4x = 28, PPPP) is a wild relative of wheat that carries several desirable genes for genetic improvement. Here, we identified black-grained lines PB31334 and PB31340 from wheat—A. cristatum derivatives, which exhibited significantly higher anthocyanin content and possibly increased amino acid content compared with common wheat. These lines were identified as wheat—A. cristatum 6P (6A) disomic substitution lines, with the alien chromosome 6P from A. cristatum responsible for the black grain trait, as revealed by genetic analysis of four segregated populations created by crossing PB31334 and PB31340 with Fukuho and Xinong979. Additionally, three lines were identified, including telosomic lines carrying the short arm (6PS) and the long arm (6PL) of alien chromosome 6P, as well as a 6PL-deletion line lacking a partial segment of the long arm (bin 6–17). The line with 6PL displayed the black grain trait, whereas the other two did not. The gene was localized to the 6PL (bin 6–17) region without affecting the grain number per spike or thousand-grain weight. Notably, the total anthocyanin content increased in 6PL telosomic line and was positively correlated with grain coloration. The newly identified 6PL chromosomal region is a valuable resource rich in anthocyanins, offering a promising avenue for increasing the nutritional content of wheat.

Rye (Secale cereale L.), a close relative of wheat (Triticum aestivum L.), has significantly contributed to wheat breeding, exemplified by the global utilization of T1RS·1BL translocation lines. This highlights the strategic importance of integrating elite genes from related species into modern crop-breeding programs. This review explores the historical contributions of rye to wheat breeding and its potential in future applications. We delve into the impact of biotechnological approaches in unlocking the genetic repertoire of rye to bolster wheat improvement. Key strategies include goal-directed germplasm innovation, in-depth understanding of genetic basis, multi-omic big data and artificial intelligence (AI)-aided precision breeding, and strengthened global collaboration. These efforts are expected to maximize the potential of rye in sustainable wheat breeding.

Uncovering desirable alien genes from wild species is important for increasing genetic variation and ensuring wheat production. Here, we identify a type-B response regulator (RR) AcRR1 of Agropyron cristatum. Ectopic expression of AcRR1 in common wheat increases the grain number per spike without decreasing the grain weight, thereby enhancing the grain yield by 9.7‒12.3% under field conditions. Expression of the AcRR1 gene also promotes plant growth and shortens the duration of vernalization in the transgenic plants. We reveal that AcRR1 reprogrammes diverse transcriptional processes in wheat by activating the expression of TaWOX11-2D and TabHLH25-5B-TaFTs, which are involved in floret fertility and early heading. Our results demonstrate that AcRR1 from A. cristatum is a valuable alien gene with the capacity to activate genetic networks for wheat yield formation, offering a promising avenue for enhancing wheat productivity through the introduction of alien genes.

Wide hybridization is crucial for broadening the genetic basis of common wheat. Agropyron cristatum (2n = 4x = 28, PPPP), a wild relative of wheat, harbors numerous favorable genes for genetic improvement. The variability related to the expression of alien genes in different wheat backgrounds is a crucial factor that limits the effective utilization of these genes. In this study, the introduction of chromosome 6P from A. cristatum into different wheat backgrounds resulted in different leaf colors: green in plants with the Fukuho background and yellow‒green in plants with the Jimai 22 background. Genetic analysis suggested that yellow‒green leaves were caused by gene interactions between chromosome 6P and genes from the Jimai 22 background, which negatively affected agronomic traits. To determine the locus on chromosome 6P responsible for yellow‒green leaves, six wheat–A. cristatum deletion lines and five wheat–A. cristatum translocation lines were crossed with Jimai 22 to produce F1 progeny for leaf color investigation. We found that the F1 progeny carrying the short arm of chromosome 6P (6PS) presented yellow–green leaves, and the relevant locus was ultimately mapped to 6PS (0.81-1.00). A total of 50 A. cristatum genes related to chlorophyll catabolite reductase and chloroplast development were annotated within this interval. A locus on chromosome 6P of A. cristatum that caused a yellow–green leaf in the Jimai 22 background was mapped to chromosome 6PS (0.81-1.00). This study provides valuable germplasm for the study of leaf color and guidance for the use of valuable genes on A. cristatum chromosome 6P.

