scholarly journals Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 504 ◽  
Author(s):  
Yunpeng Cao ◽  
Xiaoxu Li ◽  
Lan Jiang
Keyword(s):  
Fruit Quality ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Integrative Analysis ◽  
Bimolecular Fluorescence Complementation ◽  
Pear Fruit ◽  
Cell Content ◽  
Tandem Gene Duplication ◽  
Stone Cell ◽  
Chinese White

Stone cell content is an important factor affecting pear fruit flavor. Lignin, a major component of pear stone cells, hinders the quality and value of commercial fruit. The completion of the Chinese white pear (Pyrus bretschneideri) genome sequence provides an opportunity to perform integrative analysis of the genes encoding the eleven protein families (i.e., PAL, C4H, 4CL, HCT, C3H, CSE, CCoAOMT, CCR, F5H, COMT, and CAD) in the phenylpropanoid pathway. Here, a systematic study based on expression patterns and phylogenetic analyses was performed to identify the members of each gene family potentially involved in the lignification in the Chinese white pear. The phylogenetic analysis suggested that 35 P. bretschneideri genes belong to bona fide lignification clade members. Compared to other plants, some multigene families are expanded by tandem gene duplication, such as HCT, C3H, COMT, and CCR. RNA sequencing was used to study the expression patterns of the genes in different tissues, including leaf, petal, bud, sepal, ovary, stem, and fruit. Eighteen genes presented a high expression in fruit, indicating that these genes may be involved in the biosynthesis of lignin in pear fruit. Similarly to what has been observed for Populus trichocarpa, a bimolecular fluorescence complementation (BiFC) experiment indicated that P. bretschneideri C3H and C4H might also interact with each other to regulate monolignol biosynthesis in P. bretschneideri, ultimately affecting the stone cell content in pear fruits. The identification of the major genes involved in lignin biosynthesis in pear fruits provides the basis for the development of strategies to improve fruit quality.

scholarly journals CAD Genes: Genome-Wide Identification, Evolution, and Their Contribution to Lignin Biosynthesis in Pear (Pyrus bretschneideri)

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1444
Author(s):  
Kaijie Qi ◽  
Xiaofei Song ◽  
Yazhou Yuan ◽  
Jianping Bao ◽  
Xin Gong ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Gene Families ◽  
Cell Number ◽  
Segmental Duplications ◽  
Pear Fruit ◽  
Gene Expressions ◽  
Cell Content ◽  
Stone Cell ◽  
Gene Pairs

The synthetic enzyme cinnamyl alcohol dehydrogenase (CAD) is involved in responses to various stresses during plant growth. It regulates the monolignol biosynthesis and catalyzes hydroxyl cinnamaldehyde reduction to the corresponding alcohols. Although the CAD gene families have been explored in some species, little known is in Rosaceae. In this study, we identified 149 genes in Pyrus bretschneideri (PbrCAD), Malus domestica (MDPCAD), Prunus mume (PmCAD) and Fragaria vesca (mrnaCAD). They were phylogenetically clustered into six subgroups. All CAD genes contained ADH-N and ADH-zinc-N domains and were distributed on chromosomes unevenly. Dispersed and WGD/segmental duplications accounted the highest number of evolutionary events. Eight collinear gene pairs were identified among the four Rosaceae species, and the highest number was recorded in pear as five pairs. The five PbrCAD gene pairs had undergone purifying selection under Ka/Ks analysis. Furthermore, nine genes were identified based on transcriptomic and stone cell content in pear fruit. In qRT-PCR, the expression patterns of PbrCAD1, PbrCAD20, PbrCAD27, and PbrCAD31 were consistent with variation in stone cell content during pear fruit development. These results will provide valuable information for understanding the relationship between gene expressions and stone cell number in fruit.

scholarly journals Selenium Increases Fruit Quality By Reducing Ethylene Production And The Stone Cell Content In Pear (Pyrus Ussuriensis)

