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


Thambugala D, Ragupathy R, Cloutier S (2016) Structural organization of fatty acid desaturase loci in linseed lines with contrasting linolenic acid contents. Funct Integr Genomics 16:429-439

Plain language summary

Flax is the richest plant source of omega-3 fatty acids because 50-60% of its oil is linolenic acid, a highly unsaturated fat. The fatty acid composition of linseed depends greatly on the activity of fatty acid desaturase enzymes which are encoded by three pairs of genes: sad1, sad2, fad2a, fad2b, fad3a and fad3b. First, SAD1 and SAD2 use the saturated oil molecule called stearic acid as a substrate and perform a first desaturation step to produce oleic acid, a monounsaturated fat. Oleic acid is further desaturated by the action of FAD2A and FAD2B to form linoleic acid which, in turn, will be desaturated into linolenic acid by FAD3A and FAD3B, both polyunsaturated fats. Here, we looked at the structural organization of these genes in the genome of flax varieties with high and moderate linolenic acid content. These loci had a higher than average gene content and desaturase genes co-located with other genes involved in lipid and sugar metabolisms. The fad2b region harbors seven copies of the gene in both varieties. This may explains why it is possible to produce low linolenic acid linseed by knocking off the single fad3a and fad3b genes but it has not been possible to produce a true low linoleic/low linolenic acid variety.


© 2016, Her Majesty the Queen in Right of Canada as represented by: Minister of Agriculture. Flax (Linum usitatissimum L.), the richest crop source of omega-3 fatty acids (FAs), is a diploid plant with an estimated genome size of ~370 Mb and is well suited for studying genomic organization of agronomically important traits. In this study, 12 bacterial artificial chromosome clones harbouring the six FA desaturase loci sad1, sad2, fad2a, fad2b, fad3a and fad3b from the conventional variety CDC Bethune and the high linolenic acid line M5791 were sequenced, analysed and compared to determine the structural organization of these loci and to gain insights into the genetic mechanisms underlying FA composition in flax. With one gene every 3.2–4.6 kb, the desaturase loci have a higher gene density than the genome’s average of one gene per 7.8–8.2 kb. The gene order and orientation across the two genotypes were generally conserved with the exception of the sad1 locus that was predicted to have additional genes in CDC Bethune. High sequence conservation in both genic and intergenic regions of the sad and fad2b loci contrasted with the significant level of variation of the fad2a and fad3 loci, with SNPs being the most frequently observed mutation type. The fad2a locus had 297 SNPs and 36 indels over ~95 kb contrasting with the fad2b locus that had a mere seven SNPs and four indels in ~110 kb. Annotation of the gene-rich loci revealed other genes of known role in lipid or carbohydrate metabolic/catabolic pathways. The organization of the fad2b locus was particularly complex with seven copies of the fad2b gene in both genotypes. The presence of Gypsy, Copia, MITE, Mutator, hAT and other novel repeat elements at the desaturase loci was similar to that of the whole genome. This structural genomic analysis provided some insights into the genomic organization and composition of the main desaturase loci of linseed and of their complex evolution through both tandem and whole genome duplications.