Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating fungal diseases of wheat worldwide. It is essential to discover more sources of stripe rust resistance genes for wheat breeding programs. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for the construction of high-density genetic maps. In this study, a set of 200 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Chuanmai 42 (CH42) and Chuanmai 55 (CH55) was used to construct a high-density genetic map and to identify quantitative trait loci (QTLs) for stripe rust resistance using SLAF-seq technology. A genetic map of 2828.51 cM, including 21 linkage groups, contained 6732 single nucleotide polymorphism markers (SNP). Resistance QTLs were identified on chromosomes 1B, 2A, and 7B; Qyr.saas-7B was derived from CH42, whereas Qyr.saas-1B and Qyr.saas-2A were from CH55. The physical location of Qyr.saas-1B, which explained 6.24–34.22% of the phenotypic variation, overlapped with the resistance gene Yr29. Qyr.saas-7B accounted for up to 20.64% of the phenotypic variation. Qyr.saas-2A, a minor QTL, was found to be a likely new stripe rust resistance locus. A significant additive effect was observed when all three QTLs were combined. The combined resistance genes could be of value in breeding wheat for stripe rust resistance.

Wheat (Triticum aestivum L.) is rich in tandem repeats, and this is helpful in studying its karyotypic evolution. Some tandem repeats have not been assembled into the wheat genome sequence. Alignment using the blastn tool in the B2DSC web server indicated that the genomic sequence of 5B chromosome (IWGSC RefSeq v2.1) does not contain the tandem repeat pTa-275, and the tandem repeat (GA)₂₆ distributed throughout the whole 5B chromosome. The nondenaturing fluorescence in situ hybridization (ND-FISH) using the oligonucleotide (oligo) probes derived from pTa-275 and (GA)₂₆ indicated that one signal band of pTa-275 and two signal bands of (GA)₂₆ appeared on the 5B chromosome of Chinese Spring wheat, indicating the aggregative distribution patterns of the two kinds of tandem repeats. Single-copy FISH indicated that the clustering region of pTa-275 and the two clustering regions of (GA)₂₆ were located in ~160–201 Mb, ~153–157 Mb, and ~201–234 Mb intervals, respectively. Using ND-FISH and single-copy FISH technologies, the translocation breakpoint on the 5BS portion of the translocation T7BS.7BL-5BS, which exists widely in north-western European wheat cultivars, was located in the region from 157,749,421 bp to 158,555,080 bp (~0.8 Mb), and this region mainly contains retrotransposons, and no gene was found. The clustering regions of two kinds of tandem repeats on wheat chromosome 5B were determined and this will be helpful to improve the future sequence assembly of this chromosome. The sequence characteristics of the translocation breakpoint on the translocation T7BS.7BL-5BS obtained in this study are helpful to understand the mechanism of wheat chromosome translocation.

Germplasm is the material basis for crop genetic improvement and related basic research. Knowledge of genetic diversity present in wheat is the prerequisite for wheat breeding and improvement. Non-denaturing fluorescence in situ hybridization (ND-FISH) is a powerful tool to distinguish chromosomal polymorphisms and evaluate genetic diversity in wheat. In this study, ND-FISH using Oligo-pSc119.2-1, Oligo-pTa535-1, and Oligo-(GAA)₇ as probes were used to analyze the genetic diversity among 60 International Maize and Wheat Improvement Center (CIMMYT) derived wheat lines, and 93 cultivated wheat and landraces from the Chinese wheat core germplasm. A total of 137 polymorphic FISH patterns were obtained, in which 41, 65, and 31 were from A-, B-, and D-genome chromosomes, respectively, indicating polymorphism of B-genome > A-genome > D-genome. In addition, 22 and 51 specific FISH types were observed in the two germplasm resource lines. Twelve types of rearrangements, including seven new translocations, were detected in all 153 wheat lines. Genetic relationships among 153 wheat lines were clustered into six groups. Our research provides cytological information for rational utilization of wheat germplasm resources.

