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

Abstract

BackgroundFlax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax.ResultsCombined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (FST = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r2) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species.ConclusionsBased on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.

Pedigrees and genetic base of flax cultivars registered in Canada

“…These results suggest that Canadian flax cultivars have similar backgrounds, a relatively narrow genetic base, and low genetic diversity. This corroborates the results of Soto-Cerda et al (2013a) that show all 31 Canadian cultivars present in a germplasm collection of 407 core collection flax accessions cluster together on the basis of 414 neutral DNA markers. While the entire core collection has 2202 alleles, the Canadian cultivars only have 1081.…”

“…Molecular evaluation via 448 microsatellite markers has demonstrated that the core collection has abundant genetic diversity and a weak population structure, making it suitable for association mapping of agronomic and quality traits in flax (Soto-Cerda et al 2013b). Important agronomic traits such as seed yield, oil content and quality, fiber traits, and disease resistance have been phenotyped at multiple locations and years (unpublished data).…”

Genetic diversity, population structure and association analysis in linseed (Linum usitatissimum L.)

“…Several linear and mixed models have been proposed to correct the population structure and reduce the false positive factors (Pritchard et al 2000;Price et al 2006;Yu et al 2006). Association mapping in linseed have been carried out for various agronomic and seed quality traits (Soto-Cerda et al 2013 using SSR markers. Soto-Cerda et al (2013) identified 12 QTLs for six agronomic traits while 9 QTLs were identified for seed quality traits (Soto-Cerda et al 2014).…”

“…Association mapping in linseed have been carried out for various agronomic and seed quality traits (Soto-Cerda et al 2013 using SSR markers. Soto-Cerda et al (2013) identified 12 QTLs for six agronomic traits while 9 QTLs were identified for seed quality traits (Soto-Cerda et al 2014). In the present investigation only 1 QTL was potentially identified for days to 50% flowering.…”

Analysis of genetic diversity in Indian and exotic linseed germplasm and identification of trait specific superior accessions

“…Later it was introduced into New World (The Americas) after vast spread throughout Asia and Europe (Soto-Cerda 2013). Indian subcontinent near the Mediterranean Sea is known to have high biological diversity of genus (Genesar and Morris, 2003;Fu, 2005;Kaur 2017).…”