The wheat (Triticum aestivum) brassinazole-resistant 2 (TaBZR2) gene is identified as significantly associated with drought tolerance by genome-wide association study (GWAS), and a chloroplast pentatricopeptide repeat (PPR) protein gene TaPPR13 functioned as a positive drought stress regulator downstream of TaBZR2. Overexpression of TaPPR13 enhanced the antioxidative defense system, whereas knockdown of TaPPR13 led to the accumulation of reactive oxygen species (ROS) and caused abnormalities in chloroplast thylakoids under drought stress conditions. RNA-seq analysis showed that overexpression of TaPPR13 significantly upregulated the expression of nuclear-encoded genes involved in ROS scavenging and the abscisic acid (ABA) signaling pathway. Furthermore, TaPPR13 interacted with TaAOR1 and TaSIG5 to facilitate detoxification and regulate chloroplast gene expression, thereby enhancing drought tolerance. Overexpression of TaPPR13 and TaAOR1 mediated stomatal closure to reduce water loss, improving photosynthetic capacity and conferring a yield advantage under drought stress. These findings show that TaPPR13 promotes retrograde signaling to alter nuclear gene expression, with the TaBZR2-TaPPR13-TaAOR1/TaSIG5 module representing a novel signaling pathway that likely plays a pivotal role in drought stress response.

A wheat-rye 2R (2D) substitution line with PmYT9 conferring powdery mildew resistance was characterized. PmYT9 was mapped to a 14. 55 Mb interval on 2RL. A homozygous translocation line carrying PmYT9 was developed. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), poses a significant threat to wheat (Triticum aestivum L.) production. The identification and utilization of novel resistance genes from wheat relatives are an effective strategy for sustainable disease management. Rye (Secale cereale L. RR), a tertiary gene pool of wheat, harbors abundant genetic diversity. In this study, we developed a novel wheat-rye derivative line, YT9, by crossing hexaploid triticale 09R1-16 with wheat breeding line PB9. Genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), and agronomic trait evaluations confirmed that YT9 was a stable 2R (2D) substitution and T1BL·1RS translocation line with favorable performance. Resistance phenotyping and microscopic observation of fungal growth revealed that YT9 exhibited resistance to Bgt from the three-leaf stage. Genetic analysis localized the resistance gene to chromosome arm 2RL of rye, designated PmYT9. To map PmYT9, 60Coγ-ray irradiation was employed to induce chromosomal structure variants. Integrated GISH, molecular marker analysis, and disease response assessment delimited PmYT9 to a 14.55 Mb interval (831.45–846.00 Mb) on the Lo7 rye reference genome, flanked by markers SW11163 and X2RL78. Additionally, a homozygous T7DS·7DL-2RL translocation line carrying PmYT9 was developed. This study expands the genetic diversity of wheat powdery mildew resistance, provides elite germplasm for wheat resistance breeding, and establishes a foundation for the molecular cloning of PmYT9.

Exploring novel genetic variation for target traits is crucial for advancing wheat breeding and genetic improvement. Since 1990, we have been transferring genes from Agropyron cristatum, a promising wild relative genetic resource featuring robust spike morphology and stress tolerance, into common wheat by distant hybridization. To efficiently harness A. cristatum genes, we de novo assembled a 25.62-Gb high-quality genome of an autotetraploid accession Z559 with 28 chromosomes, and uncovered its specific genome features and an extensive repertoire of genes associated with yield and resistance to abiotic and biotic stresses. We systematically characterized A. cristatum genome introgressions by resequencing 431 wheat– A. cristatum derivatives and cloned the gene AcGNS1 , which functions in the regulation of grain number per spike in wheat. Subsequently, we developed an optimized genome-selection model for wheat– A. cristatum breeding derivatives, enabling the rapid selection of new potential varieties. These findings demonstrate a genomic breeding strategy for leveraging novel genetic resources of wild relatives and advancing wheat improvement. ### Competing Interest Statement The authors have declared no competing interest.

Increasing wheat yield is a key approach to ensuring global food security and an enduring focus in crop breeding. Here, we assembled a panel of 3,030 wheat lines to dissect the genetic mechanisms of yield improvement. We conducted large-scale field trials across five ecological environments over two consecutive years to evaluate yield performance and constructed a haplotype atlas using the Wheat 660K genotype array. 234 quantitative trait loci (QTLs) and 522 haplotype blocks (HBs) were identified for 14 traits through genome-wide association studies (GWAS), including 10 QTLs and 35 HBs associated with grain yield. Genomic analysis revealed that wheat yield improvement is primarily driven by changes in the epistatic network rather than the introduction of new haplotype segments. SNPs or HBs explain 53.3%-62.9% of the phenotypic variation in yield, whereas epistasis explains 70.4%, highlighting the role of epistasis in yield improvement. Moreover, yield improvement is significantly correlated with the accumulation of favorable epistatic modules. Pedigree-based analysis revealed that the modules remained relatively stable under the pressure of breeding selection, while new favorable modules were also created during hybrid breeding, highlighting that crop design breeding should be based on genetic modules. This study provides insights into genetic mechanism of wheat yield improvement and guidance for designing future wheat in the era of artificial intelligence. ### Competing Interest Statement The authors have declared no competing interest.

