Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

Abstract

<jats:title>Abstract</jats:title> <jats:p>Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6,200 SNP markers Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise F st comparison revealed a great degree of divergence ( F st &gt; 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p &lt; 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r= 0.251, 0.349 respectively and p &lt; 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within &lt; 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st &gt; 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree assists to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.</jats:p>

Genome-wide signatures in flax pinpoint to adaptive evolution along its ecological gradient

“…The genetic structure observed in this experiment is consistent with what was establish in previous works, which demonstrated the clustering of accessions attributed to their eco-geographic origin [31,54]. The relatively high differentiation and high concentration of private haplotypes in populations dominated by South Asian accessions may suggest the adaptation of the crop to warm regions [55,56]. This is unlike the cool and/or temperate habitats where flax is widely grown [57].…”

“…This is unlike the cool and/or temperate habitats where flax is widely grown [57]. Flax in this warm South Asian region might also be adapted to short-day photoperiod given that flax accessions from this region differ from the common flax adapted to grow under the long-day seasons of most cooler regions [56,58]. In a similar way, the higher rate of private haplotypes in the Abyssinian population may be attributable to adaptation of the crop to the equatorial re-gion, with equinox effects, elevation-induced cool temperate climate and windstorms [31,59].…”

Rapid transgenerational adaptation in response to intercropping increases facilitation and reduces competition

“…ProSpecieRara ensures the preservation of rare traditional varieties 55 . Furthermore, studies have shown that linseed varieties have higher genetic variability than fiber flax and should therefore be considered as valuable genetic resources 56,57 .…”