Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F₇ recombinant inbred line (RIL) population lacking the Yr18 gene, a near-isogenic line (NIL) population was developed to map the resistance gene. An all-stage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exome-capture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on 1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge, the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases threatening the yield and stability of wheat production in China and many other countries. Identification and utilization of new genes for durable stripe rust resistance are important for ongoing control of this disease. The objectives of this study were to identify quantitative trait loci (QTL) associated with adult-plant stripe rust resistance in the Chinese wheat landrace Yibinzhuermai (YBZR) and to provide wheat breeders with new sources of potentially durable resistance. A total of 117 recombinant inbred lines (RILs) (F_5:8) derived from a cross between YBZR and highly susceptible cultivar Taichung 29 (TC29) were assessed for stripe rust severity in field experiments at Wenjiang in 2016 and 2017 and Chongzhou in 2016, 2017, 2018, and 2019 in Sichuan following inoculation with a mixture of current Pst races. The RILs were genotyped using the Wheat55K single nucleotide polymorphism (SNP) array. Three QTL were identified on chromosome arms 6AL, 5BL and 7DS. QYr.YBZR-6AL and QYr.YBZR-7DS conferred major effects in all field environments, explaining 10.6% to 14.7% and 11.5% to 21.2% of phenotypic variation, respectively. The QTL on 5BL and 7DS likely correspond to previously known QTL, whereas QYr.YBZR-6AL is probably novel. Haplotype analysis revealed that the resistance allele at QYr.YBZR-6AL was present in 2.8% of 324 Chinese wheat landraces. SNP markers closely linked with QYr.YBZR-6AL were converted to kompetitive allele-specific PCR markers and validated in the RIL population and a subset of 92 wheat cultivars. QYr.YBZR-6AL and its markers should be useful in breeding programs to improve the level and durability of stripe rust resistance.