Investigation of genes associated with petal variations between diploid and autotetraploid in Chinese cabbage (Brassica rapa L. ssp. pekinensis) by RNA-seq and sRNA-seq

Shi, Fengyan; Wang, Yiheng; Huang, Shengnan; Dong, Shiyao; Li, Yong; Feng, Hui

doi:10.1007/s00438-020-01713-6

Cited by 3 publications

(5 citation statements)

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“…In general, leaf senescence comprises a series of molecular reactions involving various genes and TFs at different stages [ 52 ]. To excavate the entire set of senescence-associated genes (SAGs) in DLS-91, we assembled a comprehensive set of genes and TFs with functions related to leaf senescence in different plant species [ 1 , 4 , 48 , 51 , 53 , 54 , 55 , 56 , 57 , 58 , 59 ], including leaf coloration, chlorophyll biosynthesis and degradation, photosystems I and II, phytohormone signal components, chromatin mediated regulation, transcription and post-transcription, translation and post-translation mediated regulators, leaf senescence and plant immunity, and genes that are upregulated and downregulated during DLS. In total, 3003 orthologous genes with a wide range of expression levels among different time frames were identified from the complete transcriptome data ( Table 1 and Table S9 ).…”

Section: Resultsmentioning

confidence: 99%

“…Interestingly, 10 AGAMOUS-LIKE ( AGL )-MADS-box genes (BrAGL8-1, BrAGL8-2 , BrAGL8-3, BrAGL15-1, BrAGL15-2, BrAGL20-1 , BrAGL20-2, BrAGL20-3, BrAGL42-1, and BrAGL42-2) , had diverse expression patterns between DLS-42 and DLS-91 at all stages. According to the LSD database, eight of these genes participate in leaf color regulation, and AGL15 is involved in the regulation of leaf senescence in Arabidopsis ( Table S10 ) [ 48 , 57 ]. Two of these genes, BrAGL8-1 , and BrAGL15-1 , were more strongly expressed in DLS-91 than in DLS-42 at all stages, whereas BrAGL20-1 was more highly expressed in DLS-91 only at 1 and 4 DDT.…”

Section: Resultsmentioning

confidence: 99%

“…Likewise, Fang et al [47] have reported that overexpression of AGL15 delays SAG12 promoter activity and slows the senescence of sepal, petal, and silique tissues in Arabidopsis. Furthermore, TFs characterized as having a role in various trans-regulation, signaling, metabolic, and hormonal responses of senescence can be found in the LSD leaf senescence database (https://bigd.big.ac.cn/lsd/index.php, accessed on 17 March 2021) [48].…”

Section: Introductionmentioning

confidence: 99%

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Comparative Transcriptome-Based Mining of Senescence-Related MADS, NAC, and WRKY Transcription Factors in the Rapid-Senescence Line DLS-91 of Brassica rapa

Rameneni

Lee

et al. 2021

IJMS

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Leaf senescence is a developmental process induced by various molecular and environmental stimuli that may affect crop yield. The dark-induced leaf senescence-91 (DLS-91) plants displayed rapid leaf senescence, dramatically decreased chlorophyll contents, low photochemical efficiencies, and upregulation of the senescence-associated marker gene BrSAG12-1. To understand DLS molecular mechanism, we examined transcriptomic changes in DLS-91 and control line DLS-42 following 0, 1, and 4 days of dark treatment (DDT) stages. We identified 501, 446, and 456 DEGs, of which 16.7%, 17.2%, and 14.4% encoded TFs, in samples from the three stages. qRT-PCR validation of 16 genes, namely, 7 MADS, 6 NAC, and 3 WRKY, suggested that BrAGL8-1, BrAGL15-1, and BrWRKY70-1 contribute to the rapid leaf senescence of DLS-91 before (0 DDT) and after (1 and 4 DDT) dark treatment, whereas BrNAC046-2, BrNAC029-2/BrNAP, and BrNAC092-1/ORE1 TFs may regulate this process at a later stage (4 DDT). In-silico analysis of cis-acting regulatory elements of BrAGL8-1, BrAGL42-1, BrNAC029-2, BrNAC092-1, and BrWRKY70-3 of B. rapa provides insight into the regulation of these genes. Our study has uncovered several AGL-MADS, WRKY, and NAC TFs potentially worthy of further study to understand the underlying mechanism of rapid DLS in DLS-91.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative Transcriptome-Based Mining of Senescence-Related MADS, NAC, and WRKY Transcription Factors in the Rapid-Senescence Line DLS-91 of Brassica rapa

