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

Feng, Jijun; Dong, Yuchen; Liu, Wei; He, Qiuling; Daud, M. K.; Chen, Jinhong; Zhu, Shuijin

doi:10.1038/srep45711

Cited by 40 publications

(36 citation statements)

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“…To date, the FAD gene family has been identified and characterized in many plants, including 17 FADs in Arabidopsis [21], 29 in soybean [28], 31 in peanut [29], and 41 in Raymond cotton [30]. FAD genes have also been isolated from land cotton [31], sesame [32], sunflower [33] and other plants.…”

Section: Discussionmentioning

confidence: 99%

Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data

Zhao

Wang

et al. 2020

BMC Genomics

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Background: Walnut kernels contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids for humans and have important effects on growth and health. The main function of fatty acid desaturase (FAD), which is widely distributed in organisms, is to remove hydrogen from carbon chains in the biosynthesis of unsaturated fatty acids to generate C=C bonds.Results: By performing a series of bioinformatics analysis, 24 members of the JrFAD gene family were identified from the genome database of walnut, and then compared with the homologous genes from Arabidopsis. Phylogenetic analysis showed that JrFADs were classified into four subfamilies: the SAD desaturase subfamily, Δ7/Δ9 desaturase subfamily, Δ12/ω-3 desaturase subfamily and "front-end" desaturase subfamily. Meanwhile, the expression of fatty acid synthesis genes in walnut kernels at different developmental stages was analysed by transcriptome sequencing, with expression of JrFAD3-1, which encodes an enzyme involved in linolenic acid synthesis, being particularly prominent. The relative expression level of JrFAD3-1 changed dramatically with the kernel development stages and exhibited a Bell-Shaped Curve. A significant positive correlation was observed between the expression of JrFAD3-1 during 70-100 DAF (Days after flowering) and the content of alpha-linolenic acid during 100-130 DAF, with a correlation coefficient of 0.991. Additionally, JrFAD3-1 was proved closely related to homologous genes in Betula pendula and Corylus heterophylla, indicating that the conserved structure of FADs is consistent with classical plant taxonomy.Conclusion: Twenty-four members JrFADs in walnut were identified and classified into four subfamilies. JrFAD3-1 may play significant roles in the biosynthesis of polyunsaturated fatty acids in walnut.

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Section: Discussionmentioning

confidence: 99%

Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data

Zhao

Wang

et al. 2020

BMC Genomics

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“…In an upland cotton ( Gossypium hirsutum L.) study, 39 full-length FAD genes, based on database searches, were identified in tetraploid and were phylogenetically clustered into four subfamilies. Genomic localization revealed that 34 genes were mapped on 22 chromosomes, and five genes were positioned on the scaffold sequences [ 91 ].…”

Section: Discussionmentioning

confidence: 99%

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

Góralska

Bińkowski

Lenarczyk

et al. 2020

IJMS

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The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.

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“…This diversification is enabled by the presence of multigene families; whereas the Arabidopsis genome carries only one copy of AtFAD2, comparative analysis of other species reveals that many plant genomes carry multiple FAD2 homologs. For example, soybean has seven FAD2 gene family members (Lakhssassi et al, 2017), cotton has nine (Feng et al, 2017), safflower has 11 (Cao et al, 2013), and parsley (Petroselinum crispum) and carrot (Daucus carota ssp. sativus) have 17 and 24, respectively, the highest number of family members documented so far, indicating that functional divergence of FAD2 is not limited to oil seed crops (Somssich et al, 1989;Busta et al, 2018).…”

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confidence: 99%

“…In addition to encoding catalytic diversity, FAD2 homologs also show diversity in their expression patterns. While some FAD2 genes are targeted to the seeds, others are ubiquitous or specific to other organs; for example, transcript profiling of the FAD2 gene family in cotton and safflower revealed that developing seeds, roots, stems, and leaves expressed overlapping but distinct sets of FAD2 homologs (Cao et al, 2013;Feng et al, 2017). In addition, different members of the FAD2 family in soybean varied in their responsiveness to chilling and salinity (Feng et al, 2017), two abiotic stresses known to upregulate FAD2 expression (Wang et al, 2004;Kargiotidou et al, 2008;Teixeira et al, 2009;Zhang et al, 2012).…”

mentioning

confidence: 99%

“…While some FAD2 genes are targeted to the seeds, others are ubiquitous or specific to other organs; for example, transcript profiling of the FAD2 gene family in cotton and safflower revealed that developing seeds, roots, stems, and leaves expressed overlapping but distinct sets of FAD2 homologs (Cao et al, 2013;Feng et al, 2017). In addition, different members of the FAD2 family in soybean varied in their responsiveness to chilling and salinity (Feng et al, 2017), two abiotic stresses known to upregulate FAD2 expression (Wang et al, 2004;Kargiotidou et al, 2008;Teixeira et al, 2009;Zhang et al, 2012). In other species, some FAD2 genes are upregulated by biotic stresses, including viroid infection (Gadea et al, 1996), fungal infection (Wang et al, 2004), or application of fungal elicitors (Kirsch et al, 1997;Cahoon et al, 2003).…”

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confidence: 99%

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The FATTY ACID DESATURASE2 Family in Tomato Contributes to Primary Metabolism and Stress Responses

Lee

Padilla

Gupta³

et al. 2019

Plant Physiol.

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The conversion of oleic acid (C18:1) to linoleic acid (C18:2) in the endoplasmic reticulum is critical to the accumulation of polyunsaturated fatty acids in seeds and other tissues, and this reaction is catalyzed by a D12-desaturase, FATTY ACID DESATURASE2 (FAD2). Here, we report that the tomato (Solanum lycopersicum) genome harbors two genes, SlFAD2-1 and SlFAD2-2, which encode proteins with in vitro D12-desaturase activity. In addition, tomato has seven divergent FAD2 members that lack D12-desaturase activity and differ from canonical FAD2 enzymes at multiple amino acid positions important to enzyme function. Whereas SlFAD2-1 and SlFAD2-2 are downregulated by biotic stress, the majority of divergent FAD2 genes in tomato are upregulated by one or more stresses. In particular, SlFAD2-7 is induced by the potato aphid (Macrosiphum euphorbiae) and has elevated constitutive expression levels in suppressor of prosystemin-mediated responses2 (spr2), a tomato mutant with enhanced aphid resistance and altered fatty acid profiles. Virus-induced gene silencing of SlFAD2-7 in spr2 results in significant increases in aphid population growth, indicating that a divergent FAD2 gene contributes to aphid resistance in this genotype. Thus, the FAD2 gene family in tomato is important both to primary fatty acid metabolism and to responses to biotic stress.

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

Cited by 40 publications

References 50 publications

Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data

Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

The FATTY ACID DESATURASE2 Family in Tomato Contributes to Primary Metabolism and Stress Responses

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