Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome

Abstract

BackgroundFlax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome.ResultsThe physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding.ConclusionThe first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.

Natural Hypolignification Is Associated with Extensive Oligolignol Accumulation in Flax Stems

“…In addition to providing novel information about the transcriptional regulation of lignification in flax plants, our study suggests that the natural hypolignification of outer stem tissues is associated with the accumulation of a wide range of phenolics. Recently, a number of tools have been developed for flax, including highdensity microarrays, cDNA libraries, physical and genetic maps, molecular markers, and mutant populations, which should allow an integrated approach to investigate different processes in this biologically interesting species (Cloutier et al, 2010;Fénart et al, 2010;Ragupathy et al, 2011;Venglat et al, 2011).…”

Analysis of genetic diversity in Indian and exotic linseed germplasm and identification of trait specific superior accessions

“…The oil extracted from the seeds has unique drying properties having utility in production of paints, inks, varnish and linoleum flooring (Newkirk, 2008;Czemplik 2011). Recently linseed has found application as a functional food owing to high omega-3 alpha linolenic acid content (55-57%) and seed lignans having anti-cancerous properties (Bassett 2009;Ragupathy 2011). Keeping in view of increasing demand of linseed due to numerous health benefits, there is consistent need to increase genetic potential for seed yield.…”

Structural organization of fatty acid desaturase loci in linseed lines with contrasting linolenic acid contents

“…This is in line with the relatively low content of repetitive sequences of the flax genome (Cullis 2005;Ragupathy et al 2011;Wang et al 2012). With one gene every 3.2-4.6 kb, the desaturase loci have a gene density that is approximately twice that of the genome's average, making them gene-rich regions.…”