SSR-based population structure, molecular diversity and linkage disequilibrium analysis of a collection of flax (Linum usitatissimum L.) varying for mucilage seed-coat content |
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Authors: | Braulio J. Soto-Cerda Iván Maureira-Butler Gastón Mu?oz Annally Rupayan Sylvie Cloutier |
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Affiliation: | 1. Agriaquaculture Nutritional Genomic Center, CGNA (R10C1001), Genomics and Bioinformatics Unit, INIA, Km. 10 Camino Caj??n??Vilc??n, Temuco, Chile 2. Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada 3. Centro de Biotecnolog??a del Gran Concepci??n, Facultad de Ciencias Biol??gicas, Universidad Andr??s Bello, Sede Concepci??n, Autopista Concepci??n, 7100, Talcahuano, Chile
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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 (??st) 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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