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Abstract <p>Oxidative stress is a complex chemical and physiological phenomenon caused by biotic and abiotic stresses in plants, which is the result of the excess reactive oxygen species (ROS). Therefore, maintaining the basal level of ROS is essential for the cell. In plant cells, ROS production is carefully controlled through enzymatic antioxidant defense systems. Superoxide dismutase (SOD) is one of the essential enzymes in the plant antioxidant defense system response to ROS produced by oxidative stress. Due to the important role of SODs in the response of plants to abiotic stresses, the evolutionary and functional study of this gene family can play an important role in the use of these genes in <i>Brassica napus</i> breeding programs. In this study 30 genes encoding SODs were identified, which based on the phylogenetic tree, belong to three groups, including Cu/ZnSOD (14 genes), FeSOD (10 genes), and MnSOD (6 genes). Segmental duplication and polyploidy were the main factors in the expansion of this family, and all genes evolved under negative selection. The in silico analysis of the SOD gene promoters revealed the presence of 73 type <i>cis</i>-elements associated with site-binding, light, tissue and development, stresses, hormones, and unknown function. The most abundant regulatory element was related to MYB with a frequency of 141, which was identified in 30 <i>BnSOD</i> genes. On the other hand, the post-transcriptional regulation of 11 SOD genes is affected by miRNA molecules. Codon usage bias analysis indicated the low bias of <i>BnSOD</i> genes and their preference for A/T ending codons. Based on RNA-seq results, <i>BnSODs</i> expression in distinct tissues (roots, stems, leaves, flowers, seeds, and silique) of <i>B. napus</i> is dynamic, and some of them showed tissue-specific expression while some genes have similar expression patterns in tissues. The expression pattern of some <i>BnSOD</i> genes in response to salinity and cadmium stress by qRT-PCR showed that the expression of <i>BnMSD1</i> and <i>BnFSD1</i>/6 genes are induced in response to these stresses. The results indicated that <i>BnSODs</i> may have various functions in <i>B. napus</i> tissues and <i>BnMSD1</i> and <i>BnFSD1/</i>6 were identified as promising candidate genes for developing abiotic stress-tolerant <i>B. napus</i>.</p>

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Systematic Study of the SOD Genes in Allotetraploid Rapeseed: Genome Wide Identification, Molecular Evolution, Codon Usage Bias, and Expression Profiling

  • 期刊论文

  • 发表日期：

    2026年8月2日

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  • M. Kanani Sarcheshmeh,
  • A. Aalami,
  • A. Abedi

摘要

Abstract

Oxidative stress is a complex chemical and physiological phenomenon caused by biotic and abiotic stresses in plants, which is the result of the excess reactive oxygen species (ROS). Therefore, maintaining the basal level of ROS is essential for the cell. In plant cells, ROS production is carefully controlled through enzymatic antioxidant defense systems. Superoxide dismutase (SOD) is one of the essential enzymes in the plant antioxidant defense system response to ROS produced by oxidative stress. Due to the important role of SODs in the response of plants to abiotic stresses, the evolutionary and functional study of this gene family can play an important role in the use of these genes in Brassica napus breeding programs. In this study 30 genes encoding SODs were identified, which based on the phylogenetic tree, belong to three groups, including Cu/ZnSOD (14 genes), FeSOD (10 genes), and MnSOD (6 genes). Segmental duplication and polyploidy were the main factors in the expansion of this family, and all genes evolved under negative selection. The in silico analysis of the SOD gene promoters revealed the presence of 73 type cis-elements associated with site-binding, light, tissue and development, stresses, hormones, and unknown function. The most abundant regulatory element was related to MYB with a frequency of 141, which was identified in 30 BnSOD genes. On the other hand, the post-transcriptional regulation of 11 SOD genes is affected by miRNA molecules. Codon usage bias analysis indicated the low bias of BnSOD genes and their preference for A/T ending codons. Based on RNA-seq results, BnSODs expression in distinct tissues (roots, stems, leaves, flowers, seeds, and silique) of B. napus is dynamic, and some of them showed tissue-specific expression while some genes have similar expression patterns in tissues. The expression pattern of some BnSOD genes in response to salinity and cadmium stress by qRT-PCR showed that the expression of BnMSD1 and BnFSD1/6 genes are induced in response to these stresses. The results indicated that BnSODs may have various functions in B. napus tissues and BnMSD1 and BnFSD1/6 were identified as promising candidate genes for developing abiotic stress-tolerant B. napus.