Caixia Lan

The hybridization‐led integration of the D‐genome into domesticated tetraploid wheat gave rise to allohexaploid wheat, the most cultivated wheat globally grown across diverse environmental conditions. However, the regulatory mechanisms by which this genomic integration confers increased environmental adaptability in allohexaploid remains largely unexplored. Here, we investigated the change of transcriptome, chromatin interactome and metabolome in three independent polyploidization events. Our findings reveal that polyploidization triggers the activation of defense‐related genes through a comprehensive reorganization of the epigenome and 3D chromatin architecture. Furthermore, polyploidization significantly enriches secondary metabolites—specifically alkaloids and flavonoids—which are pivotal for environmental adaptation. We further found that B‐subgenome genes TaRLK‐1B and TaRLK‐3B are activated via de novo chromatin interactions to enhance alkali stress tolerance, whereas TaGT‐2D boosts UV‐B resistance through the accumulation of glycosylated flavonoids. These results shed light on the mechanistic basis of enhanced adaptability in hexaploid wheat, especially to salt, alkali, and UV‐B stress, and highlight the indispensable contribution of the D‐genome to the evolutionary success of the allohexaploid lineage.

Stripe rust, caused by Puccinia striiformis f. sp. tritici , can cause severe yield losses in wheat ( Triticum aestivum L.) during epidemics. Breeding resistant wheat varieties remains the most cost-effective approach to manage this disease; and the identification of new resistance loci is essential for maintaining genetic diversity. The CIMMYT-derived wheat line ‘Kijil’ was highly resistant to stripe rust in both Mexican and Chinese environments. A population of 153 F₅ recombinant inbred lines (RILs) was derived from a cross between Kijil and the susceptible parent ‘Apav#1’. The population was phenotyped for stripe rust resistance across seven environments in two countries and genotyped using a genotyping-by-sequencing (GBS) platform. Inclusive composite interval mapping (ICIM) was used to construct a genetic map and identify significant resistance quantitative trait loci (QTLs) using 5,468 polymorphic markers. Mapping revealed the known resistance loci Yr29 , Yr30 and QYr.hzau-3AS , along with two novel loci, QYr.hzau-2BS and QYr.hzau-5DL , across both Chinese and Mexican rust environments. Among these, QYr.hzau-2BS accounted for 11.75% to 19.19% of the phenotypic variance. A corresponding KASP marker, KASP_2BS, was developed to facilitate marker-assisted selection. Based on the mapping interval, two candidate genes underlying this locus were predicted. Further analysis revealed that Yr29 showed significant additive effects with other stripe rust resistance genes/loci, and the combination of Yr29 , Yr30 , and QYr.hzau-2BS reduced disease severity by up to 67.8%. Our findings suggest that Kijil and RILs carrying Yr29 , Yr30, and QYr.hzau-2BS can serve as valuable donors for breeding wheat varieties with improved stripe rust resistance.

The genetic basis of wheat yield is highly complex, being collectively influenced by key traits such as plant morphology, spike structure, and grain morphology. Therefore, exploring the genetic regulatory mechanisms underlying yield-related traits is crucial for breeding high-yield wheat varieties. In the present study, a panel of 372 wheat landraces from Gansu province, China, was phenotyped four yield-related traits: spike length (SL), spikelet number per spike (SNS), grain number per spike (GNS), and thousand−kernel weight (TKW) over four years across five field environments at two locations (Qingshui and Lanzhou) in Gansu province. Genotyping was performed using a 16K SNP array, and genome-wide association studies (GWAS) were conducted on the multi-environment phenotypic data employing the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), Compressed Mixed Linear Model (CMLM), Fixed and Random Model Circulating Probability Unification (FarmCPU), Mixed Linear Model (MLM) and Multi-Locus Mixed Model (MLMM) models. In total, we identified nine loci for SL, four loci for GNS, one loci for SNS, and five loci for TKW. The phenotypic variation explained (PVE) by these loci ranged from 2.0% to 22.0%. Each locus exhibits 2–4 haplotypes and showed significant differences between haplotypes. Furthermore, 16 candidate genes associated with panicle traits were predicted and they encoded proteins such as squamosa promoter-binding protein, F-box family protein, ferredoxin-NADP-oxidoreductase 2, aspartic proteinase Asp1, Pre-mRNA splicing factor and so on. These results provide novel genetic loci for wheat yield improvement, offering valuable resources for future breeding programs.

