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

ABSTRACT: The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. 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 B. napus plants. Based on the results, BnATGs 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 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs 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 B. napus.

SUBMITTER: Eshkiki EM

PROVIDER: S-EPMC7594038 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundHigh-affinity nitrate transporter 2 (NRT2) genes have been implicated in nitrate absorption and remobilization under nitrogen (N) starvation stress in many plant species, yet little is known about this gene family respond to various stresses often occurs in the production of rapeseed (Brassica napus L.).ResultsThis report details identification of 17 NRT2 gene family members in rapeseed, as well as, assessment of their expression profiles using RNA-seq analysis and qRT-PCR assays. In this study, all BnNRT2.1 members, BnNRT2.2a and BnNRT2.4a were specifically expressed in root tissues, while BnNRT2.7a and BnNRT2.7b were mainly expressed in aerial parts, including as the predominantly expressed NRT2 genes detected in seeds. This pattern of shoot NRT expression, along with homology to an Arabidopsis NRT expressed in seeds, strongly suggests that both BnNRT2.7 genes play roles in seed nitrate accumulation. Another rapeseed NRT, BnNRT2.5 s, exhibited intermediate expression, with transcripts detected in both shoot and root tissues. Functionality of BnNRT2s genes was further outlined by testing for adaptive responses in expression to exposure to a series of environmental stresses, including N, phosphorus (P) or potassium (K) deficiency, waterlogging and drought. In these tests, most NRT2 gene members were up-regulated by N starvation and restricted by the other stresses tested herein. In contrast to this overall trend, transcription of BnNRT2.1a was up-regulated under waterlogging and K deficiency stress, and BnNRT2.5 s was up-regulated in roots subjected to waterlogging. Furthermore, the mRNA levels of BnNRT2.7 s were enhanced under both waterlogging stress and P or K deficiency conditions. These results suggest that these three BnNRT2 genes might participate in crosstalk among different stress response pathways.ConclusionsThe results presented here outline a diverse set of NRT2 genes present in the rapeseed genome that collectively carry out specific functions throughout rapeseed development, while also responding not just to N deficiency, but also to several other stresses. Targeting of individual BnNRT2 members that coordinate rapeseed nitrate uptake and transport in response to cues from multiple stress response pathways could significantly expand the genetic resources available for improving rapeseed resistance to environmental stresses.

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

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