A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

Wang, Runze; Xue, Yongsong; Fan, Jing; Yao, Jia‐Long; Qin, Mengfan; Lin, Tao; Lian, Qiang; Zhang, Mingyue; Li, Xiaolong; Li, Jiaming; Sun, Manyi; Song, Bobo; Zhang, Jiaying; Zhao, Kunkun; Chen, Xu; Hu, Hongju; Fei, Zhangjun; Xue, Cheng; Wu, Jun

doi:10.1186/s13059-021-02531-8

Cited by 41 publications

(30 citation statements)

References 132 publications

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“…In the latest study, herbaceous peony increased the layers of thickened secondary cells and lignin accumulation, resulting in enhanced stem strength and demonstrably straight stems [ 33 ]. There was a positive correlation between lignin, cellulose, and stone cell contents in 206 sand pear cultivars [ 34 ]. Therefore, we speculated that low lignin synthesis might lead to low peel hardness and easy cracking.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

Yang

Zhang

Pan

et al. 2022

IJMS

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Watermelon (Citrullus lanatus) is an important horticultural crop worldwide, but peel cracking caused by peel hardness severely decreases its quality. Lignification is one of the important functions of class III peroxidase (PRX), and its accumulation in the plant cell wall leads to cell thickening and wood hardening. For in-depth physiological and genetical understanding, we studied the relationship between peel hardness and lignin accumulation and the role of PRXs affecting peel lignin biosynthesis using genome-wide bioinformatics analysis. The obtained results showed that lignin accumulation gradually increased to form the peel stone cell structure, and tissue lignification led to peel hardness. A total of 79 ClPRXs (class III) were identified using bioinformatics analysis, which were widely distributed on 11 chromosomes. The constructed phylogenetics indicated that ClPRXs were divided into seven groups and eleven subclasses, and gene members of each group had highly conserved intron structures. Repeated pattern analysis showed that deletion and replication events occurred during the process of ClPRX amplification. However, in the whole-protein sequence alignment analysis, high homology was not observed, although all contained four conserved functional sites. Repeated pattern analysis showed that deletion and replication events occurred during ClPRXs’ amplification process. The prediction of the promoter cis-acting element and qRT-PCR analysis in four tissues (leaf, petiole, stem, and peel) showed different expression patterns for tissue specificity, abiotic stress, and hormone response by providing a genetic basis of the ClPRX gene family involved in a variety of physiological processes in plants. To our knowledge, we for the first time report the key roles of two ClPRXs in watermelon peel lignin synthesis. In conclusion, the extensive data collected in this study can be used for additional functional analysis of ClPRXs in watermelon growth and development and hormone and abiotic stress response.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

Yang

Zhang

Pan

et al. 2022

IJMS

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“…This is opposed by PbBZR1, which suppresses the activation of the promoters of lignin biosynthesis genes PbCOMT3 and PbHCT6 , and transient silencing PbBZR1 in pear increased lignin content and induced the expression of 15 lignin biosynthetic genes (Cao et al, 2020). Wang et al (2021) have characterized a NAC TF, PbrNSC (NAC STONE CELL PROMOTING FACTOR), which is phylogenetically related to AtNST1/2/3, as a regulator of lignocellulose formation associated with stone cells in pear fruit by integrating co‐expression networks and eQTLs (expression QTL) in 206 pear cultivars. The dual‐luciferase assay showed that PbrNSC could activate the PbrMYB169 , Pbr4CL4 , and PbrLAC4 promoters and genetic complementation experiments showed that PbrNSC could rescue the pendent inflorescence stem of nst1 / nst3 Arabidopsis , which is a symptom of suppressed SCW thickenings (Wang et al, 2021).…”

Section: Transcriptional Regulation Of Fleshy Fruit Lignificationmentioning

confidence: 99%

“…Wang et al (2021) have characterized a NAC TF, PbrNSC (NAC STONE CELL PROMOTING FACTOR), which is phylogenetically related to AtNST1/2/3, as a regulator of lignocellulose formation associated with stone cells in pear fruit by integrating co‐expression networks and eQTLs (expression QTL) in 206 pear cultivars. The dual‐luciferase assay showed that PbrNSC could activate the PbrMYB169 , Pbr4CL4 , and PbrLAC4 promoters and genetic complementation experiments showed that PbrNSC could rescue the pendent inflorescence stem of nst1 / nst3 Arabidopsis , which is a symptom of suppressed SCW thickenings (Wang et al, 2021). MicroRNAs (miRNAs) have also been implicated in lignification processes.…”

