Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax (Linum usitatissimum L.)

Abstract

Powdery mildew is one of the most important diseases of flax and is particularly prejudicial to its yield and oil or fiber quality. This disease, caused by the obligate biotrophic ascomycete Oïdium lini, is progressing in France. Genetic resistance of varieties is critical for the control of this disease, but very few resistance genes have been identified so far. It is therefore necessary to identify new resistance genes to powdery mildew suitable to the local context of pathogenicity. For this purpose, we studied a worldwide diversity panel composed of 311 flax genotypes both phenotyped for resistance to powdery mildew resistance over 2 years of field trials in France and resequenced. Sequence reads were mapped on the CDC Bethune reference genome revealing 1,693,910 high-quality SNPs, further used for both population structure analysis and genome-wide association studies (GWASs). A number of four major genetic groups were identified, separating oil flax accessions from America or Europe and those from Asia or Middle-East and fiber flax accessions originating from Eastern Europe and those from Western Europe. A number of eight QTLs were detected at the false discovery rate threshold of 5%, located on chromosomes 1, 2, 4, 13, and 14. Taking advantage of the moderate linkage disequilibrium present in the flax panel, and using the available genome annotation, we identified potential candidate genes. Our study shows the existence of new resistance alleles against powdery mildew in our diversity panel, of high interest for flax breeding program.

Keywords: GBS; flax (Linum usitatissimum L.); genetic diversity; genome wide association studies (GWAS); powdery mildew.

Figure 1

SNPs density on 15 chromosomes among the entire flax panel containing 5,464,275 SNPs per 100 kb window.

Figure 2

Circleplot of private SNPs by flax type (Fiber type colored in blue, Oil type in orange and Wild type in green) with a 100 kb binwidth.

Figure 3

Scatter plot from DAPC (AM, America; EU, Europe; AS, Asia; ME, Middle-East).

Figure 4

Membership probability of the flax panel for k = 4 (AM, America; EU, Europe; AS, Asia; ME, Middle-East).

Figure 5

Linkage disequilibrium by flax type (A) and among sub-populations (B). Cultivated flax corresponds to the sum of oil and fiber flax (i.e. excluding wild type). AM, America; EU, Europe; AS, Asia; ME, Middle-East.

Figure 6

Manhattan and Quantile-quantile plots showing the significant markers detected by mixed linear model for powdery mildew in 2018 (A) and in 2019 (B). The red horizontal line represents the Bonferroni adjusted genome-wide significance threshold (á = 0.05/1,693,910 = 2.95e-08) and the blue horizontal line the FDR threshold (q = 0.05).