Background: Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. Results: We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. Conclusions: The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.

Summary: Powdery mildew poses a significant threat to global wheat production and most cloned and deployed resistance genes for wheat breeding encode nucleotide‐binding and leucine‐rich repeat (NLR) immune receptors. Although two genetically linked NLRs function together as an NLR pair have been reported in other species, this phenomenon has been relatively less studied in wheat. Here, we demonstrate that two tightly linked NLR genes, RXL and Pm5e, arranged in a head‐to‐head orientation, function together as an NLR pair to mediate powdery mildew resistance in wheat. The resistance function of the RXL/Pm5e pair is validated by mutagenesis, gene silencing, and gene‐editing assays. Interestingly, both RXL and Pm5e encode atypical NLRs, with RXL possessing a truncated NB‐ARC (nucleotide binding adaptor shared by APAF‐1, plant R proteins and CED‐4) domain and Pm5e featuring an atypical coiled‐coil (CC) domain. Notably, RXL and Pm5e lack an integrated domain associated with effector recognition found in all previously reported NLR pairs. Additionally, RXL and Pm5e exhibit a preference for forming hetero‐complexes rather than homo‐complexes, highlighting their cooperative role in disease resistance. We further show that the CC domain of Pm5e specifically suppresses the hypersensitive response induced by the CC domain of RXL through competitive interaction, revealing regulatory mechanisms within this NLR pair. Our study sheds light on the molecular mechanism underlying RXL/Pm5e‐mediated powdery mildew resistance and provides a new example of an NLR pair in wheat disease resistance.

Optimizing supplemental irrigation (SI) measures and enhancing stem lodging resistance can be the keys to achieving a high and stable yield and high efficiency in wheat. The experiment was established as a two-factor field trial in 2018–2020. We used four SI combinations at different stages: rain-fed (T0), SI at jointing (T1), SI at jointing + anthesis (T2), and SI at regreening + jointing + anthesis (T3) with ‘Bainong4199’ (BN4199) and ‘Zhoumai18’ (ZM18) as experimental materials. We researched the effects of different SI combinations on the stem characteristics, stem vigor, grain filling, and yield of winter wheat. The results suggest that the basal internode at the anthesis stage grew with the increase in SI amount, but the stem fracture resistance of T1 and T2 was higher than that of T0 and T3. As grain filling continued, the lodging index increased and stem vigor decreased. In comparison with T3, the average stem lodging index of T2 decreased by 21.92% for ‘BN4199’ and 36.63% for ‘ZM18’, but the WUE increased by 29.76% and 14.92%, respectively. The grain yield increased with the increase in irrigation times during the growth period; there was no significant difference between T2 and T3 in 2018–2019. In a biennial comparison, the grain yield of all treatments in 2019–2020 was significantly lower than those in 2018–2019, and the grain yield of ‘ZM 18’ was lower than that of ‘BN 4199’. Correlation analysis displayed that there were significant positive correlations between post-anthesis stem vigor and the dry matter contribution rate of post-anthesis to grains and between the grain filling rate at 21–28 days after anthesis (DAA) and stem strength at 30 DAA. In summary, selecting a high-yield lodging-resistant wheat variety with SI at jointing and anthesis was beneficial for forming strong stems and maintaining higher stem vigor at the later growth stage for grain filling, which reduced lodging risk and ensured high yield and high WUE.

Increasing wheat (Triticum aestivum L.) planting density is the most effective production management method for increasing yields; however, excessive crop populations under high planting densities may experience elevated risk of stem lodging. We conducted this study to assess the relationship between reduced lodging and increased yield, investigate the effects of planting density on wheat population structure, stem strength, and material transport, and provide a basis for rationale planting densities. The experiments were carried out using a split-plot design with three replicates. The main plots contained two wheat varieties: Bainong 5819 (BN5819) and Bainong 4199 (BN4199), and the sub-plots contained four planting density treatments: 90 × 10⁴ plants/ha (D1), 180 × 10⁴ plants/ha (D2), 270 × 10⁴ plants/ha (D3), and 360 × 10⁴ plants/ha (D4). A two-year field trial was conducted in 2021–2023. The relationships between population structure characteristics, changes in stem strength, activation, and retransport of stem material after anthesis, and achievement of high and stable yields were investigated at the different planting densities. When the planting density of wheat increased from D1 to D4 treatment, the activity of fructan hydrolase was significantly increased. Compared with D1 treatment, the highest activity of fructan hydrolase was increased by 457.47 μg/h/g under D4 treatment. At the same time, the increase of density also increased the contribution rate of dry matter accumulation (CDMA) to grain after anthesis increased, with the highest increase in CDMA at 33.67%, which significantly reduced stem strength. Correlation analysis revealed a significant negative association between CDMA and stem strength. Specifically, CDMA levels were significantly lower with the D3 treatment than the D4 treatment, while stem strength remained higher after anthesis as an adaptive response to mitigate lodging risk. Stem storage compounds can promote grain filling and a weight increase in inferior grains. The number of spikes per unit area increased significantly with increasing planting density, but the number of grains per spike and 1000-grain weight decreased significantly. In two years, the number of spikes in D3 treatment increased by a maximum of 211.67 × 10⁴ ha⁻¹ and 99.17 × 10⁴ ha⁻¹, respectively, compared to D1 and D2 treatments. The number of grains per spike was significantly higher than that of D4 treatment, the highest being 3.68 grains. Therefore, in the North China Plain with suitable water, fertilizer, and temperature, the sowing density of 270 × 10⁴ plants/ha established population structure, significantly reduced CDMA, maintained post-anthesis stem strength, enhanced resilience of stems against post-anthesis lodging, and resulted in high yields by stabilizing the number of grains per spike and increasing the number of wheat spikes.

Based on previous research, we hypothesized that an SeVI and SeMet combined application at different growth stages could increase the yield and Se concentration and decrease Cd concentration in wheat grains. To verify this hypothesis, we designed a pot experiment throughout the wheat growth period and investigated the effects of SeIV, SeVI, and SeMet applied individually or in combination at different growth stages on yield traits; Cd absorption and transport; and Se content under Cd stress. The results indicated that grain yield was the highest under the SeVI individual application treatment and the SeVI (at the seedling, jointing, and heading stages) and SeMet (at the filling stage) combined application treatment (3 + 1 treatment), showing a more than 42% increase compared with the Cd-only control treatment (CK). Under the 5 mg/kg Cd stress, the grain Cd content in the 3 + 1 treatment was 34.1% lower than that in CK and over 14.1% lower than those in Se individual treatments. Furthermore, grain Se content was the highest under the 3 + 1 treatment, being 160.8%, 99.7%, and 39.5% higher than those in the SeIV, SeVI, and SeMet individual treatments under 5 mg/kg Cd stress. This may be attributed to early SeVI application in the 3 + 1 treatment, which enhanced yield traits and effectively promoted the retention of Cd in the middle and lower organs, reducing its transport to the grains. Furthermore, the SeMet application enhanced Se translocation to the grains, further reducing Cd content and increasing the Se concentration. In conclusion, the combined application of SeVI (at the seedling, jointing, and heading stages) and SeMet (at the filling stage) helped achieve the desired outcomes of high grain yield, low Cd content, and Se enrichment under Cd stress.