Characterization of adult plant leaf rust resistance loci in an international wheat collection using a re-sequencing genotyping system

Leaf rust, caused by the fungus Puccinia triticina , is one of the most destructive diseases affecting global wheat production. Developing disease-resistant wheat varieties is the most cost-effective and environmentally friendly approach to managing this disease. We phenotyped a collection of 559 wheat accessions from five continents for resistance to leaf rust in field trials at three locations in China (Zhoukou, Henan; Wuhan, Hubei; and Xinxiang, Henan) during the 2020–2021, 2021–2022, and 2022–2023 cropping seasons, followed by best-linear-unbiased-estimation analysis across environments. These accessions were genotyped using the MGISEQ-2000 re-sequencing platform, and a genome-wide association analysis was subsequently performed. Twenty-four stable leaf rust resistance loci across 15 chromosomes were identified. Among these, 11 loci may represent new sources of resistance. Notably, Lr.hzau-2BS.1 and Lr.hzau-7AL were consistently detected across all three environments and BLUE. Lr.hzau-2BS.1 has the highest frequency in European wheat accessions, whereas Lr.hzau-7AL is most prevalent in South American accessions. Gene-expression analysis identified 101 candidate genes associated with these loci. Closely linked Kompetitive Allele Specific PCR (KASP) markers, 2B-209172 and 7A-348992 , were developed for Lr.hzau-2BS.1 and Lr.hzau-7AL , respectively. Chinese wheat varieties Mianmai 45 and Liaomai 16, which carry resistance alleles at both loci and exhibit < 5 % leaf rust severity, represent valuable sources of leaf rust resistance for wheat breeding programs. These newly identified resistance loci and their KASP markers provide valuable resource for their exploitation in wheat breeding.