2021 ◽  
Author(s):  
Chi Yuan ◽  
Haidong Bu ◽  
Jiaming Zhao ◽  
Jiaojiao Liu ◽  
Hui Yuan ◽  
...  
Keyword(s):  
Fruit Quality ◽  
Ethylene Production ◽  
Lignin Biosynthesis ◽  
Essential Trace Element ◽  
Pear Fruit ◽  
Cell Content ◽  
Stone Cell ◽  
Titratable Acid ◽  
Biosynthesis Gene ◽  
Key Genes

Abstract Background:Selenium (Se) is an essential trace element for both animals and plants. Se treatment can increase fruit Se concentration and shelf life. However, the mechanism underlying Se-delayed fruit ripening is still unclear.Results:In this research, two groups of Se (A and B treatments) were used to treat ‘Nanhong’ pear fruit. The results showed that these treatments could greatly increase the Se content but decreased the titratable acid content. Treatment A significantly decreased ethylene production, and the key genes controlling ethylene production, PuACSs and PuERF2, were inhibited by Se treatment. In addition, treatment A significantly decreased the stone cell content, and one lignin biosynthesis gene, PuC4H, was downregulated by treatment A.Concusions:Se treatment increased the Se content in pear fruit. In addition, Se decreased ethylene production and the stone cell content. Moreover, the key genes for ethylene production (PuACSs and PuERF2) and lignin biosynthesis (PuC4H) were also inhibited by Se treatment.

scholarly journals Cinnamate-4-Hydroxylase Gene Is Involved in the Step of Lignin Biosynthesis in Chinese White Pear

2015 ◽  
Vol 140 (6) ◽  
pp. 573-579 ◽  
Author(s):  
Shutian Tao ◽  
Danyang Wang ◽  
Cong Jin ◽  
Wei Sun ◽  
Xing Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Enzymatic Reactions ◽  
Cell Content ◽  
Stone Cell ◽  
Chinese White ◽  
Essential Enzyme ◽  
Main Component ◽  
Lignin Metabolism

Lignin is the main component of stone cells, and stone cell content is one of the crucial factors for fruit quality in chinese white pear (Pyrus ×bretschneideri). The lignin biosynthesis pathway is complex and involves many enzymatic reactions. Cinnamate-4-hydroxylase [C4H (EC.1.14.13.11)] is an essential enzyme in lignin metabolism. This study was conducted to investigate the effect of bagging on lignin metabolism during fruit development in chinese white pear. The study showed that bagging had little effect on stone cell content, lignin content, C4H activity, and C4H gene expression and that there was a positive correlation between C4H gene expression and lignin content as well as stone cell content. Moreover, a full-length complementary DNA (cDNA) encoding C4H (PbrC4H, GenBank accession number KJ577541.1) was isolated from chinese white pear fruit. The cDNA is 1515 bp long and encodes a protein of 504 amino acids. Sequence alignment suggested that the deduced protein belongs to the P450 gene family and that C4H might be located subcellularly in the cell membrane. The results indicate that bagging cannot change the lignin and stone cell content significantly and that C4H catalyzes a step in lignin biosynthesis. These findings provide certain theoretical references and practical criteria for improving the quality of chinese white pear.

scholarly journals Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aisajan Mamat ◽  
Kuerban Tusong ◽  
Juan Xu ◽  
Peng Yan ◽  
Chuang Mei ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Cell Formation ◽  
Parenchyma Cell ◽  
Lignin Biosynthesis ◽  
Cell Content ◽  
Stone Cell ◽  
Fruit Samples

AbstractKorla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.

scholarly journals A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri

2018 ◽  
Vol 5 (7) ◽  
pp. 171463 ◽  
Author(s):  
Yunpeng Cao ◽  
Shumei Li ◽  
Yahui Han ◽  
Dandan Meng ◽  
Chunyan Jiao ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Functional Divergence ◽  
Sugar Content ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
World Market ◽  
Pear Fruit ◽  
Rosaceae Species ◽  
Chinese White

