Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax ( Linum usitatissimum L.)

• Published in: International journal of molecular sciences Vol. 23; no. 9; p. 4960
• Main Authors: You, Frank M, Rashid, Khalid Y, Zheng, Chunfang, Khan, Nadeem, Li, Pingchuan, Xiao, Jin, He, Liqiang, Yao, Zhen, Cloutier, Sylvie
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 29-04-2022; MDPI
• Subjects: Alleles; Barley; Binding sites; Breeding; Chromosome 5; Chromosomes; Cloning; core collection; Crop diseases; Defoliation; Disease Resistance - genetics; Erysiphe; Flax; Flax - genetics; Fungi; Genes; Genes, Plant; genome-wide associate study (GWAS); Genome-wide association studies; Genome-Wide Association Study - methods; Genomes; genomic prediction (GP); Genomics; Haplotypes; Interleukin 1; Kinases; Linum usitatissimum; Mathematical models; Nucleotides; Oidium lini; Pathogens; Phenotypes; Plant Breeding - methods; Plant diseases; Plant Diseases - genetics; Plant Diseases - microbiology; Plant resistance; Powdery mildew; powdery mildew (PM) resistance; Protein kinase; Proteins; Quantitative genetics; Quantitative trait loci; quantitative trait loci (QTL); quantitative trait nucleotides (QTNs); Ratings & rankings; Reproducibility of Results; Single-nucleotide polymorphism; Statistical analysis; Statistical models; Wheat; core collection; quantitative trait nucleotides (QTNs); quantitative trait loci (QTL); flax; genomic prediction (GP); genome-wide associate study (GWAS); Linum usitatissimum L; powdery mildew (PM) resistance
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms23094960

Powdery mildew (PM), caused by the fungus
in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (
) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010-2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (
= 10-30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (
= 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (
= 0.93) than those constructed using the 247,160 genome-wide random SNP (
= 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4-5.6 Mb and 9.4-16.9 Mb) and 13 (4.7-5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.