Section: Transcriptional Regulation Of Fleshy Fruit Lignificationmentioning

confidence: 99%

“…This indicates a conserved function of the AtMYB85 and AtMYB58 clades among species and implies that these two clades are the major regulators of lignin biosynthesis in fruits. Three lignin‐related NACs have been reported, PbrNCS, EjNAC1 and EjNAC3, and the former two have homology with AtVND7 and AtNST1/2/3 respectively, although the latter is not related to any other NAC members associated with SCW changes (Xu et al, 2015; Ge et al, 2017; Wang et al, 2021). A PbrNCS‐PbrMYB169 cascade has been shown to be involved in lignification in pear stone cells, and EjNACs and EjMYBs also operate in loquat fruit, but so far there is no evidence that the NAC‐MYB cascade operates in lignification of loquat and other fruits and this needs further study.…”

Section: Transcriptional Regulation Of Fleshy Fruit Lignificationmentioning

confidence: 99%

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Transcriptional regulation of fleshy fruit texture

Shi

et al. 2022

JIPB

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Fleshy fruit texture is a critically important quality characteristic of ripe fruit. Softening is an irreversible process which operates in most fleshy fruits during ripening which, together with changes in color and taste, contributes to improvements in mouthfeel and general attractiveness. Softening results mainly from the expression of genes encoding enzymes responsible for cell wall modifications but starch degradation and high levels of flavonoids can also contribute to texture change. Some fleshy fruit undergo lignification during development and post‐harvest, which negatively affects eating quality. Excessive softening can also lead to physical damage and infection, particularly during transport and storage which causes severe supply chain losses. Many transcription factors (TFs) that regulate fruit texture by controlling the expression of genes involved in cell wall and starch metabolism have been characterized. Some TFs directly regulate cell wall targets, while others act as part of a broader regulatory program governing several aspects of the ripening process. In this review, we focus on advances in our understanding of the transcriptional regulatory mechanisms governing fruit textural change during fruit development, ripening and post‐harvest. Potential targets for breeding and future research directions for the control of texture and quality improvement are discussed.

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“…Additional limitations of the use of RNA-seq data for variant calling are due to more complicated bioinformatics processing. Specific pipelines must be used to reduce possible false positives resulting from mapping errors induced by splicing events, RNA editing and allele-specific expressions [127,128].…”

Section: Rna Sequencingmentioning

confidence: 99%

DNA-Based Technologies for Grapevine Biodiversity Exploitation: State of the Art and Future Perspectives

et al. 2022

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The cultivated grapevine, Vitis vinifera subsp. vinifera L., is represented by an enormous population of varieties and clones. They arise from the accumulation of gametic and somatic mutations during centuries of sexual and asexual propagation. These varieties represent a vast reservoir of traits/alleles that could be useful in improving the berry quality as well as against environmental stresses. However, most of them are still unexploited. For this reason, an efficient characterization system is essential to define the varietal identity, avoid cases of synonymy (identical genotypes but different names) and homonymy (same names but different genotypes) and deepen our understanding of the existing diversity within the grape germplasm. The plethora of DNA-based high-throughput technologies currently available provides promising tools for the analysis of diversity, overcoming many of the limitations of phenotypic-based diversity analyses. However, the analysis of intra-varietal diversity remains challenging. In this scenario, after summarizing the causes and consequences of grapevine genetic inter- and intra-varietal diversity, we review the DNA-based technologies used for varietal genotyping, emphasizing those able to distinguish clones within a variety. This review provides an update on the technologies used to explore grapevine diversity, the knowledge of which is necessary for an efficient exploitation and conservation of the grapevine germplasm.

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A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

Cited by 41 publications

References 132 publications

Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

Transcriptional regulation of fleshy fruit texture

DNA-Based Technologies for Grapevine Biodiversity Exploitation: State of the Art and Future Perspectives

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