Transcriptome profiling reveals differentially expressed genes associated with wizened flower bud formation in Chinese pear (<i>Pyrus bretschneideri</i> Rehd.)

Liu, Ya; Zhang, Shaoling; Gu, Chao; Tao, Shutian; Wang, Dong Sheng; Guo, Xian Ping; Qi, Kai

doi:10.1080/14620316.2016.1142359

Cited by 8 publications

(4 citation statements)

References 25 publications

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“…Genome-wide transcriptome analysis is useful for rapidly analyzing the expression patterns of members of each gene family and understanding the regulatory network of various metabolic pathways. At present, although transcriptome analysis has been used to analyze pear peel color, flower bud and aroma formation and other aspects [ 24 – 27 ], transcriptome analysis of stone cells formation has not been reported.…”

Section: Introductionmentioning

confidence: 99%

Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents

et al. 2017

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Stone cell content is thought to be one of the key determinants for fruit quality in pears. However, the molecular mechanism of stone cell development remains poorly understood. In this study, we found that the stone cell clusters (SCCs) distribution and area in 'Dangshan Su' (with abundant stone cells) were higher as compared to 'Lianglizaosu' (low stone cell content bud sport of 'Dangshan Su') based on the histochemical staining, and the correlations of lignin content with stone cell content and SCC area was significant. The fruits of 'Dangshan Su' and 'Lianglizaosu' at three different developmental stages (23 and 55 days after flowering and mature) were sampled for comparative transcriptome analysis to explore the metabolic pathways associated with stone cell development. A total of 42444 unigenes were obtained from two varieties, among which 7203 differentially expressed genes (DEGs) were identified by comparison of the six transcriptomes. Specifically, many DEGs associated with lignin biosynthesis were identified, including coumaroylquinate 3-monooxygenase (C3H), shikimate O-hydroxycinnamoyltransferase (HCT), ferulate 5-hydroxylase (F5H), cinnamyl alcohol dehydrogenase (CAD) and peroxidase (POD), as well as genes related to carbon metabolism, such as sorbitol dehydrogenase-like (SDH-like) and ATP-dependent 6-phosphofructokinase (ATP-PFK). At the peak of the stone cell content (55 days after flowering), the expression level of these genes in 'Dangshan Su' was significantly increased compared with 'Lianglizaosu', indicating that these genes were closely related to stone cell development. We validated the transcriptional levels of 33 DEGs using quantitative realtime polymerase chain reaction (qRT-PCR) analysis. The results were consistent with the transcriptome analysis, indicating the reliability of transcriptome data. In addition, subcellular localization analysis of three DEGs in lignin synthesis (PbC3H, PbF5H and PbPOD) revealed that these proteins are mainly distributed in the cell membrane and cytoplasm. These results provide new insights into the molecular mechanism of stone cell formation.

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Section: Introductionmentioning

confidence: 99%

Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents

et al. 2017

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“…CTK is associated with a variety of plant physiological processes, like leaf senescence, seed fatty acid production ( Wu et al, 2017 ), flower organ development and pod formation ( Liu et al, 2016 ), and seed yield ( Murai, 2014 ). The hormone also contributes to plant responses to a number of abiotic stresses, like salinity ( Joshi et al, 2018 ), temperature ( Bielach, Hrtyan & Tognetti, 2017 ), and drought ( Golan et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

Hamid,

Jacob,

Ghorbanzadeh

et al. 2024

PeerJ

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Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress.

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“…In pear orchards, wizened bud occurrence is frequently observed, which impedes flower bud growth, resulting in a great loss of yield [6]. According to the present study, more than 60% of buds presented a wizened performance in '710' sand pear trees at the time of flower bud differentiation (Figure 1A,B), indicating that '710' sand pear trees have a typical character of wizened bud formation and could be used as interesting material to investigate the underlying mechanism.…”

Section: Discussionmentioning

confidence: 99%

“…bretschneideri. ), showing the occurrence of wizened bud, and results in a great loss of pear production [5,6]. Moreover, previous studies demonstrated that wizened bud formation is closely related to management practices and the nutritional status of buds [6,7].…”

Section: Introductionmentioning

confidence: 98%

Morpho-Physiological and Transcriptome Analyses Provide Insights into the Wizened Bud Formation in Pear Trees

Shi

Hussain

et al. 2022

Agronomy

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Wizened buds are frequently observed in pear (Pyrus spp.) trees, which greatly reduces the yield. However, little is known about the mechanism of wizened bud formation. Here, we analyzed physiological and transcriptomic differences between normal buds and wizened buds of ‘710’ pear trees. The results indicated that the sorbitol and boron (B) contents, during bud differentiation, were significantly reduced in wizened buds. The microscopic observation and transcriptome analysis revealed that the collapse of the organ structure and cell wall loosening process may have a close relation with wizened bud formation. Moreover, reduced transcript levels of PpyMYB39.1 and its downstream genes (PpyHT1, PpyHT2, PpyPMEI1 and PpyPMEI2) were found in wizened buds. However, the transcript levels of pentose and glucuronate interconversion pathway genes (PpyPME3, PpyPL18.1, PpyPL18.2, PpyPG1 and PpyPG2) and the concentration of pectin-degradation-related enzymes were increased in wizened buds. Correspondingly, the pectin concentration was significantly reduced in wizened buds. Taken together, PpyMYB39.1 may promote pectin degradation and decrease carbohydrate transport by regulating its downstream genes and is supposed to play a vital role in the wizened bud formation resulting from the cell wall loosening process. Our study provides fundamental insights into wizened bud formation and strategies to reduce the wizened bud occurrence in pear trees.

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Transcriptome profiling reveals differentially expressed genes associated with wizened flower bud formation in Chinese pear (Pyrus bretschneideri Rehd.)

Cited by 8 publications

References 25 publications

Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents

Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

Morpho-Physiological and Transcriptome Analyses Provide Insights into the Wizened Bud Formation in Pear Trees

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