Decoding Flax Genome for Structural Genomics and Functional Insights into Yield Genes

Flax (Linum usitatissimum) is among the world's earliest domesticated and important crop plants contributing fibre, oil and health promoting products. It is a diploid plant (n=15 chromosomes) with estimated nuclear DNA content C=373 Mb. For accelerating gene discovery and enrichment of genomic resources, whole-genome shotgun sequencing was performed to develop an integrated, ordered physical and functional sequence resource that describes flax gene-space in a structured whole-genome context.  The de novo assembly represents deep-coverage (94× raw/69× filtered) short-sequence reads that covered 302Mb of non-redundant sequence representing 81% genome coverage. Projection of complementary DNA sequence onto deep whole-genome sequence framework supports 43,384 protein-coding genes with 86% homology with Arabidopsis. Up to 93% of published flax ESTs aligned to predicted genes, indicating excellent coverage and accuracy at gene level. Whole genome sequence of flax was used to identify and characterize one of the intrinsic yield genes, bri1 (Brassinosteroid insensitive 1) involved in fibre development of diverse plant species. Identified flax bri1 (Lubri1) is 3735 bp and 5’ RACE combined with sequence confirmation of genomic fragment revealed presence of three introns in the coding sequence. Functionality of GFP tagged Lubri1 has been determined by complementation of Arabidopsis (bri1-301/bri1 null) and localization studies showed it is targeted to plasma membrane. Since, At-BRI1 (At4g39400) is intron-less, the evolutionary and functional implication of intron retention in Lubri1 is investigated. Flax transformation with LuBRI1 is in progress to assess function of Lubri1 in fibre development. Our goal is to apply genome-assisted research to enhance fibre production in flax.