Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (18): 3744-3765.doi: 10.3864/j.issn.0578-1752.2025.18.012

• HORTICULTURE • Previous Articles     Next Articles

Based on Transcriptomics and Proteomics to Provide Insights into the Molecular Mechanisms of Calyx Abscission in Korla Xiangli

LIN Yan(), ZHENG LingLing, TIAN Jia, WEN Yue(), CHEN Chen, WANG Lei   

  1. Institute of Horticulture, Xinjiang Agricultural University/Xinjiang Forestry and Fruit Efficient Cultivation and High Value Utilization Engineering Technology Research Center, Urumqi 830052
  • Received:2025-05-05 Accepted:2025-06-24 Online:2025-09-18 Published:2025-09-18
  • Contact: WEN Yue

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Abstract:

【Objective】Calyx abscission in Korla Xiangli contributes to the improvement of fruit quality. Through multi-omics integrated analysis, the molecular mechanism of calyx abscission in Korla Xiangli was explored. The differentially expressed genes and proteins during the abscission process, as well as the involved metabolic pathways and signal transduction pathways were identified. This enriched the understanding of the abscission mechanism of calyx and provided a theoretical basis for further research on the abscission mechanism of calyx in Korla Xiangli. It also laid the foundation for the application of physiological and molecular techniques in regulating calyx abscission in Korla Xiangli in production. 【Method】Using Korla Xiangli pear as the research material, the clayx abscission zone of decalyx fruits and the corresponding parts of the abscission zone of persistent calyx fruits at the critical period of abscission zone formation were selected as research objects. Transcriptome and proteome sequencing, along with integrated analysis were performed. Multiple bioinformatics tools were employed to screen differentially expressed genes and proteins. The genes and proteins related to abscission were analyzed in detail, and the metabolic pathways and signal transduction pathways they participated in were identified. Finally, the differentially expressed genes were verified by quantitative real-time PCR (qRT-PCR). 【Result】A total of 393 differentially expressed genes were obtained through transcriptome analysis. These genes were mainly enriched in cell wall biosynthesis, plant-type cell wall organization or biogenesis, plant-type cell wall biosynthesis, plant-type secondary cell wall biosynthesis, phenylpropanoid metabolic processes, etc., as well as metabolic pathways, biosynthesis of secondary metabolites, and mutual Pentose and glucuronate interconversions, which indicated that most differentially expressed genes were involved in cell wall metabolism. A total of 256 differentially expressed proteins were obtained through proteome analysis. The integrated analysis showed that the differentially expressed genes and proteins were mainly enriched in pathways of plant hormone signal transduction, pentose and glucuronate interconversions, zeatin biosynthesis, and phenylpropanoid biosynthesis. Plant hormone-related genes (e.g., ethylene-responsive transcription factors, indole-3-acetic O-methyltransferase gene) and genes/proteins involved in cell wall degradation (e.g., pectin lyase gene, pectin esterase gene, polygalacturonase gene, peroxidase gene) were screened out, playing critical roles in calyx abscission of Korla Xiangli. In addition, the expression trends of 10 differentially expressed genes verified by qRT-PCR were consistent with the sequencing results. 【Conclusion】The regulation mechanism of calyx abscission in Korla Xiangli was determined from the levels of gene transcription and protein expression. Genes and proteins related to plant hormones and cell wall degrading enzymes were screened out, and clarified that the calyx abscission process of Korla Xiangli mainly involved in pathways such as phenylpropanoid biosynthesis, plant hormone signal transduction, pentose and glucuronate interconversions.

