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Whole-genome mining and in silico analysis of FAD gene family in Brassica juncea

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Abstract

Brassica juncea is one of important oilseed crops, and FA compositions determine quality of vegetable oil. Although fatty acid desaturases (FADs) are mainly responsible for modifying seed FA compositions, genome-wide analysis of FAD gene family in B. juncea (BjuFAD) is not reported. Here, we identified 57 BjuFAD genes in B. juncea genome using homology searches. These FAD genes were unevenly distributed in 16 chromosomes and 3 scaffolds. Phylogenetic analysis showed that BjuFAD genes were divided into seven subfamilies. Exon–intron organizations, intron patterns and MEME motifs were highly conserved within each of BjuFAD subfamilies. Moreover, subcellular locations of deduced BjuFAD proteins and cis-acting elements in BjuFAD promoters were predicted and analyzed using online software. In addition, 16 SSR loci were totally found in BjuFAD genes/promoters. This work provides a basis for further function study of BjuFAD genes in quality improvement of B. juncea seed oil and in plant development as well as stress response.

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Fig. 1

Abbreviations

FA:

Fatty acid

FAD:

Fatty acid desaturase

MEME:

Multiple expectation maximization for motif elicitation

NJ:

Neighbour-joining

SSR:

Simple sequence repeats

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Acknowledgements

This work was supported by National Key R&D Program of China (2016YFD0100506), Chongqing Research Program of Basic Research and Frontier Technology (cstc2015jcyjBX0143), National Natural Science Foundation of China (31871549), “111” Project of China (B12006).

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Author notes

  1. Yufei Xue, Chengyan Chai and Baojun Chen contributed equally to this work.

Authors and Affiliations

  1. College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China

    Yufei Xue, Chengyan Chai, Baojun Chen, Xiaofeng Shi, Bitao Wang, Fanrong Mei, Manlin Jiang, Xueli Liao, Xia Yang, Chenglong Yuan, Lin Zhang & Yourong Chai

  2. Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China

    Yufei Xue, Baojun Chen, Xiaofeng Shi, Bitao Wang, Fanrong Mei, Manlin Jiang, Xueli Liao, Xia Yang, Chenglong Yuan, Lin Zhang & Yourong Chai

  3. Chongqing Rapeseed Engineering Research Center, Southwest University, Chongqing, 400715, China

    Yufei Xue, Chengyan Chai, Baojun Chen, Xiaofeng Shi, Bitao Wang, Fanrong Mei, Manlin Jiang, Xueli Liao, Xia Yang, Chenglong Yuan, Lin Zhang & Yourong Chai

  4. Chongqing Key Laboratory of Crop Quality Improvement, Southwest University, Chongqing, 400715, China

    Yufei Xue, Chengyan Chai, Baojun Chen, Xiaofeng Shi, Bitao Wang, Fanrong Mei, Manlin Jiang, Xueli Liao, Xia Yang, Chenglong Yuan, Lin Zhang & Yourong Chai

  5. Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Chongqing, 400715, China

    Yufei Xue, Chengyan Chai, Baojun Chen, Xiaofeng Shi, Bitao Wang, Fanrong Mei, Manlin Jiang, Xueli Liao, Xia Yang, Chenglong Yuan, Lin Zhang & Yourong Chai

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  1. Yufei Xue
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Correspondence to Yourong Chai.

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Xue, Y., Chai, C., Chen, B. et al. Whole-genome mining and in silico analysis of FAD gene family in Brassica juncea. J. Plant Biochem. Biotechnol. 29, 149–154 (2020). https://doi.org/10.1007/s13562-019-00516-0

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