Genome wide association study reveals novel QTL for barley yellow dwarf virus resistance in wheat

Abstract

Background: Barley yellow dwarf (BYD) is an important virus disease that causes significant reductions in wheat yield. For effective control of Barley yellow dwarf virus through breeding, the identification of genetic sources of resistance is key to success. In this study, 335 geographically diverse wheat accessions genotyped using an Illumina iSelect 90 K single nucleotide polymorphisms (SNPs) bead chip array were used to identify new sources of resistance to BYD in different environments.

Results: A genome-wide association study (GWAS) performed using all the generalised and mixed linkage models (GLM and MLM, respectively) identified a total of 36 significant marker-trait associations, four of which were consistently detected in the K model. These four novel quantitative trait loci (QTL) were identified on chromosomes 2A, 2B, 6A and 7A and associated with markers IWA3520, IWB24938, WB69770 and IWB57703, respectively. These four QTL showed an additive effect with the average visual symptom score of the lines containing resistance alleles of all four QTL being much lower than those with less favorable alleles. Several Chinese landraces, such as H-205 (Baimazha) and H-014 (Dahongmai) which have all four favorable alleles, showed consistently higher resistance in different field trials. None of them contained the previously described Bdv2, Bdv3 or Bdv4 genes for BYD resistance.

Conclusions: This study identified multiple novel QTL for BYD resistance and some resistant wheat genotypes. These will be useful for breeders to generate combinations with and/or without Bdv2 to achieve higher levels and more stable BYD resistance.

Keywords: BYD resistance; Genome-wide association study; Novel QTL; SNP; Wheat.

Fig. 1

An estimation of the most probable number of clusters (K), based on 20 independent runs and K ranging from 2 to 8

Fig. 2

Population structure of the 335 wheat accessions. Three subpopulations (K = 3) were produced on genetic diversity detected by 4560 SNP markers, each are presented by a different colour

Fig. 3

Manhattan plots and Quantile-quantile (Q-Q) plots for genome wide association study (GWAS) of BYD resistance in 335 wheat accessions. a Manhattan plot in Q method; b Manhattan plot in K method; c Q-Q plot in K method. In Manhattan plots, significant association was identified using criterion of –log10 (P) > 3 (P < 0.001). Q-Q plots were displayed in marker–trait association analysis. The black line represents the expected line under the null distribution, while the red symbol in the observed –log10 (P) for BYD resistance

Fig. 4

Average symptom scores of genotypes with resistance alleles. 0: without any tolerance alleles, 1–4: with 1–4 resistance alleles

Fig. 5

BYD symptom severity scores in wheat. Score 0, whole plant without symptoms; score 1, few leaves showing discoloration; score 2, about 20% leaf area has discoloration; score 3, 40% leaf area shows yellowing; score 4, 60%, leaf area shows yellowing; score 5, most of plant affected (photos were taken from field trials of the current experimental)