Screening and verification of reference genes for analysis of gene expression in winter rapeseed (Brassica rapa L.) under abiotic stress

Ma, Lan; Wu, Junyan; Qi, Weiliang; Coulter, Jeffrey A.; Fang, Yan; Li, Xuecai; Liu, Lijun; Jin, Jiaojiao; Niu, Zaoxia; Yue, Jinli; Sun, Weizheng

doi:10.1371/journal.pone.0236577

Cited by 24 publications

(20 citation statements)

References 52 publications

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“…It is well known that winter B. rapa is widely grown in northern China, and the ecological conditions in this region are cruel. Winter B. rapa is subject to various abiotic adversities throughout the reproductive period, and varieties with strong cold tolerance tend to display other types of abiotic resistanc 26,30 . However, individual genes show opposite results under different abiotic stresses, implying the complexity of the response of winter B. rapa to abiotic stresses.…”

Section: Discussionmentioning

confidence: 99%

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Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

Bai

et al. 2021

Preprint

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Winter Brassica rapa is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. APX plays important roles in response of this plant to abiotic stress and in scavenging free radicals. In this study, 59 DEPs were isolated and identified from winter B. rapa and B. napus using bidirectional electrophoresis, and APX was found to be differentially expressed in these two species. Therefore, the roles of APX proteins in the cold response and superoxide metabolism pathways in both rapeseed species were further investigated. And comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profile in APX gene family. Most of the BrAPX genes were specifically expressed under low temperature stress and behaved significantly differently in cold-tolerant and cold-sensitive varieties. qPCR was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress, and these candidate genes and proteins may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

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Section: Discussionmentioning

confidence: 99%

“…After treatment for 0 h (CK), 3 h and 24 h, the growth cones and leaves were collected according to the method described above 30 .…”

Section: Methodsmentioning

confidence: 99%

Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

Bai

et al. 2021

Preprint

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“…The PCR reactions were run in three technical replicates, as described in [35]. The PCR primers and probes (Table 1) were designed using Primer Express Software v 3.0.1 (Applied Biosystems by Life Technologies, Foster City, CA, USA) to amplify separately the PIP1 and Actin gene [36] as an endogenous reference gene. QuantStudio Design and Analysis Software v. 1.5.0 was used to analyse the data.…”

Section: Osmotic Potentialmentioning

confidence: 99%

Deacclimation of Winter Oilseed Rape—Insight into Physiological Changes

et al. 2020

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Climate changes, which result in the occurrence of periods with relatively high temperatures during the winter, can lead to the deacclimation of cold-hardened plants and cause problems with their winter survival. The aim of these studies was to investigate the physiological changes (photosynthesis and water relations including aquaporin expression) that accompany deacclimation process in the economically important winter oilseed rape plants. The effect of deacclimation on frost tolerance was also estimated for two tested cultivars: semi-dwarf and plants of a normal height. After cold acclimation at 4 °C (compared to the unacclimated control) the typical changes that accompany cold acclimation such as an increase in the content of water-soluble sugars or a lower water content in the leaves, which lead to an increased frost tolerance, were observed. Deacclimation partially or completely reversed these changes, which resulted in a decreased frost tolerance that was accompanied by a decrease in the content of sugars and an increase of the osmotic potential. The chemical composition of the leaves, which was measured using FT-Raman spectroscopy also clearly confirmed the metabolic differences between the cold-acclimated and deacclimated plants. The plants were significantly different in regard to the content of the various pigments as well as fatty acids and polysaccharides. The phenomenon of a deacclimation-induced decrease in aquaporin PIP1 accumulation, which was accompanied by unchanged PIP1 transcript accumulation, will be discussed in the aspects of the water relations and decreased frost tolerance in deacclimated plants.

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“…Leaves and growth cones were sampled at 0 h (CK), 3 h, and 24 h (same photoperiod and light intensity as above) after different abiotic stress treatments, and immediately frozen in liquid nitrogen and stored at −80 °C for further analysis. For each type and duration of stress treatment, three separate pots were used as replicates (Ma et al, 2020).…”

Section: Plant Growth and Cold Treatmentsmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the Ascorbate Peroxidase (APX) Gene Family of Winter Rapeseed (Brassica rapa L.) Under Abiotic Stress

Bai³

et al. 2022

Front. Genet.

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Winter Brassica rapa (B. rapa) is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. Ascorbate peroxidase (APX) plays important roles in the response of this plant to abiotic stress and in scavenging free radicals. In this study, the roles of APX proteins in the cold response and superoxide metabolism pathways in rapeseed species were investigated, and a comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profiles in the APX gene family was conducted. Most BrAPX genes were specifically expressed under cold stress and behaved significantly differently in cold-tolerant and weakly cold-resistant varieties. Quantitative real-time-PCR (qRT-PCR) was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress. The expression of five BrAPX genes was significantly upregulated in growth cones at 3 h of cold stress, while their expression was significantly lower at 24 h than at 3 h. The expression of Bra015403 and Bra003918 was significantly higher in “Longyou-7” growth cones than in other treatments. Five BrAPXs (Bra035235, Bra003918, Bra033040, Bra017120, and Bra031934) were closely associated with abiotic stress responses in B. rapa. These candidate genes may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

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Screening and verification of reference genes for analysis of gene expression in winter rapeseed (Brassica rapa L.) under abiotic stress

Cited by 24 publications

References 52 publications

Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

Deacclimation of Winter Oilseed Rape—Insight into Physiological Changes

Genome-Wide Identification and Analysis of the Ascorbate Peroxidase (APX) Gene Family of Winter Rapeseed (Brassica rapa L.) Under Abiotic Stress

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