Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut

Luo, Xiaomei; Liu, Juncheng

doi:10.3390/genes10080605

Cited by 6 publications

(6 citation statements)

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“…This study shows that sugar beet has the best growth state in high pH environment, and low soil pH affects sugar beet photosynthesis. Similarly, phenotypic and physiological analyses revealed that the optimum pH of iron walnut was 4-5 ( Luo and Liu, 2019 ), and the net photosynthetic rate significantly declined under non-optimal pH conditions. Moreover, it has recently been reported that low pH affected ROS and MG metabolisms in Citrus roots and leaves, and the negative effect was more significant in roots than in leaves ( Long et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, it was reported that iron walnut growth was better in pH 4-5 and pH 5-6 treatments than in pH 3-4 and pH 6-7 treatments. Transcriptome analyses revealed that the pathways involved in polyamine metabolisms participated in iron walnut acid stress tolerance ( Luo and Liu, 2019 ). Moreover, under alkaline conditions, high rhizosphere pH inhibits plant growth by imposing an adverse effect on roots elongation and disrupting cellular ionic homeostasis and pH.…”

Section: Introductionmentioning

confidence: 99%

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Physiological and Proteomic Analysis of Different Molecular Mechanisms of Sugar Beet Response to Acidic and Alkaline pH Environment

et al. 2021

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Soil pH is a major constraint to crop plant growth and production. Limited data are available on sugar beet growth status under different pH conditions. In this study, we analyzed the growth status and phenotype of sugar beet under pH 5, pH 7.5, and pH 9.5. It was found that the growth of sugar beet was best at pH 9.5 and worst at pH 5. The activities of superoxide dismutase (SOD) and peroxidase (POD) in leaves and roots increased as pH decreased from 9.5 to 5. Moreover, compared with pH 9.5, the levels of soluble sugar and proline in leaves increased significantly at pH 5. To explore the mechanisms of sugar beet response to different soil pH environments, we hypothesized that proteins play an important role in plant response to acidic and alkaline pH environment. Thus, the proteome changes in sugar beet modulated by pH treatment were accessed by TMT-based quantitative proteomic analysis. A total of three groups of differentially expressed proteins (DEPs) (pH 5 vs. pH 7.5, pH 9.5 vs. pH7.5 and pH 5 vs. pH 9.5) were identified in the leaves and roots of sugar beet. Several key proteins related to the difference of sugar beet response to acid (pH 5) and alkaline (pH 9.5) and involved in response to acid stress were detected and discussed. Moreover, based on proteomics results, QRT-PCR analysis confirmed that expression levels of three N transporters (NTR1, NRT2.1, and NRT2.5) in roots were relatively high under alkaline conditions (pH 9.5) compared with pH 5 or pH 7.5. The total nitrogen content of pH 9.5 in sugar beet was significantly higher than that of pH 7.5 and pH 5. These studies increase our understanding of the molecular mechanism of sugar beet response to different pH environments.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Physiological and Proteomic Analysis of Different Molecular Mechanisms of Sugar Beet Response to Acidic and Alkaline pH Environment

et al. 2021

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“…Based on the genomic data for walnut (J. regia and J. sigillata) available from the NCBI (Martinez-Garcia et al, 2016;Luo and Liu, 2019b), 21 pairs of primers (Table 2) were obtained after two rounds of screening. Then, the fluorescent amplification products were sequenced on an ABI 3730 DNA analyser (Applied Biosystems), and allele sizing was performed using Gene Mapper™ 4.1 software (Applied Biosystems).…”

Section: Ssr Analysismentioning

confidence: 99%

Distinguishing Sichuan Walnut Cultivars and Examining Their Relationships with Juglans regia and J. sigillata by FISH, Early-Fruiting Gene Analysis, and SSR Analysis

Luo

Chen

2020

Front. Plant Sci.

