Association mapping analysis of a core collection of flax (Linum usitatissimum L.)

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Soto-Cerda, Braulio
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BMC Plant Biology
Linseed oil (Linum usitatissimum L.) is valued for its food and non-food applications. Although Canada is the world’s largest linseed producer and exporter, linseed remains a minor crop in part because its yield has been stagnating over the last decade compared to other oilseeds. Narrow genetic base, absence of an efficient hybrid production system and limited genomic tools for linseed breeding are the main factors hindering yield and quality improvements. Here, we characterized the Canadian flax core collection of 407 accessions with 448 genome-wide simple sequence repeat markers and, using association mapping (AM), we demonstrated its potential for the improvement of seed quality and agronomic traits. Genetic structure analyses assigned all accessions to two major groups that were weakly differentiated (FST = 0.094). Genetic diversity was abundant in the total panel (5.32 alleles per locus) with weak familial relatedness (mean = 0.287) for most individual pairs. Linkage disequilibrium (LD) decayed relatively quickly with an average genome-wide LD of ~1 cM. AM for seven seed quality traits including oil content (OIL), palmitic acid (PAL), stearic acid (STE), oleic acid (OLE), linoleic acid (LIO), linolenic acid (LIN) and iodine value (IOD) identified nine stable candidate QTL. LIO and LIN QTL co-localized with previously identified QTL and some mapped in the vicinity of genes known to be involved in the fatty acid biosynthesis pathway. AM conducted for nine agronomic traits including yield, bolls per area (BPA), seeds per boll (SPB), thousand seed weight (TSW), start of flowering (FL5%), end of flowering (FL95%), plant height (PH), plant branching (PB) and lodging (LDG) identified twelve significant marker-trait associations for six of the traits. The associated markers explained between 0.5 to 18.5% of the phenotypic variation, with Lu526 and Lu2532 associated with TSW and Lu943 associated with flowering being the most promising for marker-assisted selection. Statistical simulation for five markers associated with TSW indicated that the favorable alleles have additive effects. None of the accessions carried the five favorable alleles but a few breeding lines had four, indicating that further improvement of TSW and yield could be achieved through marker assisted breeding
Association mapping, Linseed, Marker-assisted selection, Molecular breeding
Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types. 13:78