Genome-wide association study and genomic selection of flax powdery mildew in Xinjiang Province

Abstract

Flax powdery mildew (PM), caused by Oidium lini, is a globally distributed fungal disease of flax, and seriously impairs its yield and quality. To data, only three resistance genes and a few putative quantitative trait loci (QTL) have been reported for flax PM resistance. To dissect the resistance mechanism against PM and identify resistant genetic regions, based on four years of phenotypic datasets (2017, 2019 to 2021), a genome-wide association study (GWAS) was performed on 200 flax core accessions using 674,074 SNPs and 7 models. A total of 434 unique quantitative trait nucleotides (QTNs) associated with 331 QTL were detected. Sixty-four loci shared in at least two datasets were found to be significant in haplotype analyses, and 20 of these sites were shared by multiple models. Simultaneously, a large-effect locus (qDI 11.2) was detected repeatedly, which was present in the mapping study of flax pasmo resistance loci. Oil flax had more QTL with positive-effect or favorable alleles (PQTL) and showed higher PM resistance than fiber flax, indicating that effects of these QTL were mainly additive. Furthermore, an excellent resistant variety C120 was identified and can be used to promote planting. Based on 331 QTLs identified through GWAS and the statistical model GBLUP, a genomic selection (GS) model related to flax PM resistance was constructed, and the prediction accuracy rate was 0.96. Our results provide valuable insights into the genetic basis of resistance and contribute to the advancement of breeding programs.

Keywords: flax; genome-wide association study (GWAS); genomic selection (GS); powdery mildew (PM); quantitative trait loci (QTL).

Figure 1

Resistance phenotypes. (A) Disease index (DI). (B) Correlation analysis of DI. (C) Classification of powdery mildew (PM) resistance: HS, high susceptible; S, susceptible; MR, moderately resistant; R, resistant; HR, high resistant. (D) Geographical distribution of resistant varieties: green represents highly resistant varieties, blue represents moderately resistant varieties, and orange represents resistant varieties. Different letters denote significant differences at the p< 0.05 level found by MRT. *** p<0.001.

Figure 2

Screening and comparison of the obtained quantitative trait loci (QTLs) and candidate gene. (A) Repeated detection of QTL screening in different years. (B) Haplotype analysis of SNP15090, Y1–Y4, and M representing the 2017, 2019, 2020, 2021, and average datasets. (C) The distribution of 64 stable resistance loci on chromosomes. (D) Class distribution of disease resistance-related genes (DRGs) located within 54-kb flanking regions of QTLs. (E) Duplication between the resistance loci utilized in this investigation and those used in previous studies. The difference between haplotypes was analyzed by t-tests.

Figure 3

Analysis of the peak for chromosome 11 and candidate genes. (A–D) Manhattan plots based on GLM-2021 (A), MLM-2021 (B), MLM-mean (C), and mrMLM-2021 (D). (E, F) Local Manhattan plot surrounding the peak on chromosome 11. (E) GLM-2021. (F) MLM-mean. (G) MLM-mean. (H) LD heatmap. (I) Gene structure of Lus10042068. (J, K) Haplotype analysis based on the lead single-nucleotide polymorphism (SNP) (SNP450497) of 2021 (J) and mean (K). (L) The distribution of allele frequencies of strong SNP was distributed in oil and fiber subpopulations. The AA and GG alleles are shown in blue and red, respectively. The difference between haplotypes was analyzed by t-tests.

Figure 4

Cluster analysis of the association panel based on a set of 64 stable large-effect quantitative trait loci (QTLs). (A) The accessions were grouped into three clusters, and the QTLs were assigned to four subgroups. Tag QTNs of QTLs were chosen for analysis. Red indicates the presence of positive-effect or favorable alleles (PQTLs) in the accessions; blue indicates the absence of PQTLs. (B) The number of oil and fiber materials included in the materials clustered into three clusters. (C) DI, disease index; NPQTL, the number of QTLs with positive-effect alleles. (D) Violin plot of QTLs clustered into four groups. (E) Set A, the number of materials that contain this group of QTLs; Set B, number of materials excluding this group of QTLs. Different letters denote significant differences at the p< 0.05 level found by MRT.

Figure 5

Distribution of number of quantitative trait loci (QTLs) with positive-effect or favorable alleles (NPQTL) in flax accessions. (A) Heatmap of disease index and NPQTL in resistant and susceptible individuals. (B) Comparison of disease index (DI) of oil and fiber in flax. (C) Comparison of NPQTL of oil and fiber in flax. The difference between subpopulations was analyzed by t-tests.

Figure 6

Genomic selection for flax powdery mildew. (A) Prediction accuracy of GBLUP and rrBLUP. (B) Relative efficiency of GBLUP and rrBLUP. (C) Correlation between training population size and prediction accuracy. (D) Correlation between observed and predicted values. Different letters denote significant differences at the p< 0.05 level found by MRT. * p<0.05, **** p<0.0001, ns: no significant.