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears ( Pyrus bretschneideri ) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRK s into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11 , PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRK s that might contribute to fructose efflux in the pear fruit.

scholarly journals The Effect of Different Pollination on the Expression of Dangshan Su Pear MicroRNA

2017 ◽  
Vol 2017 ◽  
pp. 1-18 ◽  
Author(s):  
Xi Cheng ◽  
Chongchong Yan ◽  
Jinyun Zhang ◽  
Chenhui Ma ◽  
Shumei Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Fruit Quality ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Cell Content ◽  
Qrt Pcr ◽  
Stone Cell ◽  
Negative Effect

The high-throughput sequencing of pear “Dangshan Su” × “Yali” (whose fruits lignin and stone cell content are high and quality is poor) and pear “Dangshan Su” × “Wonhwang” (whose fruits with low content of lignin and stone cell and the quality are better ) found that the expressions of these two miRNAs (pyr-1809 and pyr-novel-miR-144-3p) were significantly different; their corresponding target genes encode two kinds of laccase (Pbr018935.1 and Pbr003857.1). qRT-PCR results showed that these two enzymes are involved in the formation of lignin and stone cells and the existence of these two miRNAs has a negative effect on them. It was concluded that the effect of pollination on the development of stone cells may affect the synthesis of lignin, through the regulation of laccase controlled by miRNAs, and ultimately affect the formation of stone cell and fruit quality.

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

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xueqiang Su ◽  
Yu Zhao ◽  
Han Wang ◽  
Guohui Li ◽  
Xi Cheng ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Major Gene ◽  
Lignin Biosynthesis ◽  
Functional Identification ◽  
Key Factors ◽  
Pear Fruit ◽  
Positive Role ◽  
Factors Affecting ◽  
Chinese White ◽  
Key Enzyme

Abstract 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.

scholarly journals Genome-Wide Comparative Analysis of the β-glucosidase Family in Five Rosaceae Species and their Potential Role on Lignification of Stone Cells in Chinese White Pear

2020 ◽  
Author(s):  
Han Wang ◽  
Yang Zhang ◽  
Yu Zhao ◽  
Wenlong Han ◽  
Jinjin Lu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Prunus Avium ◽  
Expression Patterns ◽  
Cell Development ◽  
Glycoside Hydrolase Family ◽  
Pear Fruit ◽  
Stone Cell ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome

Abstract Background: The β-glucosidase BGLU in the glycoside hydrolase family 1 (GH1) is involved in the sugar metabolism of the plant and plays an important role in maintaining the normal physiological function of the plant. Recent studies had shown that β-glucosidase was involved in plant lignification. The lignification in pear fruit is closely related to the formation of pear stone cells, but the BGLU genes family has not been identified in pears.Result: A total of 343 BGLU genes were identified from five species of Rosaceae (Pyrus bretschneideri, Prunus mume, Malus domestica, Prunus avium, Fragaria vesca). According to phylogenetic analysis, 50 PbBGLUs were divided into 8 groups. 298 syntenic pairs were found in intra- and inter-species collinear analysis of five Rosaceae species, found that pears and apples had more syntenic pairs than pear and the other three Rosaceae species. The Ka/Ks analysis of duplication PbBGLU genes in pear indicated that the main mode of expansion of the PbBGLUs was segmental replication and was mainly affected by purification. qRT-PCR showed that the three gene expression patterns of PbBGLU1, PbBGLU15 and PbBGLU16 were basically consistent with the change trend of pear fruit lignin and stone cell content, and may be involved in lignification and stone cell development of pear fruit. Subcellular localization showed that these three candidate genes were all located on the cell wall.Conclusion: In this study, a genome-wide analysis of BGLU genes in five Rosaceae species was carried out, and three candidate genes related to lignification and stone cell development of pear fruits were identified, which laid the foundation for a deeper understanding of the function of BGLU genes in pear fruits and potential in changing pear fruit quality.

