Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Abstract

Backgrounds: Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs).Results: 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions: This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.

Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis)

“…In addition to the response to biotic and abiotic stresses, other regulatory elements were also identified in the promoter of these genes, such as Box 4, G-Box, I-box, SP1, AAGAA-motif, AC-I, CAT-box, and RY-element which implies the contribution of these genes in response to light and also expressed in various plant tissues. However, the presence of specific regulatory elements is not the definitive reason for the response of these genes to certain hormones or stresses, thus, the use of laboratory methods such as qRT-PCR is necessary to accurately determine the function of these genes (Hajiahmadi et al 2020).…”

Burden tests can be used to map causal genes for a simple metabolic trait in an exome‐sequenced polyploid mutant population

“…To investigate whether burden tests can be applied to the Cadenza population, we measured the fatty acid composition of lipids in individual M 4 grains (caryopses) from 1188 exome‐sequenced lines using gas chromatography and calculated the proportion of unsaturated fatty acids that are polyunsaturated (ω‐6 desaturation efficiency or ω‐6DE), which is a simple adaptive metabolic trait (Menard et al ., 2017) and a determinant of edible oil quality (Hajiahmadi et al ., 2020). As summarized in Figure 1a, we extracted a list of putative deleterious mutations in the M 2 population (Krasileva et al ., 2017) using BioMart within EnsemblPlants (https://plants.ensembl.org/biomart/martview) and collapsed them by gene and by homoeologous group (triad) (Ramírez‐González et al ., 2018).…”

“…We identified three genes and two triads that are significantly ( P < 0.05) associated with ω‐6DE, after applying Bonferroni correction (Figures 1b,c and S1). The three genes TraesCS6A02G280000 , TraesCS6B02G309400 and TraesCS6D02G260200 form one triad and are predicted to encode homologues of FATTY ACID DESATURASE 2 (FAD2) (Hajiahmadi et al ., 2020). FAD2 is a microsomal ω‐6 fatty acid desaturase that is known to control ω‐6DE in Arabidopsis thaliana seeds (Menard et al ., 2017; Okuley et al ., 1994).…”

“…FAD2 is a microsomal ω‐6 fatty acid desaturase that is known to control ω‐6DE in Arabidopsis thaliana seeds (Menard et al ., 2017; Okuley et al ., 1994). Hexaploid wheat contains eleven putative FAD2 genes (Hajiahmadi et al ., 2020), and TraesCS6A02G280000 ( TaFAD2.1 ), TraesCS6B02G309400 ( TaFAD2.6 ) and TraesCS6D02G260200 ( TaFAD2.8 ) are the most strongly expressed in developing grains of cv. Azhurnava (Figure 1d; Ramírez‐González et al ., 2018).…”