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

Authors: HOQUE, AHASANUL - North Dakota State University; Fiedler, Jason; RAHMAN, MUKHLESUR - North Dakota State University

Submitted to: BMC Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2020
Publication Date: 8/14/2020
Citation: Hoque, A., Fiedler, J.D., Rahman, M. 2020. Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection. BMC Genetics. 21:557. https://doi.org/10.1186/s12864-020-06922-2.
DOI: https://doi.org/10.1186/s12864-020-06922-2

Interpretive Summary: Flax is an important oilseed crop used for human nutrition and industrial processes. To meet the yield and quality demands of the flax market in the future, molecular breeding tools are required to accelerate the breeding to develop new cultivars. In this study, we began to develop these tools by characterizing the genetic diversity of a global germplasm panel that is available to the North Dakota State University breeding program. We evaluated diversity metrics, identified sub-population structures in these lines, and characterized the relatedness of the lines in one sub-population vs another. Sub-population designations are largely grouped with geographical origin and lines with a sub-population are relatively related to each other. This information is useful for researchers to establish trait mapping populations and is useful for breeders because it has highlighted the most advantageous crosses to increase genetic gain.

Technical Abstract: 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 Fst comparison revealed a great degree of divergence (Fst > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 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 < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 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 (Fst > 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.