Identification and validation of stripe rust resistance on 7BL in wheat cultivar Aikang 58 through linkage and association analysis

A genomic region spanning over 30 Mb on chromosome arm 7BL carring multiple loci for durable resistance to stripe rust was identified in wheat cultivar Aikang 58. GWAS and sweep selection analyses revealed the specific genomic regions on chromosome arm 7BL with artificial selection signals in different breeding groups. High-throughput molecular markers have been developed to accelerate the deployment of YrAK58.1 , YrAK58.2 , YrAK58.3 in breeding programs. Stripe rust caused by Puccinia striiformis f. sp. tritici ( Pst ) is a serious disease affecting wheat production in China. Wheat cultivar Aikang 58 (AK58) has exhibited effective resistance to stripe rust since its release in 2005. But the genetic basis of its stripe rust resistance remains unknown. Two genetic populations from the crosses of Avocet S/AK58 (128 recombinant inbred lines) and Kenong 9204/AK58 (1,042 F 2:3 families) were used to dissect the genetic basis of stripe rust resistance in AK58, respectively. In addition, Panel 1 consisting of 688 wheat accessions were used for genome-wide association study (GWAS) and sweep selection analysis to validate the presence of the resistance haplotype of the target region and Panel 2 consisting of 388 Chinese cultivars and breeding lines was genotyped using molecular markers to evaluate the prevalence and distribution of the resistant loci in AK58. The genetic populations were evaluated for stripe rust responses at Yangling and Guiyang over five cropping seasons (2017-2022) and genotyped using GBW16 K SNP array and KASP markers. Using quantitative trait loci (QTLs) analysis, seven QTL were detected on chromosome arms 1BL, 2BS, 2BL, 5BL and 7BL (three QTLs). Among them, QYrak . nwafu-2BL identified as Yr5b conferred all-stage resistance to Pst race V32L; three QTL within the 7BL chromosome arm region 715.77-733.25 Mb based on Chinese Spring RefSeq v.2.1, were designated YrAK58 . 1, YrAK58 . 2 and YrAK58 . 3 , respectively. YrAK58 . 1 confirmed as Yr6 , and YrAK58 . 2 conferred all-stage resistance to multiple Pst races and were also effective in field environments. YrAK58 . 3 contributed stable resistance in all field environments. The remaining QTL were environment-dependent with minor effect. GWAS and sweep selection analyses revealed specific genomic regions with artificial selection signals for the three QTL on chromosome arm 7BL in different breeding groups. A haplotype combination of high-throughput molecular markers tightly flanking Yr6, YrAK58 . 2 and YrAK58 . 3 detected all three genes in 3.6% of entries in Panel 2. The same marker set can be used to further exploit the resistance gene combination in breeding programs.