The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding.

The root is an important organ by which plants directly sense variation in soil moisture. The discovery of drought stress-responsive genes in roots is very important for the improvement of drought tolerance in wheat varieties via molecular approaches. In this study, transcriptome sequencing was conducted on the roots of drought-tolerant wheat cultivar YH1818 seedlings at 0, 2, and 7 days after treatment (DAT). Based on a weighted gene correlation network analysis of differentially expressed genes (DEGs), 14 coexpression modules were identified, of which five modules comprising 3107 DEGs were related to 2 or 7 DAT under drought stress conditions. A total of 223,357 single-nucleotide polymorphisms (SNPs) of these DEGs were retrieved from public databases. Using the R language package and GAPIT program, association analysis was performed between the 223,357 SNPs and the drought tolerance coefficient (DTC) values of six drought resistance-related traits in 114 wheat germplasms. The results revealed that 18 high-confidence SNPs of 10 DEGs, including TaPK, TaRFP, TaMCO, TaPOD, TaC3H-ZF, TaGRP, TaDHODH, TaPPDK, TaLectin, and TaARF7-A, were associated with drought tolerance. The RT–qPCR results confirmed that these genes were significantly upregulated by drought stress at 7 DAT. Among them, TaARF7-A contained three DTC-related SNPs, which presented two haplotypes in the tested wheat germplasms. YH1818 belongs to the Hap1 allele, which is involved in increased drought tolerance. This study revealed key modules and candidate genes for understanding the drought-stress response mechanism in wheat roots.

Structural variation (SV) serves as a fundamental driver of phenotypic diversity and environmental adaptation in plants and animals, significantly influencing key agronomic traits in crops. Common wheat (Triticum aestivum L.), an allohexaploid species, harbors extensive chromosomal SVs and distant hybridization-induced recombination events that provide critical resources for genetic improvement. This study utilizes non-denaturing fluorescence in situ hybridization (ND-FISH) and oligonucleotide multiplex probe-based FISH (ONPM-FISH) to analyze the karyotypes of 153 BC₁F₄–BC₁F₆ lines derived from the hybrid line Xiaoyan 7430 and common wheat Yannong 1212. The results revealed that Xiaoyan 7430 carries 8 alien chromosome pairs and 20 wheat chromosome pairs (lacking 6B), and Yannong 1212 contains 21 pairs of wheat chromosomes. The parental lines exhibited presence/absence variations (PAVs) on chromosomes 2A, 6A, 5B, 1D, and 2D. Chromosomal variations, including numerical chromosomal variation (NCV), structural chromosomal variation (SCV), and complex chromosomal variation (CCV), were detected in the progeny lines through ONPM-FISH analysis. The tracking of alien chromosomes over three consecutive generations revealed a significant decrease in transmission frequency, declining from 61.82% in BC₁F₄ to 26.83% in BC₁F₆. Telosomes were also lost during transmission, declining from 21.82% in BC₁F₄ to 9.76% in BC₁F₆. Alien chromosome 1J^S, 4J, and 6J exhibited the highest transmission stability and were detected across all three generations. Association analysis showed that YN-PAV.2A significantly affected the length/width ratio (LWR) and grain diameter (GD); YN-PAV.6A, XY-PAV.6A, and PAV.5B increased six grain traits (+2.25%~15.36%); YN-PAV.1D negatively affected grain length (GL) and grain circumference (GC); and XY-PAV.2D exerted positive effects on thousand-grain weight (TGW). Alien chromosomes differentially modulated grain characteristics: 1J^S and 6J both reduced grain length and grain circumference; 1J^S increased LWR; and 4J negatively impacted TGW, grain width (GW), GD, and grain area (GA). Meanwhile, increasing alien chromosome numbers correlated with progressively stronger negative effects on grain traits. These findings elucidate the genetic mechanisms underlying wheat chromosomal variations induced by distant hybridization and their impact on wheat grain traits, and provide critical intermediate materials for genome design breeding and marker-assisted selection in wheat improvement.