Stripe rust, caused by Puccinia striiformis f. sp. tritici , can cause severe yield losses in wheat ( Triticum aestivum L.) during epidemics. Breeding resistant wheat varieties remains the most cost-effective approach to manage this disease; and the identification of new resistance loci is essential for maintaining genetic diversity. The CIMMYT-derived wheat line ‘Kijil’ was highly resistant to stripe rust in both Mexican and Chinese environments. A population of 153 F₅ recombinant inbred lines (RILs) was derived from a cross between Kijil and the susceptible parent ‘Apav#1’. The population was phenotyped for stripe rust resistance across seven environments in two countries and genotyped using a genotyping-by-sequencing (GBS) platform. Inclusive composite interval mapping (ICIM) was uesd to construct a genetic map and identify significant resistance quantitative trait loci (QTLs) using 5,468 polymorphic markers. Mapping revealed the known resistance loci Yr29 , Yr30 and QYr.hzau-3AS , along with two novel loci, QYr.hzau-2BS and QYr.hzau-5DL , across both Chinese and Mexican rust environments. Among these, QYr.hzau-2BS accounted for 11.75% to 19.19% of the phenotypic variance. A corresponding KASP marker, KASP_2BS, was developed to facilitate maker-assisted selection. Based on the mapping interval, four candidate genes underlying this locus were predicted. Further analysis revealed that Yr29 showed significant additive effects with other stripe rust resistance genes/loci, and the combination of Yr29 , Yr30 , and QYr.hzau-2BS reduced disease severity by up to 67.8%. Our findings suggest that Kijil and RILs carrying Yr29 , Yr30, and QYr.hzau-2BS can serve as valuable donors for breeding wheat varieties with improved stripe rust resistance. Author summary: Stripe rust is an important disease that seriously threatens the yield and quality of wheat. It is crucial to explore new resistant resources and cultivate durable resistant varieties in the current breeding programme. In this study, we analysed the genetic basis of resistance to stripe rust in the wheat line “Kijil”, which has broad-spectrum resistance to stripe rust. Through genetic mapping, we identified five quantitative trait loci for stripe rust, including two new resistance loci. A closely linked KASP marker, KASP_2BS, was developed for the QYr.hzau-2BS , which can be used for rapid and accurate screening of resistant plants in early breeding populations. Meanwhile, within this QTL region, we screened four candidate genes based on expression analysis. In addition, it was found that polymerization of QYr.hzau-2BS with known resistance genes, Yr29 and Yr30 , significantly enhanced resistance and reduced disease severity to low levels and near immunity. In conclusion, this study provides new genetic resources, practical molecular markers and effective gene polymerization strategies for breeding wheat for stripe rust resistance. ‘Kijil’ and the lines containing resistance loci have important breeding utilization value.

Summary: Drought stress significantly reduces crop yield by triggering abscisic acid (ABA) accumulation in plants. It involves the suppression of CYP707A genes, which encode enzymes that catalyze ABA. However, little is known about epigenetic control in the CYP707A gene‐mediated drought stress response in wheat. In this study, we reported that TaCYP707A‐6A/6B/6D but not TaCYP707A‐5A/5B/5D participates in drought response in common wheat. Disruption of TaCYP707A‐6B showed enhanced drought tolerance but also decreased fertility. Expression of TaCYP707A‐6B is negatively associated with H3K27me3 level. An evolutionarily conserved CTCTGYTY motif cluster (binding site for a Jumonji H3K27me3 demethylase) was found in the intron of TaCYP707A‐6B as well as the intron of CYP707A homologs in other plant species. Blocking the CTCTGYTY motif by dead Cas9 (dCas9) maintained a high level of H3K27me3 on the CYP707A gene, while decreasing its expression level leading to enhanced drought tolerance in both wheat and Arabidopsis. In particular, the mutant in which the intron bound by H3K27me3 demethylase was cut out without change of splicing pattern showed enhanced drought tolerance. Therefore, our study provides a novel approach to improve plant drought tolerance by manipulating an evolutionarily conserved cis‐element bound by histone demethylases in the intron of CYP707A genes.

Stripe or yellow rust (YR) caused by Puccinia striiformis tritici (Pst) is an important foliar disease affecting wheat production globally. Resistant varieties are the most economically and environmentally effective way to manage this disease. The common winter wheat (Triticum aestivum L.) cultivar Luomai 163 exhibited resistance to the Pst races CYR32 and CYR33 at the seedling stage and showed a high level of adult plant resistance in the field. To understand the genetic basis of YR resistance in this cultivar, 142 F₅ recombinant inbred lines (RILs) derived from cross Apav#1 × LM163 and both parents were genotyped with the 16K SNP array and bulked segregant analysis sequencing. The analysis detected a major gene, YrLM163, at the seedling stage associated with the 1BL.1RS translocation. Additionally, three genes for resistance at the adult plant stage were detected on chromosome arms 1BL (Lr46/Yr29/Pm39/Sr58), 6BS, and 6BL in Luomai 163, whereas Apav#1 contributed resistance at a quantitative trait locus (QTL) on 2BL. These QTL explained YR disease severity variations ranging from 6.9 to 54.8%. The kompetitive allele-specific PCR (KASP) markers KASP-2BL, KASP-6BS, and KASP-6BL for the three novel loci QYr.hzau-2BL, QYr.hzau-6BS, and QYr.hzau-6BL were developed and validated. QYr.hzau-1BL, QYr.hzau-2BL, and QYr.hzau-6BS showed varying degrees of resistance to YR when present individually or in combination based on genotype and phenotype analysis of a panel of 570 wheat accessions. Six RILs combining resistance alleles of all QTL, showing higher resistance to YR in the field than Luomai 163 with disease severities of 10.7 to 16.0%, are important germplasm resources for breeding programs to develop YR-resistant wheat varieties with good agronomic traits.