Powdery mildew is a serious disease caused by Blumeria graminis f. sp. tritici (Bgt) that critically threatens the yield and quality of wheat (Triticum aestivum L.). Using effective powdery mildew resistance genes is the optimal method for controlling this disease. Against the background of high genetic homogeneity among the modern commercial cultivars that are mainly derived from conventional interbreeding, the resistance genes from wheat relatives have especially prominent advantages. Octoploid triticale, produced from common wheat and rye (Secale cereale L.) through distant hybridization, is a new synthetic species and valuable gene donor for wheat improvement. In this study, we developed the wheat–rye line YT5 through the hybridization of octaploid triticale and two wheat lines. YT5 was confirmed to be a 6RL ditelosomic addition and 1R (1B) substitution line using genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), multicolor GISH (mc-GISH) and molecular marker analysis. Genetic analysis showed that the powdery mildew resistance in YT5 was derived from the rye chromosome arm 6RL. After inoculation with different Bgt isolates at the seedling stage, YT5 had compound reaction patterns with both obvious spores and hypersensitivity, and it gradually became highly resistant until the adult-plant stage, thus showing a resistance response significantly different from the reported Pm genes from rye chromosome 6RL. YT5 also showed promising agronomic performance, so it is expected to be an elite resistance donor for wheat improvement. To promote the transfer of the chromosome arm 6RL of YT5 in marker-assisted selection (MAS) breeding, we selected and verified two 6RL-specific kompetitive allele-specific PCR (KASP) markers that can be applied to efficiently detect this chromosome arm in different wheat backgrounds.

A novel locus on Agropyron cristatum chromosome 6P that increases grain number and spikelet number was identified in wheat–A. cristatum derivatives and across 3 years. Agropyron cristatum (2n = 4x = 28, PPPP), which has the characteristics of high yield with multiple flowers and spikelets, is a promising gene donor for wheat high-yield improvement. Identifying the genetic loci and genes that regulate yield could elucidate the genetic variations in yield-related traits and provide novel gene sources and insights for high-yield wheat breeding. In this study, cytological analysis and molecular marker analysis revealed that del10a and del31a were wheat–A. cristatum chromosome 6P deletion lines. Notably, del10a carried a segment of the full 6PS and 6PL bin (1–13), while del31a carried a segment of the full 6PS and 6PL bin (1–8). The agronomic characterization and genetic population analysis confirmed that the 6PL bin (9–13) brought about an increase in grain number per spike (average increase of 10.43 grains) and spikelet number per spike (average increase of 3.67) over the three growing seasons. Furthermore, through resequencing, a multiple grain number locus was mapped to the physical interval of 593.03–713.89 Mb on chromosome 6P of A. cristatum Z559. The RNA-seq analysis revealed the expression of 537 genes in the del10a young spike tissue, with the annotation indicating that 16 of these genes were associated with grain number and spikelet number. Finally, a total of ten A. cristatum-specific molecular markers were developed for this interval. In summary, this study presents novel genetic material that is useful for high-yield wheat breeding initiatives to meet the challenge of global food security through enhanced agricultural production.

