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.
Highlights
Flax (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
In 2009, the Total Utilization Flax GENomics (TUFGEN; http://www.tufgen.ca) project was initiated in Canada to generate genomics resources for flax and to develop a comprehensive knowledge of its unique genome with specific goals in applied genomics aiming at the improvement of flax as a total utilization crop
A total of 43,776 bacterial artificial chromosomes (BAC) clones from the library of the flax cultivar CDC Bethune was used to construct the first genome-wide physical map and to generate BAC-end sequences (BES), annotation of which unearthed the uniqueness of the flax genome
Summary
Flax (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. 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. Flax (Linum usitatissimum L.) was domesticated for its seed oil and stem fibres nearly 7,000 years ago, during the Neolithic period [1]. Is considered the wild progenitor of cultivated flax, Linum usitatissimum L. The latter is a self pollinated diploid species with a chromosome number of 2n = 30 [4]. Flax nuclear DNA with ~35% highly repetitive tandemly arrayed sequences, ~15% middle repetitive fraction and ~50% low-copy number fraction is reported to be somewhat different from other plant genomes characterized to date [7]. A high-density microarray platform was recently developed which is suitable for analyzing differential gene expression of biologically relevant samples [12]
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