In Silico Analyses of Autophagy-Related Genes in Rapeseed (<i>Brassica napus</i> L.) under Different Abiotic Stresses and in Various Tissues

• Main Authors: Elham Mehri Eshkiki, Zahra Hajiahmadi, Amin Abedi, Mojtaba Kordrostami, Cédric Jacquard
• Format: Article
• Language: English
• Published: MDPI AG 2020-10-01
• Series: Plants
• Subjects: codon usage bias; duplication; expression pattern; gene family; gene ontology
• Online Access: https://www.mdpi.com/2223-7747/9/10/1393

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. <i>Brassica napus</i> (<i>B. napus</i>)<i> </i>is among the most important oilseed crops, but <i>ATGs</i> are largely unknown in this species. Therefore, a genome-wide analysis of <i>the B. napus ATG</i> gene family (<i>BnATGs</i>) was performed. One hundred and twenty-seven ATGs were determined due to the <i>B. napus</i> genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in <i>BnATGs</i>. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of <i>B. napus</i> plants. Based on the results, <i>BnATGs</i> are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 <i>BnATGs</i>. In general, 127 simple sequence repeat marker (SSR) loci were also detected in <i>BnATGs</i>. Based on the RNA-seq data, the highest expression in root and silique was related to <i>BnVTI12e</i>, while in shoot and seed, it was <i>BnATG8p</i>. The expression patterns of the most <i>BnATGs</i> were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in <i>B. napus</i>.