Leaf pubescence is an important trait closely associated with plant adaptability to specialized habitats. Baimaomai (BMM) is a wheat (Triticum aestivum L.) landrace originating from the high-altitude, drought-prone environment of Sichuan Province, China with long, dense leaf pubescence. A population of 234 recombinant inbred lines (F₁₀) developed from the cross between Chuanmai104 (CM104), which lacks leaf pubescence, and BMM with pubescent leaves, was used to conduct a phenotypic evaluation of leaf pubescence. Three quantitative trait loci (QTLs) were detected on chromosome arms 7BS, 3DL and 3AL using a high-density wheat 50K single-nucleotide polymorphism array in four environments. The QTLs were designated QLp.saas-7BS, QLp.saas-3DL and QLp.saas-3AL. QLp.saas-3AL, derived from BMM, and QLp.saas-3DL, derived from CM104, were new minor-effect loci. QLp.saas-7BS, derived from BMM, was a novel major-effect locus detected in all environments and was localized in a 0.48 Mb interval on chromosome arm 7BS based on the wheat ‘Chinese Spring’ reference genome. QLp.saas-7BS explained up to 40.77% of the total phenotypic variance. KASP markers tightly linked to QLp.saas-7BS were developed and verified. The present results provide valuable information for further fine mapping, cloning, and marker-assisted selection with QLp.saas-7BS in wheat.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a persistent threat to wheat production in China. The Sichuan cultivar Chuanmai 62 (CM62) has exhibited stable adult-plant resistance (APR) for over a decade. To elucidate its genetic basis, we evaluated a recombinant inbred line population (CM62 × Avocet S) across 13 environments and genotyped it using the 55K SNP array. QTL mapping identified six QTL distributed on chromosomes 1BL, 2AS, 2BL, 5AL (two loci), and 5BL. Among these, three major QTL (QYr.CM62-1BL, QYr.CM62-2AS, and QYr.CM62-2BL) were detected. Notably, QYr.CM62-2BL was the preeminent locus, explaining 8.97–50.59% of phenotypic variance and exhibiting high stability across 11 of the 13 environments; this locus is closely linked to the previously reported QYR1 region, although whether it is allelic to QYR1 remains unclear. QYr.CM62-2AS corresponded to Yr17/YrM1225, while QYr.CM62-1BL aligned with Yr29. A significant finding was the identification of QYr.CM62-5BL, a novel minor-effect QTL mapped to the rearranged 5BL·7BL segment resulting from a 5B/7B reciprocal translocation present in both parents. Furthermore, two Kompetitive Allele-Specific PCR (KASP) markers (KASP-AX-109507945 and KASP-AX-109844182) were developed for QYr.CM62-2BL. Polymorphism screening of 328 cultivars confirmed their utility for marker-assisted selection. Collectively, our results demonstrate that the durable APR in CM62 is governed by multiple additive QTL. The newly developed KASP markers, together with the novel QYr.CM62-5BL locus and prioritized candidate genes from in silico annotation of the QYr.CM62-2BL interval, provide valuable genetic resources for pyramiding resistance alleles and future map-based cloning in wheat breeding programs.

Allopolyploidy increases its evolutionary potential by fixing heterosis and the advantage of gene redundancy. Allelic combinations generated from genetic recombination potentially provide many variations to the selection pools for evolution. May there be any relationship between allopolyploidization and genetic recombination? To study the impact of polyploidy on genetic recombination, we selected wheat as a model and simulated its evolution pathway of allopolyploidy by developing synthetic hexaploid wheat. The change of homologous chromosome recombination were investigated on their diploid DD and tetraploid AABB genomes after their allohexaploidization, respectively. The genetic recombination of the ancestral diploid genome of Aegilops tauschii was enhanced significantly more than 2 folds after their hexaploidization. Hexaploidization enhancing genetic recombination of the ancestral diploid D genome was firstly reported to be a new way to increase evolutionary potential of wheat, which is beneficial for wheat to conquer their narrow origination of D genome, quickly spread and make it a major crop of the world. Finally, re-synthetizing hexaploid wheat using diverse Ae. tauschii species with tetraploid wheat can be considered as a pleiotropic strategy to speed adaptive evolution of bread wheat in breeding processes by increasing both gene allele types and genetic recombination variations.