Key words: Korla Xiangli, calyx, abscission zone, transcriptome, proteome

Fig. 1

The external morphological changes of the abscission zone of decalyx fruit and the corresponding parts of the abscission zone of the persistent calyx in the fruits during the calyx abscission of Korla Xiangli A1: The early stage of the formation of the calyx abscission zone of the decalyx fruit; A2: The critical period of the formation of the calyx abscission zone of the decalyx fruit. The area circled in red was the calyx abscission zone; A3: The late stage of the formation of the calyx abscission zone of the decalyx fruit; B1: The early stage of the formation of the corresponding part of calyx abscission zone of the persistent calyx fruit; B2: The critical period of the formation of the corresponding part of calyx abscission zone of the persistent calyx fruit; B3: The late formation of the corresponding part of calyx abscission zone of the persistent calyx fruit"

Table 1

qRT-PCR specific primers"

基因编号 Gene ID 正向引物 Forward primer (5′-3′) 反向引物 Reverse primer (5′-3′)
Psin03G014400 GGACAAAAGATCAGCAGCCTAC ACCTGAGAAAGCTTGCCAAG
Psin05G015600 TGCAGCTGAAATTCGTGACC CCTCAGCTGTCTCAAATGTGC
Psin01G012900 TCTCTTCTTCGGCTCCACTTC AAATCCCCGTGCAGAATTCC
Psin03G003950 ACGACAACCTTGCACCTTTG TTTGATCACTGTGGAGGAGACC
Psin12G002990 ACAGCCTAACAGCAAACCAG TCAGGCCAACAGCAGAAAAC
Psin01G002910 TGCTTGATGACACACCAACC AAGAAACAACTCCCGGACAC
Psin01G014890 ACTTTCGACAATGGCGGTTC GCTCAATGACTCCTTTGGTTCC
Psin10G013480 AACAATTTGGGGGTCAAGGG TCAGTGCAAGTAACGTCGTC
Psin03G018850 GTTCCATGTATCCTTGCAACGG AACAACTTGTCGGCTGAACC
Psin02G000220 GTTCCATGTATCCTTGCAACGG AACAACTTGTCGGCTGAACC

Table 2

Sample sequencing and data comparison statistics"

样品
Sample		 原始序列数
Raw reads		 有效序列数
Valid reads		 有效碱基数
Valid bases		 基因组比对序列数
Reads mapped		 Q20
(%)		 Q30
(%)
T-L-1 53100666 51652274 7.75 47429147(91.82%) 97.70 93.25
T-L-2 49583548 48231834 7.23 44281991(91.81%) 97.62 93.07
T-L-3 50550552 49112684 7.37 45132315(91.90%) 97.58 92.97
S-LD-1 59022886 57275596 8.59 52859617(92.29%) 97.76 93.44
S-LD-2 64312592 62558674 9.38 57688769(92.22%) 97.70 93.28
S-LD-3 52419448 51073616 7.66 47107851(92.24%) 97.77 93.43

Fig. 2

Principal component analysis diagram among samples"

Fig. 3

Venn diagram of differentially expressed genes"

Fig. 4

Heatmap of differentially expressed genes"

Fig. 5

Bubble plots of GO and KEGG enrichment for differentially expressed genes A and B represent the GO and KEGG enrichment maps of differentially expressed genes, respectively"

Table 3

Functional enrichment analysis of the first 20 GO terms of differential gene expression"

