Overview
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Key numbers
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- Gong et al. BMC Plant Biology (2022) 22:425
- cantly affected by flooding; however, stomatal conductance was altered considerably 0–5 days after flooding, and the
- net photosynthesis rate changed substantially 5–10 days after flooding. In addition, the root activity of waterlogging-
- tolerant varieties was substantially higher after flooding for 10 days than that of the control. This implies that the effect
- the 20 selected DEGs, including genes such as mitogen-activated protein kinase 3 (MPK3) and calcium-binding protein 4
- (CML4), approximately 80% of the gene expression patterns were consistent with our RNA-seq dataset.
- *Correspondence: zhanfengsong_saas@163.com
- © The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
- licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
- mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
- Gong et al. BMC Plant Biology (2022) 22:425 Page 2 of 18
- ment, yield, and quality (1, 2). Waterlogging damage to waterlogged seedlings with benzyladenine relieved most
- ucts in the root system. More so, waterlogging results revealed that 1-aminocyclopropane-1-carboxylic acid,
- stress reactions. Hypoxia causes a breakdown in the equi- transcripts (20, 21). Micro RNAs may also be involved
- ing, and accumulation of free radicals, which damages root length (22). However, research on the molecular
- membrane permeability (3, 4). waterlogging has been scanty. In this study, RNA-seq was
- world after tomato (6, 7). More so, it is the principal spice additional functional, physiological, and biochemical
- all vegetables (8). Furthermore, peppers are a source of ance in pepper, which is necessary for the development of
- both of which have high growth potential (9–11). Results
- cial pepper production. Pepper is a shallow-rooted plant waterlogging-sensitive “Chuan Teng No.6” (S) hot pep-
- making it ideal for growing in dry climates (7). Pepper is No.10” (T) variety. The phenotypic differences between
- considerably affects the yield and quality of the grown S was nearly 50% after a waterlogging treatment of 10
- Gong et al. BMC Plant Biology (2022) 22:425 Page 3 of 18
- d, whereas the leaf wilting rate of T was approximately The findings revealed that an average of 92.9% of reads
- 10%; therefore, the waterlogging tolerance properties of were mapped to the reference genome (Table S4). Of
- ent (Fig. 1A). Statistical analysis of plant weight follow- introns, and 23% to intergenic regions (Table S5). Fol-
- increased at 5 days after treatment (dat) but decreased 40,540 known genes and 5,204 novel genes were obtained
- at10 dat. T, in contrast, was less affected by waterlogging, and used in computing the fragment per kilobase of tran-
- rate than T at 5 dat, although the weight of S decreased as Differentially expressed genes (DEGs)
- a result of wilting at 10 dat. Conversely, the growth rate between waterlogging‑sensitive and ‑tolerant varieties
- of T was lower at 10 dat than at 5 dat, but its weight still A core set of DEGs at the three time points of the water-
- showed a gradual increase (Fig. 1C). Conclusively, these logging stress treatment in the two pepper varieties was
- different molecular regulatory mechanisms. regulated genes) between the two pepper varieties (S0CK
- varieties under control and waterlogging treatment con- T5CK was similar (1,842 DEGs, including 1,276 upreg-
- from each sample (Table S1). The mean GC content was regulated genes) were noted (Fig. 2A). Furthermore, the
- 42.15%. Following filtering, the Q20 and Q30 were equal number of DEGs gradually increased at 5 dat and 10 dat
- to or greater than 97.65% and 93.22%, respectively (Table after the waterlogging treatment ended. Approximately
- S2). Clean reads of all samples were then mapped to a 2,903 DEGs (including 1,424 upregulated genes and 1,479
- ribosomal RNA (rRNA) database. Following the removal downregulated genes) were found between S5T and T5T
- of rRNA reads, the remaining ~ 98% unmapped reads (at 5 dat) (Fig. 2A). Furthermore, 4,116 DEGs (includ-
- per reference genome ’Zunla-1’ (version 2.0) (Table S3). genes) were found between S10T and T10T (at 10 dat)
- of the plant; down, underground part of the plant. Error bars indicate the SD (n ≥ 3) of three biological replicates. Asterisks indicate statistically
Methods (brief)
- *Correspondence: zhanfengsong_saas@163.com
- ment (Fig. 1B). Furthermore, when the growth rate of the sample.
- RNA samples obtained from the roots of both S and T After 5 days, the number of DEGs between S5CK and
- ditions were obtained at 0, 5, and 10 dat. These samples ulated genes and 566 downregulated genes) (Fig. 2A).
- from each sample (Table S1). The mean GC content was regulated genes) were noted (Fig. 2A). Furthermore, the
- S2). Clean reads of all samples were then mapped to a 2,903 DEGs (including 1,424 upregulated genes and 1,479
- for the major samples were further mapped to the pep- ing 2,350 upregulated genes and 1,766 downregulated
- waterlogging-tolerant peppers was 6,606 (2,487 upregu- treated samples were analyzed and the 4 comparison
- on variety and treatment, the naming of the samples is
- Samples were first washed with deionized water, then to calculate an FPKM value to quantify gene expres-
- frozen in liquid nitrogen (N2), and stored at − 80 °C for sion abundance (58). DEGs between different samples
- Table 1 The samples list from the reference set.
- Fresh leaf samples (0.1 g) were finely pulverized in 2 mL Determination of GABA content
- containing 1 mM EDTA and 2% (w/v) PVP. Samples acetic acid. The purification of GABA was performed as
- Next, plant leaves were collected to determine the con- β-tubulin was used as an internal control. qRT-PCR was per-
- centrations of photosynthetic pigments. Samples (0.5 g of
- compared the control and treatment samples taken at the same time USA. 2000;1158-249.
- annuum) as Determined by HPLC. J Food Sci. 1988;53(5):1440–3.
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