Comparative Transcriptomic Analysis Provides Insight into the Domestication and Improvement of Pear (<i>P. pyrifolia</i>) Fruit

Li, Xiaolong; Liu, Lun; Ming, Meiling; Hu, Hongju; Zhang, Mingyue; Fan, Jing; Song, Bobo; Zhang, Shaoling

doi:10.1104/pp.18.01322

Cited by 37 publications

(28 citation statements)

References 51 publications

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“…In contrast, the higher nucleotide diversity in NBS-encoding genes of cultivated groups in Europe might have occurred due to distinct selection pressure imposed by the cultivated habitats [41]. A recent study has shown that several regions with NBS-encoding genes had higher nucleotide diversity in landraces than the wild pear group [42]. The latter results, along with our findings, indicate that the genetic diversity of similar genes can be altered differently due to preferential selection of traits during independent domestication events as observed in pear [3].…”

Section: Discussionmentioning

confidence: 99%

“…To investigate the expression of the NBS-encoding genes that have signatures of selection, four pear genotypes representing two cultivated and two wild accessions at three different fruit developmental stages (small, enlarged, and mature) were used. The RNAseq data of 12 samples were obtained from a previous study [42]. To investigate the expression changes of the NBS-encoding genes after inoculation with A. alternata, RNA-seq data of two pear species (P. calleryana and P. pyrifolia: 'Hongfen' pear) were used generated from previous study [19,20].…”

Section: Genome-wide Expression Analysis Of the Nbs-encoding Genesmentioning

confidence: 99%

“…For gene expression validation, four pear accessions (PyW13, PyW14, PyI1 and PyL2) at enlarged stage were chosen for quantitative real time PCR (RT-qPCR) analysis. For expression validation of Pbr025269.1 with RT-qPCR, ten Asian cultivated (PyL2, PyL7, PyL8, PyL9, PyL10, PyL11, PyI1, PyI9, PyI11, PyI14) and seven Asian wild (PyW5, PyW6, PyW7, PyW9, PyW12, PyW13, PyW14) pear accessions were chosen from a previous study [42]. Plant Total RNA Isolation Kit plus was used to extract total RNA from pear fruits at the enlarged stage, and DNase I was used to remove the genomic DNA contamination.…”

Section: Real-time Pcr Analysismentioning

confidence: 99%

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Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

et al. 2020

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Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. Results In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. Conclusion Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

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Section: Discussionmentioning

confidence: 99%

Section: Genome-wide Expression Analysis Of the Nbs-encoding Genesmentioning

confidence: 99%

Section: Real-time Pcr Analysismentioning

confidence: 99%

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Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

et al. 2020

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“…To solve this problem, many studies have been conducted on stone cells, and some progress has been made in revealing the biosynthetic and regulatory processes of pear stone cells and lignin [6, 39, 40]. However, the existing research has mainly concentrated on pear fruit after 15 DAP, and pear fruit in this period already contains a large number of stone cells [5, 41, 42]. The molecular mechanisms of stone cell formation and development in early fruit development (before 15 DAP) remain unclear.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis

Zhao

Wang

et al. 2019

BMC Plant Biol

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Background The content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in ‘Dangshan Su’ pear fruit 15-145 days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched. Results In this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in ‘Dangshan Su’ pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis. Conclusions Our results revealed that ‘Dangshan Su’ pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in ‘Dangshan Su’ pear and plays a positive role in lignin biosynthesis.

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“…These varieties are often used as pollen parents in Dangshan County, Anhui Province, China. Previous studies have shown that the 'Yali' has a high stone cell content, but the 'Cuiguan' has a low stone cell content [28,30]. However, the effect that the pollen parents with different stone cell levels have on the formation of stone cells in the fruit of 'Lianglizaosu' remains unknown.…”

Section: Introductionmentioning

confidence: 99%

Effects of Metaxenia on Stone Cell Formation in Pear (Pyrus bretschneideri) Based on Transcriptomic Analysis and Functional Characterization of the Lignin-Related Gene PbC4H2

Cheng

Zhang

Wang

et al. 2020

Forests

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The deposition of lignin in flesh parenchyma cells for pear stone cells, and excessive stone cells reduce the taste and quality of the fruit. The effect of metaxenia on the quality of fruit has been heavily studied, but the effect of metaxenia on stone cell formation has not been fully elucidated to date. This study used P. bretschneideri (Chinese white pear) cv. ‘Yali’ (high-stone cell content) and P. pyrifolia (Sand pear) cv. ‘Cuiguan’ (low-stone cell content) as pollination trees to pollinate P. bretschneideri cv. ‘Lianglizaosu’ separately to fill this gap in the literature. The results of quantitative determination, histochemical staining and electron microscopy indicated that the content of stone cells and lignin in YL fruit (‘Yali’ (pollen parent) × ‘Lianglizaosu’ (seed parent)) was significantly higher than that in CL fruit (‘Cuiguan’ (pollen parent) × ‘Lianglizaosu’ (seed parent)). The transcriptome sequencing results that were obtained from the three developmental stages of the two types of hybrid fruits indicated that a large number of differentially expressed genes (DEGs) related to auxin signal transduction (AUX/IAAs and ARFs), lignin biosynthesis, and lignin metabolism regulation (MYBs, LIMs, and KNOXs) between the CL and YL fruits at the early stage of fruit development. Therefore, metaxenia might change the signal transduction process of auxin in pear fruit, thereby regulating the expression of transcription factors (TFs) related to lignin metabolism, and ultimately affecting lignin deposition and stone cell development. In addition, we performed functional verification of a differentially expressed gene, PbC4H2 (cinnamate 4-hydroxylase). Heterologous expression of PbC4H2 in the c4h mutant not only restored its collapsed cell wall, but also significantly increased the lignin content in the inflorescence stem. The results of our research help to elucidate the metaxenia-mediated regulation of pear stone cell development and clarify the function of PbC4H2 in cell wall development and lignin synthesis, which establishes a foundation for subsequent molecular breeding.

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Comparative Transcriptomic Analysis Provides Insight into the Domestication and Improvement of Pear (P. pyrifolia) Fruit

Cited by 37 publications

References 51 publications

Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis

Effects of Metaxenia on Stone Cell Formation in Pear (Pyrus bretschneideri) Based on Transcriptomic Analysis and Functional Characterization of the Lignin-Related Gene PbC4H2

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