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

Content Provider	Springer Nature Link
Author	Thambugala, Dinushika Ragupathy, Raja Cloutier, Sylvie
Copyright Year	2016
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.
Starting Page	429
Ending Page	439
Page Count	11
File Format	PDF
ISSN	1438793X
Journal	Functional & Integrative Genomics
Volume Number	16
Issue Number	4
e-ISSN	14387948
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2016-05-03
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Flax Genome organization Structural genomics Fatty acid desaturase Bacterial artificial chromosome Linolenic acid Cell Biology Plant Genetics & Genomics Microbial Genetics and Genomics Biochemistry Bioinformatics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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