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.
Highlights
The 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
Two of the genes encode FAD3-type enzymes localized in the endoplasmic reticulum (ER) (FAD3-1 and FAD3-2) and three genes encode FAD7/ 8-type enzymes in the chloroplast (FAD7/8-1, FAD7/8-2, FAD7/8-3) (Figure 1; only the encoded polypeptide sequences from G. raimondii are shown for clarity)
Five omega-3 fatty acid desaturase (FAD)-type genes were identified in cotton, two of which encode ER-localized enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2 and FAD7/8-3) (Table 1; Figure 1)
Summary
The 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 perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. G. hirsutum (the source of upland cotton) was subsequently domesticated for fiber production in the last few thousand years in the New World, and as such, is an interesting model system for use in the study of genome evolution, and for studying the role of polyploidy in crop development and domestication [6]. Development of upland cotton varieties with improved tolerance to low temperature stress could improve the agronomic performance of the crop and thereby significantly impact the cotton industry [12,14]
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