Whole-Genome Resequencing of Early Flowering (epi) Mutant Lines from Flax (Linum usitatissimum) Cultivar ‘Royal’ Induced Using a Hypomethylating Agent 5-azacytidine

Flowering time is a complex trait, an estimated 306 genes condition photoperiod, ambient temperature, vernalization, aging, circadian clock, hormonal, sugar and autonomous pathways (Bouche et al. 2015). Three early flowering lines including RE2 were developed from the flax cultivar ‘Royal’ using the DNA demethylating agent 5-azacytidine (Fieldes and Amyot 1999). Whole genome resequencing of ‘Royal’ and its three derivatives was done to characterize SNPs in the mutants including the gene space known to be involved in flowering time to identify diagnostic markers to develop early maturing cultivars for the Canadian prairies. Illumina paired-end sequencing yielded ~129 million processed reads which were mapped against the flax reference genome (Wang et al. 2012). The average coverage is 15.4X and a total of 160,547 SNPs were called using GATK unified genotyper. RE2, the least photo-sensitive line of the early flowering derivatives of Royal (Sun, 2015), exhibited 5,188 homozygous SNPs distributed on the 15 chromosomes. A total of 880 SNPs were inside protein coding genes, 12 of which were associated with flowering pathways. Interestingly, a SNP was identified in the flax gene Lus10002974, an orthologue of Arabidopsis PHOTOPERIOD-INDEPENDENT EARLY FLOWERING-1 (PIE; AT3G12810), encoding a major chromatin remodeling protein associated with epigenetic regulation. Positional, as well as functional, impact of these SNPs will be presented.

References:

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Fieldes, M. A. and Amyot, L. M. (1999) J. Heredity, 90:199-206.

Jia Sun. M.Sc. Thesis (2015) Department of Plant Sciences, University of Saskatchewan, 113p.

Wang et al. (2012) Plant J. 72:461-473.