title: Structural organization of fatty acid desaturase loci in linseed lines with contrasting linolenic acid contents.
abstract: 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.
authors.affiliation: Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada.
authors.forename: Dinushika
authors.initials: D
authors.lastname: Thambugala
authors.affiliation: Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada.
authors.forename: Raja
authors.initials: R
authors.lastname: Ragupathy
authors.affiliation: Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada. Sylvie.J.Cloutier@agr.gc.ca.|Ottawa Research and Development Centre, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada. Sylvie.J.Cloutier@agr.gc.ca.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Cloutier
mesh_terms: D044943:Fatty Acid Desaturases / Q000235:genetics* / Q000378:metabolism; D019597:Flax / Q000235:genetics* / Q000378:metabolism; D018745:Genome, Plant; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D056916:Segmental Duplications, Genomic / Q000235:genetics; D017962:alpha-Linolenic Acid / Q000235:genetics* / Q000378:metabolism
chemical_list: D017962:alpha-Linolenic Acid; D044943:Fatty Acid Desaturases
keywords: Bacterial artificial chromosome; Fatty acid desaturase; Flax; Genome organization; Linolenic acid; Structural genomics