Identification of differentially expressed genes involved in amino acid and lipid accumulation of winter turnip rape (Brassica rapa L.) in response to cold stress

Abstract

Winter turnip rape (Brassica rapa L.) is an important overwintering oil crop that is widely planted in northwestern China. It considered to be a good genetic resource for cold-tolerant research because its roots can survive harsh winter conditions. Here, we performed comparative transcriptomics analysis of the roots of two winter turnip rape varieties, Longyou7 (L7, strong cold tolerance) and Tianyou2 (T2, low cold tolerance), under normal condition (CK) and cold stress (CT) condition. A total of 8,366 differentially expressed genes (DEGs) were detected between the two L7 root groups (L7CK_VS_L7CT), and 8,106 DEGs were detected for T2CK_VS_T2CT. Among the DEGs, two ω-3 fatty acid desaturase (FAD3), two delta-9 acyl-lipid desaturase 2 (ADS2), one diacylglycerol kinase (DGK), and one 3-ketoacyl-CoA synthase 2 (KCS2) were differentially expressed in the two varieties and identified to be related to fatty acid synthesis. Four glutamine synthetase cytosolic isozymes (GLN), serine acetyltransferase 1 (SAT1), and serine acetyltransferase 3 (SAT3) were down-regulated under cold stress, while S-adenosylmethionine decarboxylase proenzyme 1 (AMD1) had an up-regulation tendency in response to cold stress in the two samples. Moreover, the delta-1-pyrroline-5-carboxylate synthase (P5CS), δ-ornithine aminotransferase (δ-OAT), alanine-glyoxylate transaminase (AGXT), branched-chain-amino-acid transaminase (ilvE), alpha-aminoadipic semialdehyde synthase (AASS), Tyrosine aminotransferase (TAT) and arginine decarboxylase related to amino acid metabolism were identified in two cultivars variously expressed under cold stress. The above DEGs related to amino acid metabolism were suspected to the reason for amino acids content change. The RNA-seq data were validated by real-time quantitative RT-PCR of 19 randomly selected genes. The findings of our study provide the gene expression profile between two varieties of winter turnip rape, which lay the foundation for a deeper understanding of the highly complex regulatory mechanisms in plants during cold treatment.

Comparative Transcriptome Analysis Revealed the Freezing Tolerance Signaling Events in Winter Rapeseed (Brassica rapa L.)

“…Unfortunately, the molecular mechanisms by which B. rapa adapts to freezing stress remain poorly understood. Several studies have conducted transcriptome analysis of B. rapa under cold stress using a low accuracy B. rapa genome v1.5, v2.0, or v2.5 as the reference genome based on 4°C cold stress transcriptome analysis ( Ma et al, 2019 ; Fang et al, 2021 ). Recently, cold-responsive microRNA and metabolic change under freezing stress (-4°C, 8 h) have been reported as possible mechanisms of B. rapa response to freezing stress ( Xu et al, 2018 ; Zeng et al, 2018 ).…”

Metabolic composition of endophytes contributed to the effect of Brassica rapa L. in improving immunity

“…And it also caused differences in metabolic patterns between PR10 and other three endophytes. PR10 involved in numerous independent metabolic pathway, especially amino acid metabolisms, which may contributed to the speci c amino acid compositions of Brassica rapa L.. Fang et al (Fang et al 2021) reported that under the cold press the amino acids of Brassica rapa L were different from the normal group. suggesting that amino acid metabolism can affect some disease resistance in Brassica rapa L..…”

Transcriptome and Gut Microbiota Profiling Analysis of ANIT-Induced Cholestasis and the Effects of Da-Huang-Xiao-Shi Decoction Intervention

“…Ornithine decarboxylase (ODC) is the rate-limiting enzyme in polyamine biosynthesis that catalyzes ornithine metabolism ( 44 ). These enzymes of serine acetyltransferase 1 (SAT1) convert l- serine to O-acetyl- l- serine and played a vital role in the synthesis and metabolism of glutamate and serine ( 45 ). Interestingly, GSTT3, the largest family of GSTs, is highly expressed in the liver and plays a vital role in hepatotoxicant-induced liver damage, especially individual susceptibility, according to a prebiopsy procedure ( 46 ).…”