Rameneni

Lee

et al. 2021

IJMS

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“…A case in point is that whole genome duplication shifted the flowering time and tolerance to new environments in tetraploid Anacamptis pyramidalis [63]. Thus, based on study Brassica rapa (Chinese cabbage) by RNA-seq and sRNA-seq, it was revealed that autotetraploid one prolonged flowering time due to an increase of phyto-hormone levels including the jasmonic acid and indole-3-acetic acid, while a decrease of the abscisic acid as well as regulating of miRNA-target mRNA related to flowering period, petal growth, flowering blooming, and pollen development [64]. After polyploidisation, meiotic stability becomes important because this processing becomes complicated.…”

Section: Changing Process Of Developmentmentioning

confidence: 99%

Evolutionary Fixed Potential Agronomic Traits in Polysomic Polyploidy Plants with Special Reference to Potato

Hieu¹

2023

AJPS

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It is commonly known that polyploidization has become one of major forces for a speciation and evolution, especially with evolutionary fixed potential agronomic traits in plants. Although several studies demonstrate that allopolyploid plants were successful in developing novel crops, autopolyploid ones are also more substantial and worth exploring. Obviously, autopolyploid development via sexual or asexual pathways can lead to advantages in biomass, changing process of development, and lots of benefits on coping with climate changes do not comprehend as a whole. This review shed light on 1) gaining gigantic effect and increasing phytochemical content; 2) enhancing biotic and abiotic tolerance to adapt to climate change; 3) changing in process of development; 4) adapting ecology. Based on these benefits, this review provides breeders with several choices when they need in the breeding strategies. Also further review on prospects of polyploidy potato in food security is concerned.

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“…For example, during the formation of tumorous stem of B. juncea , DEGs is significantly enriched in glucosinolate biosynthesis pathway ( Li et al., 2020a ). In addition, there are 231 DEGs related to plant hormone signal transduction and 29 DEGs related to carotenoid biosynthesis were detected in the study of diploid and autotetraploid petal variation genes in Chinese cabbage ( Shi et al., 2020 ). At the same time, RNA-seq has also been used to study the development mechanism of plant storage organs.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of succulent stem development of Chinese kale (Brassica oleracea var. alboglabra Bailey) and its synthetic allotetraploid via RNA sequencing

Zheng

Shi²,

Zhu³

et al. 2022

Front. Plant Sci.

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Chinese kale (Brassica oleracea var. alboglabra Bailey, CC) is a succulent stem vegetable in the Brassica family. Its allotetraploid (AACC) vegetable germplasm, which was synthesized via distant hybridization with the colloquially named ‘yellow turnip’ (B. rapa L. ssp. rapifera Matzg., AA), has a swelling stem similar to CC. To address the molecular mechanism of stem development for CC and AACC, RNA sequencing (RNA-seq) was used to investigate transcriptional regulation of their stem development at three key stages including 28 days, 42 days and the bolting stage (BS) after sowing. As a result, 32,642, 32,665, 33,816, 32,147, 32,293 and 32,275 genes were identified in six corresponding cDNA libraries. Among them, 25,459 genes were co-expressed, while 7,183, 7,206, 8,357, 6,688, 6,834 and 6,814 genes were specifically expressed. Additionally, a total of 29,222 differentially expressed genes (DEGs) were found for functional enrichment as well as many genes involved in plant hormones including gibberellin (GA), abscisic acid (ABA), cytokinin (CTK) and auxin (AUX). Based on gene expression consistency between CC and AACC, the gene families including DELLA, GID, PYR/PYL, PP2C, A-ARR and AUX/IAA might be related to stem development. Among these, eight genes including Bo00834s040, Bo5g093140, Bo6g086770, Bo9g070200, Bo7g116570, Bo3g054410, Bo7g093470 and Bo5g136600 may play important roles in stem development based on their remarkable expression levels as confirmed by qRT-PCR. These findings provide a new theoretical basis for understanding the molecular mechanism of stem development in Brassica vegetable stem breeding.

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Investigation of genes associated with petal variations between diploid and autotetraploid in Chinese cabbage (Brassica rapa L. ssp. pekinensis) by RNA-seq and sRNA-seq

Cited by 3 publications

References 93 publications

Comparative Transcriptome-Based Mining of Senescence-Related MADS, NAC, and WRKY Transcription Factors in the Rapid-Senescence Line DLS-91 of Brassica rapa

Comparative Transcriptome-Based Mining of Senescence-Related MADS, NAC, and WRKY Transcription Factors in the Rapid-Senescence Line DLS-91 of Brassica rapa

Evolutionary Fixed Potential Agronomic Traits in Polysomic Polyploidy Plants with Special Reference to Potato

Transcriptomic analysis of succulent stem development of Chinese kale (Brassica oleracea var. alboglabra Bailey) and its synthetic allotetraploid via RNA sequencing

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