scholarly journals Transcriptomics of Differential Ripening in ‘d’Anjou’ Pear (Pyrus communis L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Loren Honaas ◽  
Heidi Hargarten ◽  
John Hadish ◽  
Stephen P. Ficklin ◽  
Sara Serra ◽  
...  
Keyword(s):  
Fruit Quality ◽  
Expression Patterns ◽  
Pyrus Communis ◽  
Accurate Estimation ◽  
Pear Fruit ◽  
Pome Fruit ◽  
Tissue Samples ◽  
European Pear ◽  
Fruit Maturity ◽  
Postharvest Management

Estimating maturity in pome fruits is a critical task that directs virtually all postharvest supply chain decisions. This is especially important for European pear (Pyrus communis) cultivars because losses due to spoilage and senescence must be minimized while ensuring proper ripening capacity is achieved (in part by satisfying a fruit chilling requirement). Reliable methods are lacking for accurate estimation of pear fruit maturity, and because ripening is maturity dependent it makes predicting ripening capacity a challenge. In this study of the European pear cultivar ‘d’Anjou’, we sorted fruit at harvest based upon on-tree fruit position to build contrasts of maturity. Our sorting scheme showed clear contrasts of maturity between canopy positions, yet there was substantial overlap in the distribution of values for the index of absorbance difference (IAD), a non-destructive spectroscopic measurement that has been used as a proxy for pome fruit maturity. This presented an opportunity to explore a contrast of maturity that was more subtle than IAD could differentiate, and thus guided our subsequent transcriptome analysis of tissue samples taken at harvest and during storage. Using a novel approach that tests for condition-specific differences of co-expressed genes, we discovered genes with a phased character that mirrored our sorting scheme. The expression patterns of these genes are associated with fruit quality and ripening differences across the experiment. Functional profiles of these co-expressed genes are concordant with previous findings, and also offer new clues, and thus hypotheses, about genes involved in pear fruit quality, maturity, and ripening. This work may lead to new tools for enhanced postharvest management based on activity of gene co-expression modules, rather than individual genes. Further, our results indicate that modules may have utility within specific windows of time during postharvest management of ‘d’Anjou’ pear.

scholarly journals Identification and Characterization of the CCoAOMT Gene Family in Apple, Chinese White Pear, and Peach

2021 ◽  
pp. 1-12
Author(s):  
Leli Li ◽  
Shutian Tao ◽  
Huangwei Zhang ◽  
Weijian Huang ◽  
Jim M. Dunwell ◽  
...  
Keyword(s):  
Gene Family ◽  
Prunus Persica ◽  
Lignin Content ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Pathogenic Fungi ◽  
Development Stage ◽  
Chinese White ◽  
Main Components

Lignin is one of the main components of plant cell walls, which provides mechanical support for plants and also contributes to resisting against plant pathogenic fungi. In the fruit industry, the lignin content can affect the quality of fruit. The biosynthesis of lignin involves a variety of enzymes, of which caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a class of methyltransferases that plays an essential role in lignin biosynthesis. Studies have been conducted on the CCoAOMT gene family in several species, including arabidopsis (Arabidopsis thaliana), black poplar (Populus nigra), and cotton (Gossypium hirsutum). Still, there is relatively little research on this gene family in the Rosaceae. In this study, we used bioinformatics to identify and characterize the CCoAOMT gene family in apple (Malus domestica), chinese white pear (Pyrus bretschneideri), and peach (Prunus persica). In total, 35 CCoAOMT genes were identified in the three Rosaceae species: 8 from chinese white pear, 12 from apple, and 15 from peach. By using structure analysis and collinearity analysis, we found 12 conserved motifs and 12 pairs of CCoAOMT genes with collinearity. In the phylogenetic tree, the gene family was mainly divided into two groups. The genes had different expression patterns during the growth and development stage of fruit, a finding that is consistent with the pattern of lignin accumulation. This study will be beneficial for further study of CCoAOMT genes.

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