Genome-Wide Association Studies for Pasmo Resistance in Flax (<em>Linum Usitatissimum L.</em>)

Abstract

Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype &amp;times; environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3-23%), were stable across all datasets and explained 32-64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of positive effect QTL (NPQTL) in accessions was significantly correlated with PR (R2=0.55), suggesting additive effects. NPQTL was also significantly associated with morphotype (R2=0.52) and &amp;nbsp;major positive effect QTL were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding.

Evaluation of Genomic Prediction for Pasmo Resistance in Flax

“…Four marker sets were used for GP of pasmo resistance. The first marker set contained 52,347 genome-wide SNPs (SNP-52347) that were correlated to the five-year average PS and the PS of the five individual years at a 10 -5 probability level [4]. The other three marker sets were the 500 unique QTL (SNP-500QTL), the 134 QTL statistically stable over five consecutive years (SNP-134QTL), and the 67 stable and relatively large-effect QTL (SNP-67QTL) sets previously identified for PR [4].…”

“…The first marker set contained 52,347 genome-wide SNPs (SNP-52347) that were correlated to the five-year average PS and the PS of the five individual years at a 10 -5 probability level [4]. The other three marker sets were the 500 unique QTL (SNP-500QTL), the 134 QTL statistically stable over five consecutive years (SNP-134QTL), and the 67 stable and relatively large-effect QTL (SNP-67QTL) sets previously identified for PR [4]. The SNP-500QTL dataset comprises markers for all small-or large-effects, including QTL stable across environments and environment-specific QTL identified using ten different statistical models and all six phenotypic datasets ( Figure 1).…”

“…Resistance to flax pasmo is polygenic. Our previous study reported 500 non-redundant QTL for PR from 370 diverse flax accessions of a core collection based on five-year pasmo field assessments; of those, 134 QTL were statistically stable in all five years and 67 had relatively stable and large effects [4]. The number of positive-effect QTL was also significantly negatively correlated with pasmo severity (PS), providing a way to predict PR.…”

“…Developing resistant cultivars is the most viable and effective option to control this disease that has become widespread in all flax production areas of North America and other parts of the world. Resistance to pasmo has a low heritability [3] and is quantitatively inherited [4].…”

“…Phenotypic recurrent selection is typically used to develop cultivars with improved resistance, and selection is usually carried out based on phenotypic assessments of resistance in field conditions [5]. However, field assessment of pasmo severity (PS) in germplasm and breeding lines is costly and, is heavily influenced by the environments due to strong genotype × environment (G × E) interactions [3,4].…”