Quantitative trait loci and candidate genes conferring leaf rust resistance in synthetic hexaploid wheat derived populations


You FM, Zheng C, Edwards T, Jia B, Li P, McCallum B, Pozniak CJ, Cloutier S (2023) Quantitative trait loci and candidate genes conferring leaf rust resistance in synthetic hexaploid wheat derived populations. Proc 5th Canadian Wheat Symposium, Vancouver, Nov 13-16


Synthetic hexaploid wheats (SHWs) are valuable genetic resource for broadening the genetic diversity of important agronomic traits, such as yield, drought tolerance and disease resistance, by accessing the largely untapped Aegilops tauschii genepool and introducing new allelic variation for Canadian breeding programs. Leaf rust is a widespread disease that can result in significant yield losses. To investigate allelic variations associated with leaf rust resistance, we backcrossed five SHWs (C44, C45, C52, C65 and C66) to the elite Canadian cultivar Carberry, resulting in BC1F5 populations of 133-208 individuals. These populations were sequenced using genotyping by sequencing (GBS), producing 446K-838K SNPs each. The plants were phenotyped under controlled greenhouse conditions after being inoculated with various Puccinia triticina (leaf rust) isolates, including isolate 11-180-1 TDBG for 18C52CAR and 18C66CAR, isolates 12-3 MBDS, 77-2 JBJ and 9-1 SBDG for 18C65CAR, isolates 16-273-2 TSBS, 16-252-2 TTBJ, 06-1-1 TDBG (TDBG2) and 77-2 TJBJ for 19C44CAR and 19C45CAR. The phenotypic segregations of leaf rust resistance in the populations can be explained by one, two or more major genes. Using the haplotype-based model RTM-GWAS, we identified unique quantitative trait loci (QTLs) associated with resistance against these isolates. A total of 7, 4, 3, 7 and 3 unique QTLs, explaining more than 5% of the phenotypic variation, were detected from 19C44CAR, 19C45CAR, 18C52CAR, 18C65CAR and 18C66CAR, respectively. Multiple major QTL (R2 > 10%) were identified on chr2B, 2D, 6A, 7D and in unmapped genome locations. Several resistance gene analogs co-located with the QTLs, including nucleotide binding site and leucine-rich repeat receptors (NLRs), receptor-like kinases (RLKs), and proteins with transmembrane-coiled-coil (TM-CC) domains. These QTLs and candidate genes can be used in genomic selection and for superior cross-prediction in SHW breeding. The SHW donor parents and the Carberry recurrent parent have been sequenced, and mutant populations are being developed to isolate the candidate genes.