Identification and validation of a novel locus, Qpm-3BL, for adult plant resistance to powdery mildew in wheat using multilocus GWAS

Abstract

Background Powdery mildew (PM), one of the major diseases in wheat, severely damages yield and quality, and the most economical and effective way to address this issue is to breed disease-resistant cultivars. Accordingly, 371 landraces and 266 released cultivars in Henan Province were genotyped by a 660 K microarray and phenotyped for adult plant resistance (APR) to PM from 2017 to 2020, and these datasets were used to conduct multilocus genome-wide association studies (GWASs). Results Thirty-six varieties showed stable APR in all the environments, and eleven quantitative trait nucleotides (QTNs) were found by multiple methods across multiple environments and best linear unbiased prediction (BLUP) values to be significantly associated with APR. Among these stable QTNs, four were previously reported, three were newly discovered in this study, and the others need to be further investigated. The major and newly discovered QTN, Qpm-3BL, was located at chr03BL_AX-109,052,670, while another newly discovered QTN, Qpm-1BL, was located between chr01BL_AX-108,771,002 and chr01BL_AX-110,117,322. Five and eight landraces were identified to be resistant based on Qpm-1BL (haplotype TC) and Qpm-3BL (allele T), respectively. To validate Qpm-3BL, a new kompetitive allele-specific PCR (KASP) marker was developed to scan 155 F2 individuals, and the average resistance score supported the value of Qpm-3BL in marker-assisted breeding. Near Qpm-3BL, PmBMYD was identified by KEGG, gene expression and comparative genomics analyses to be a candidate. Its resistance mechanism may involve gene tandem repeats. Conclusions This study reveals a previously unknown gene for PM resistance that is available for marker-assisted breeding.

Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions

“…Combining the GWAS results of both experiments, 71 MTAs across 16 different chromosomes were detected. The presence of many MTAs controlling PM resistance across different chromosomes was reported previously in different wheat backgrounds such as American wheat, Russian wheat, winter wheat, and other backgrounds ( Liu et al., 2017 ; Kang et al., 2019 ; Leonova, 2019 ; Alemu et al., 2021 ; Du et al., 2021 ). Most of the identified significant markers were located within gene models that functionally annotated to directly or indirectly control wheat resistance to different organisms.…”

Combining Genome-Wide Association Study and Gene-Based Haplotype Analysis to Identify Candidate Genes for Alkali Tolerance at the Germination Stage in Rice

“…Genome-wide association study (GWAS) has been widely used to identify associations between phenotypic traits and genotypes in many crops (Du et al, 2021;Ma et al, 2021a,b;Tekeu et al, 2021). Based on the GWAS using a core set of 208 rice germplasms, 6 and 14 SNPs associated with salt tolerance at the germination and seedling stages, and identified 22 candidate genes through haplotype analysis (Naveed et al, 2018).…”

Genome-wide association study of agronomic traits related to nitrogen use efficiency in Henan wheat

“…Total genomic DNAs of 244 accessions were extracted from fresh seedling leaves using a modified CTAB method, following Du et al (2021) [ 48 ]. Genotyping for all 244 wheat accessions was carried out using SNP 660 K wheat microarray developed by Zhongyujin Marker Biotechnology Co., Ltd., Beijing, China.…”