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Walnuts are economically important tree species in Sichuan Province (China) that provide heathy nuts. Fluorescence in situ hybridization (FISH) and analyses of an early-fruiting gene fragment and simple sequence repeats (SSRs) were used to distinguish Sichuan walnut cultivars and examine their relationships with Juglans regia L. and Juglans sigillata Dode. Thirty-four small chromosomes were counted in four Sichuan walnut cultivars. In the four cultivars, 5S rDNA was located in the proximal regions of two chromosomes (5 and 6), while (AG 3 T 3) 3 was located at both ends of each chromosome. The existence of the signal at both chromosome ends ensured accurate chromosome counts. 5S rDNA and (AG 3 T 3) 3 were not effective in identifying Sichuan walnut cultivars. Evolutionary analysis involving 32 early-fruiting nucleotide sequences from Sichuan walnut materials were performed with the maximum likelihood method. There were a total of 602 positions. All positions with gaps and missing data were eliminated, resulting in a final dataset of 562 positions. The ML tree with the highest log likelihood (−1607.82) revealed two obvious groups: one including materials of J. regia, which fruits 1 year after grafting, and another including materials of J. sigillata, which fruits >3 years after grafting. The early-fruiting gene fragment divided 22 walnut materials (10 walnut cultivars and 12 walnut accessions) into two groups, indicating that it was somewhat effective for distinguishing Sichuan walnut cultivars. Furthermore, 22 SSR loci were revealed to identify nine walnut cultivars. Eight cultivars were exclusively discerned by one SSR locus each: Chuanzao 1 [CUJRB307 (116) or CUJRA206a (182)], Chuanzao 2 [JSI-73 (154)], Shuangzao [CUJRB103a (123), CUJRB218 (144), JSI-71 (146), or CUJRA206a (176)], Shimianju [ZMZ11 (138)], Meigupao [CUJRB218 (149), CUJRB103a (151), or CUJRA206a (190)], Muzhilinhe [CUJRB220 (136), ZMZ11 (147), CUJRC310 (156), or JSI-73 (166)], Maerkang [CUJRA124 (154), CUJRB218 (159), or CUJRA123 (182)], Yanyuanzao [CUJRA124 (150) or CUJRA206a (192)]. The Shuling cultivar was identified by the combination of

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“…We performed cluster analysis of the DEGs in IVF and PA by using the short time-series expression miner (Stem) software (Luo and Liu, 2019). We performed functional annotation and enrichment analysis in each group for the nine clusters with p-value < 0.01 in IVF and PA, respectively ( Figure 1B, Figure 2).…”

Section: Differential Expression Analysis Of Mrnas In Adjacent Stagesmentioning

confidence: 99%

Transcriptome analysis of in vitro fertilization and parthenogenesis activation during early embryonic development in pigs

Huang

Zhang

et al. 2020

Preprint

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BackgroundParthenogenesis-activated oocytes exhibit inferior embryonic development and lower total cell count per blastocyst than fertilized embryos, thus often leading to pre-implantation failure in porcine. The mechanisms underlying the deficiencies of embryos generated from parthenogenesis activation have not been completely understood. Alternative splicing events (AS) and long intergenic non-coding RNAs (lincRNAs) have emerged as key regulators in various biological processes. However, their regulatory mechanisms for parthenogenesis have not been fully elucidated, and their relation to parthenogenesis in pig is largely unknown. ResultHere, we reconstructed 189,228 transcripts and identified 7,185 lincRNAs in a single mature oocyte and discovered three stages between in vitro fertilization (IVF) and parthenogenesis activation (PA). A large change in transcriptome occurred in early blastocyst and morula in IVF and PA, respectively, indicating tremendous alteration for the transcriptome in both processes. Compare to protein-coding genes, differential expression protein-coding genes have higher alternative splicing rate, and most transcripts possibly originated from transcription start site (TSS) and transcription terminal site (TTS) types of alternative splicing according to the average expression of 12 AS types. Most lincRNAs with remarkably stage specificity were found in both in procceses. Function prediction results suggest that the specifically expressed lincRNAs in distinct stages have different biological functions. Hub lincRNAs analysis showed that three lincRNAs may play important roles on early embryonic development, and five may function on abnormal parthenogenesis embryonic development. Comparison of the transcriptome between IVF and PA revealed that most DEGs enriched the regulation of apoptotic and late embryonic development-related process. conclusionWe performed a comprehensive comparative analysis framework of RNA-seq data, including mRNA, alternative splicing and long intergenic noncoding RNA. This work identified functional protein-coding genes and lincRNAs, and showed differences in the expression pattern of alternative splicing in IVF and PA. Which detailed the early embryonic development-related procedure in porcine, some protein-coding genes, and lincRNAs that may affect pre-implantation failure in PA embryos. This study will help future research on these genes and molecular-assisted breeding for pig parthenotes.

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Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut

Cited by 6 publications

References 59 publications

Physiological and Proteomic Analysis of Different Molecular Mechanisms of Sugar Beet Response to Acidic and Alkaline pH Environment

Physiological and Proteomic Analysis of Different Molecular Mechanisms of Sugar Beet Response to Acidic and Alkaline pH Environment

Distinguishing Sichuan Walnut Cultivars and Examining Their Relationships with Juglans regia and J. sigillata by FISH, Early-Fruiting Gene Analysis, and SSR Analysis

Transcriptome analysis of in vitro fertilization and parthenogenesis activation during early embryonic development in pigs

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