Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium

Abstract

BackgroundThe majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation.ResultsEleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings.ConclusionsThe omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0312-5) contains supplementary material, which is available to authorized users.

Genome-wide identification of membrane-bound fatty acid desaturase genes in Gossypium hirsutum and their expressions during abiotic stress

“…Similarly, the over-expression of FAD8 could also alleviate the damage of cold stress35. In this study, GhFAD8.1A was highly expressed implying its potential role in the plant tolerance to low temperature stress, which is consistent with the previous findings33536.…”

“…In most of the plant tissues, fatty acid biosynthesis occurs in the plastids by a successive concatenation of two carbon long units resulting in the formation of 16- or 18-carbon long fatty acids that predominate in the cellular membranes23. They are over 75% unsaturated and play essential roles like regulating plant growth and responding to variance in environmental signals456.…”

“…Gossypium hirsutum L., an allotetraploid species, is one of the most commonly grown cotton species for commercial production4. Originally, it was developed from two ancient diploid cotton species, G. raimondii and G. arboreum , by hybridization and chromosome doubling about 1–2 MYA3. It seems to be an interesting model system not only for the research of genome evolution, but also for studying the roles of polyploid in crop development and domestication with high research value.…”

“…The fatty acid families from G. raimondii and G. arboreum have already been identified and characterized13. In G. hirsutum , Δ12 desaturase ( FAD2 ) and Δ15 desaturase ( FAD3 and FAD7/8 ) have been studied, mainly focused on cold adaptation at seedling stages1237. Furthermore, the FAD2 - 1 was found to be a seed-specific desaturase responsible for the synthesis of polyunsaturated fatty acids in the cottonseeds27, while the FAD2 - 2 had low expression levels throughout the seed development2.…”

Environmental and varietal impact on linseed composition and on oil unidirectional expression process

“…In fact, lots of works indicated a regulation of omega-3 desaturases enzymes dependent on the growth temperature. At low temperature, the transcription of fatty acid desaturase genes (FAD) in various organs are shown to be induced (Soto-Campos et al, 2014;Yurchenko et al, 2014). For protein content, year 2013 is significantly different from years 2011 and 2012.…”