Fig. 1: Identification of a candidate gene for wheat yellow mosaic virus (WYMV) resistance based on multiple strategies.

a, b GWAS result for WYMV resistance on chromosome 2D in panel I (a) and panel II (b). The red horizontal line indicates the genome-wide significance threshold (P = 1.0e⁻⁰⁴ in panel I and P = 1.0e⁻⁰³ in panel II). Yellow background area indicates the candidate region (595.1-619.1 Mb in panel I and 596.9-613.3 Mb in panel II) on 2D. Two sides and the multiple test correction is conducted with Bonferroni method. c LOD contours for quantitative trait loci (QTL) to WYMV resistance on 2D identified by inclusive composite interval mapping (ICIM) in the UC1110/PI610750 (UP) population; d Integrated analysis of GWAS and QTL results. e Distribution of seven candidate genes in the region of 604.1–612.2 Mb. f Seven candidate genes were screened by multi-omics. Transcriptomics identified 23 differentially expressed genes (DEGs) in the target region by bulked segregant transcriptome using RNA-seq (BSR-Seq). Re-sequencing of the genome identified 17 of 23 DEGs with nonsynonymous variations or promoter variations in the target region between UC1110 and PI610750. The expression pattern identified 16 of 17 genes with a stable expression in roots and shoots in the target region, and 7 of 16 candidate genes were induced by WYMV infection. g, h Haplotype analysis indicated a 444-kb block covering the lead SNP (AX-95101589) in Panel I and a 342-kb block covering the lead SNP (BobWhite_c32336_504) in Panel II. For box-plot, the horizontal lines from top to bottom represent the maximum, first quartile, median, third quartile, and minimum of the total data, respectively. The cross in the middle of the box represents the average. n represents the number of wheat accessions with the corresponding haplotype. Statistics: for both datasets, two-sided t test was performed. n the number of wheat accessions with the corresponding haplotype. Source data are provided as a Source Data file.