The advanced model of floral morphogenesis is based largely on data from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), but this process is less well understood in the Triticeae. Here, we investigated a sterile barley (Hordeum vulgare) mutant with malformed floral organs (designated mfo1), of which the paleae, lodicules, and stamens in each floret were all converted into lemma-like organs, and the ovary was abnormally shaped. Combining bulked-segregant analysis, whole-genome resequencing, and TILLING approaches, the mfo1 mutant was attributed to loss-of-function mutations in the MADS-box transcription factor gene HvAGL6, a key regulator in the ABCDE floral morphogenesis model. Through transcriptomic analysis between young inflorescences of wild-type and mfo1 plants, 380 genes were identified as differentially expressed, most of which function in DNA binding, protein dimerization, cell differentiation, or meristem determinacy. Regulatory pathway enrichment showed HvAGL6 associates with transcriptional abundance of many MADS-box genes, including the B-class gene HvMADS4. Mutants with deficiency in HvMADS4 exhibited the conversion of stamens into supernumerary pistils, producing multiple ovaries resembling the completely sterile multiple ovaries 3.h (mov3.h) mutant. These findings demonstrate that the regulatory model of floral morphogenesis is conserved across plant species and provides insights into the interactions between HvAGL6 and other MADS-box regulators.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating disease that seriously threatens wheat yield and quality. To control this disease, host resistance is the most effective measure. Compared with the resistance genes from common wheat, alien resistance genes can better withstand infection of this highly variable pathogen. Development of elite alien germplasm resources with powdery mildew resistance and other key breeding traits is an attractive strategy in wheat breeding. In this study, three wheat-rye germplasm lines YT4-1, YT4-2, and YT4-3 were developed through hybridization between octoploid triticale and common wheat, out of which the lines YT4-1 and YT4-2 conferred adult-plant resistance (APR) to powdery mildew while the line YT4-3 was susceptible to powdery mildew during all of its growth stages. Using genomic in situ hybridization, multi-color fluorescence in situ hybridization, multi-color GISH, and molecular marker analysis, YT4-1, YT4-2, and YT4-3 were shown to be cytogenetically stable wheat-rye 6R addition and T1RS·1BL translocation line, 6RL ditelosomic addition and T1RS·1BL translocation line, and T1RS·1BL translocation line, respectively. Compared with previously reported wheat-rye derivative lines carrying chromosome 6R, YT4-1 and YT4-2 showed stable APR without undesirable pleiotropic effects on agronomic traits. Therefore, these novel wheat-rye 6R derivative lines are expected to be promising bridge resources in wheat disease breeding.

A grain weight locus from Agropyron cristatum chromosome 5P increases grain weight in different wheat backgrounds and is localized to 5PL (bin 7–12). Thousand-grain weight is an important trait in wheat breeding, with a narrow genetic basis being the main factor limiting improvement. Agropyron cristatum, a wild relative of wheat, harbors many desirable genes for wheat improvement. Here, we found that the introduction of the 5P chromosome from A. cristatum into wheat significantly increased the thousand-grain weight by 2.55–7.10 g, and grain length was the main contributor to grain weight. An increase in grain weight was demonstrated in two commercial wheat varieties, indicating that the grain weight locus was not affected by the wheat background. To identify the chromosome segment harboring the grain weight locus, three A. cristatum 5P deletion lines, two wheat–A. cristatum 5P translocation lines and genetic populations of these lines were used to evaluate agronomic traits. We found that the translocation lines harboring the long arm of A. cristatum chromosome 5P (5PL) exhibited high grain weight and grain length, and the genetic locus associated with increased grain weight was mapped to 5PL (bin 7–12). An increase in grain weight did not adversely affect other agronomic traits in translocation line 5PT2, which is a valuable germplasm resource. Overall, we identified a grain weight locus from chromosome 5PL and provided valuable germplasm for improving wheat grain weight.

Nitrogen(N)fertilizer application boosts yield and quality in crops such as wheat(Triticum aestivum L.)but raises environmental and economic concerns(Liu et al.,2019).Therefore,identifying the genes associated with N use efficiency is a major objective in wheat breeding(Liu et al.,2022b).Nitrate transporters are key factors in plant N uptake and play important roles in N responses(Schroeder et al.,2013;Fan et al.,2023).However,few studies have explored the regulation of N uptake efficiency in wheat.Here,we report the functional characterization of a gene encoding a nitrate transporter,NRT1/PTR family 6.2(TaNPF6.2,also reported as Nitrate transporter 1.4[TaNRT1.4]),and describe how it affects wheat agronomic traits by enhancing N uptake efficiency.

Flowering regulation is a reflection of plant self-adaptation to the environment and is the main determinant of plant yield. The quantitative trait loci (QTL) mapping of agronomic traits associated with the flowering stage of Agropyron Gaertn. was conducted using a cross-pollinated (CP) hybrid population with a total of 113 plant lines between A. mongolicum Keng Z2098 and A. cristatum (L.) Gaertn. Z1842 under four different environmental conditions and the genetic map constructed of 1,023 single-nucleotide polymorphism (SNP) markers. The results showed that 28 QTLs were detected on seven linkage groups. Each QTL explained 0.39–18.46