Genome-wide association studies for pasmo resistance in flax (Linum usitatissimum L.)

Citation

He, L., Xiao, J., Rashid, K.Y., Yao, Z., Li, P., Jia, G., Wang, X., Cloutier, S., You, F.M. (2019). Genome-wide association studies for pasmo resistance in flax (Linum usitatissimum L.). Frontiers in Plant Science, [online] 9 http://dx.doi.org/10.3389/fpls.2018.01982

Plain language summary

Flax is a dual-purpose crop that provides many resources for human production including linin and linseed oil. The pasmo fungal disease causes major losses in flax yield. Identification of the genetic regions associated with pasmo resistance will facilitate combating against the disease. Field pasmo resistance data obtained from five individual years and large number of genotyping-by-sequencing molecular markers were used for this study and 500 genomic regions, called quantitative trait loci (QTL) associated with pasmo resistance variation have been identified. Of these 500 regions, 67 had a large effects that explained up to 64% of the total variation for pasmo resistance in the data. The genomic regions are shown to have an additive effect with pasmo resistance. The results suggested that the 67 large effect regions are most suited for market-assisted selection and all 500 regions are effective for the genomic prediction of pasmo resistance breeding.

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 × 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 QTL with positive-effect or favorite alleles (NPQTL) in accessions was significantly correlated with PR (R 2 = 0.55), suggesting that these QTL effects are mainly additive. NPQTL was also significantly associated with morphotype (R 2 = 0.52) and major QTL with positive effect alleles 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.

Publication date

2019-01-14