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SSR-based population structure, molecular diversity and linkage disequilibrium analysis of a collection of flax (Linum usitatissimum L.) varying for mucilage seed-coat content

Abstract

Flax seed mucilage (SM) presents specific biological activities useful for the food and pharmaceutical industries. Understanding the population structure, genetic diversity and linkage disequilibrium (LD) of germplasm varying for mucilage content is pivotal for the identification of genes and quantitative trait loci underlying mucilage variation by association mapping (AM). In this study, 150 microsatellite loci were used to assess the population structure, genetic diversity and LD of a set of 60 flax cultivars/accessions capturing the breadth of SM variation in flax germplasm. STRUCTURE analysis and similarity-based methods revealed the presence of three populations reflecting mainly their geographic origins (South Asia, South America and North America), and the impact of germplasm exchange within and between North American flax breeding programs. Analysis of molecular variance showed that 78.32% of the genetic variation resided within populations and 21.68% among populations. The phi-statistic (Φst) value of 0.22 confirmed the presence of a strong population structure. A total of 408 alleles were detected, with the South American population capturing the highest overall diversity. However, the genetic diversity was narrow, as indicated by the small number of alleles per locus (2.72) and gene diversity (mean = 0.34). LD was significant between 3.9% (r 2) and 36.2% (D′) of the loci pairs (FDR < 0.05). The mean r 2 and D′ were 0.26 and 0.53, respectively. The results suggest that the collection could be useful in AM studies aimed at the discovery of genes/alleles involved in SM; however a greater diversity may be required to improve the AM resolution.

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Acknowledgments

The authors are grateful to Dr. Axel Diederichsen for supplying the germplasm, Hector Urbina for his contribution in SSR sequence analysis and annotation, Andrzej Walichnowski for technical assistance, Mike Shillinglaw for help in the preparation of figures and Joanne Schiavoni for manuscript editing. This research was funded by Agriaquaculture Nutritional Genomics Center, CGNA (R10C1001). We acknowledge INIA for its support providing experimental fields and infrastructure. Braulio Soto-Cerda was supported by Becas Chile—Comisión Nacional de Investigación Científica y Tecnológica (CONICYT).

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Supplementary material 1 (PDF 74 kb)

Supplementary material 2 (PDF 97 kb)

Supplementary material 3 (PDF 69 kb)

11032_2011_9670_MOESM4_ESM.eps

Supplementary material 4 (EPS 850 kb) Online Resource 4 Principal coordinate analysis (PCoA) based on the genetic distance matrix for the 60 flax accessions. Colour assignment is the same as Figure 1b describing the STRUCTURE analysis (blue square = South Asian, red triangle = South American, green circle = North American)

Supplementary material 5 (PDF 57 kb)

11032_2011_9670_MOESM6_ESM.eps

Supplementary material 6 (EPS 761 kb) Online Resource 6 Comparison of number of alleles for the 60 accessions and those captured by the optimum core set of 30 accessions. a Histogram of the allele frequencies for the 150 SSR loci (inner graph corresponds to the box plot of the allele frequencies). b Allele frequencies between the 60 accessions and the optimum core set of flax

11032_2011_9670_MOESM7_ESM.eps

Supplementary material 7 (EPS 819 kb) Online Resource 7 Box plot comparison between the 60 accessions (blue) and the optimum core set (brown). a Major allele frequency. b Number of alleles per locus. c Gene diversity. d Polymorphism information content (PIC) value. e Mucilage content (MIV) value. The box is representative of 50% of the data where the inner cross bar represents the median and the upper plus lower boundaries of the box locate the 75th and 25th percentile of the data set, respectively. Vertical lines indicate the maximum and minimum values of the data set

11032_2011_9670_MOESM8_ESM.eps

Supplementary material 8 (EPS 1301 kb) Online Resource 8 LD heat plots of flax accessions varying for mucilage seed coat content. a The 60 accessions. b The optimum core set. Above the diagonal coloured rectangles represent one LD value (r 2) between a pair of SSR loci. Below the diagonal is the corresponding P value. Coloured bar code for significance threshold levels in both diagonals is shown

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Soto-Cerda, B.J., Maureira-Butler, I., Muñoz, G. et al. SSR-based population structure, molecular diversity and linkage disequilibrium analysis of a collection of flax (Linum usitatissimum L.) varying for mucilage seed-coat content. Mol Breeding 30, 875–888 (2012). https://doi.org/10.1007/s11032-011-9670-y

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Keywords

  • Linum usitatissimum
  • Seed mucilage
  • Population structure
  • Genetic diversity
  • Linkage disequilibrium
  • Flax