Genetic Characterization and Association Mapping of Yield in Flax (Linum usitatissimum L.)

Flax is grown for its seed oil rich in alpha-linolenic acid. Oil production strongly depends on seed yield (SY), a complex trait determined by several yield components (YC). However, the genetic architecture of SY and its YC at the quantitative trait loci (QTL) level for flax breeding remains largely unknown. We utilized a core collection of 407 flax accessions capturing the breadth of the phenotypic diversity of the Plant Gene Resources Canada collection for association mapping. The core collection was assessed using 460 microsatellite markers and the agronomic data for SY, 1000-seed weight (TSW), number of seeds/boll (NSPB) and bolls/m² were obtained from field trials at 2 locations (Saskatoon and Winnipeg, Canada) in 2010 and 2011. The core collection showed abundant genetic diversity (allelic richness = 5.68 alleles/locus) and partitioned into two major groups weakly differentiated (F_ST = 0.09).  Linkage disequilibrium decayed relatively fast (1-1.5 cM, r² = 0.1) at the genome level. Using a mixed linear model (Q + K) a total of 288 significant marker-trait associations were identified, which delineate into 37, 56, 51 and 40 QTL for SY, TSW, NSPB and bolls/m² distributed over all linkage groups. Eight QTL were common for all traits and 27 QTL were common to at least 3 traits in agreement with a positive correlation among them in the range of  r = 0.31-0.99. Our study provides the first insights into QTL controlling SY and YC in flax that will facilitate future cost-effective marker assisted breeding.