分类
Category		 GO编号
GO number		 条目
Term		 差异基因数量
DEGs number		 校正后P值
Corrected P-value
生物过程
Biological process		 GO:0009834 植物型次生细胞壁生物合成 Plant-type secondary cell wall biogenesis 36 2.06×10-14
GO:0042546 细胞壁生物合成 Cell wall biogenesis 48 5.28×10-37
GO:0071669 植物型细胞壁组织或生物合成 Plant-type cell wall organization or biogenesis 46 9.20×10-31
GO:0009832 植物型细胞壁生物合成 Plant-type cell wall biogenesis 38 1.17×10-30
GO:0045492 木聚糖生物合成过程 Xylan biosynthetic process 20 8.92×10-26
GO:0044036 细胞壁大分子代谢过程 Cell wall macromolecule metabolic process 32 4.63×10-24
GO:0010383 细胞壁多糖代谢过程 Cell wall polysaccharide metabolic process 28 3.96×10-21
GO:0009698 苯丙烷类代谢过程 Phenylpropanoid metabolic process 35 3.24×10-22
GO:0070589 细胞组分大分子生物合成过程 Cellular component macromolecule biosynthetic process 23 9.34×10-22
GO:0044038 细胞壁大分子生物合成过程 Cell wall macromolecule biosynthetic process 23 9.34×10-22
GO:0010383 细胞壁多糖代谢过程 Cell wall polysaccharide metabolic process 28 3.96×10-21
GO:0045491 木聚糖代谢过程 Xylan metabolic process 22 4.68×10-21
GO:0010410 半纤维素代谢过程 Hemicellulose metabolic process 24 3.22×10-20
GO:0033692 细胞多糖生物合成过程 Cellular polysaccharide biosynthetic process 30 3.51×10-19
GO:0070592 多糖生物合成过程 Polysaccharide biosynthetic process 23 1.63×10-22
GO:0046274 木质素分解代谢过程 Lignin catabolic process 15 9.74×10-18
GO:0046271 苯丙烷类分解代谢过程 Phenylpropanoid catabolic process 15 9.74×10-18
分子功能
Molecular function		 GO:0016682 氧化还原酶活性，以二酚及相关物质为供体、氧为受体
Oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor		 18 2.21×10-18
GO:0052716 对苯二酚﹕氧氧化还原酶活性 Hydroquinone﹕oxygen oxidoreductase activity 15 3.05×10-18
GO:0016679 氧化还原酶活性，以二酚及相关物质为供体
Oxidoreductase activity, acting on diphenols and related substances as donors		 18 1.46×10-17

Table 4

KEGG pathway with significantly enriched differential genes"

分类
Category		 通路编号
Path number		 途径
Pathway		 差异基因数量
DEGs number		 校正后P值
Corrected P-value
代谢
Metabolism		 ko01100 代谢途径 Metabolic pathways 64 5.82×10-7
ko00040 戊糖和葡萄糖醛酸相互转化 Pentose and glucuronate interconversions 12 7.32×10-7
ko01110 次生代谢物的生物合成 Biosynthesis of secondary metabolites 34 1.39×10-3
ko00909 倍半萜和三萜生物合成 Sesquiterpenoid and triterpenoid biosynthesis 4 1.92×10-3
ko00073 角质、木栓质和蜡的生物合成 Cutin, suberine and wax biosynthesis 4 2.28×10-3
ko00908 玉米素生物合成 Zeatin biosynthesis 3 2.51×10-3
ko00520 氨基糖和核苷酸糖代谢 Amino sugar and nucleotide sugar metabolism 7 2.91×10-3
ko00940 苯丙烷生物合成 Phenylpropanoid biosynthesis 8 1.16×10-2

Fig. 6

Statistical chart of protein identification results (A) and peptide length distribution map (B)"

Fig. 7

Differential protein volcano map"

Fig. 8

GO and KEGG enrichment bubble plots of differentially expressed proteins A and B represent GO and KEGG enrichment bubble plots of differentially expressed proteins, respectively"

Table 5

GO functional enrichment analysis of the first 20 differentially expressed proteins"

分类
Category		 GO编号
GO number		 条目
Term		 差异蛋白数量
DEPs number		 校正后P值
Corrected P-value
生物过程
Biological process		 GO:0042744 过氧化氢分解代谢过程 Hydrogen peroxide catabolic process 7 1.17×10-5
GO:0006979 对氧化应激的响应 Response to oxidative stress 7 8.96×10-5
GO:0046274 木质素分解代谢过程 Lignin catabolic process 4 9.21×10-5
GO:0009627 系统获得性抗性 Systemic acquired resistance 3 5.19×10-4
GO:0009734 生长素激活的信号通路 Auxin-activated signaling pathway 5 1.80×10-3
GO:0051726 细胞周期调控 Regulation of cell cycle 2 4.49×10-3
GO:0006865 氨基酸运输 Amino acid transport 3 6.44×10-3
GO:0030036 肌动蛋白细胞骨架组织 Actin cytoskeleton organization 2 6.64×10-3
GO:0045492 木聚糖生物合成过程 Xylan biosynthetic process 2 9.16×10-3
GO:0000139 高尔基体膜 Golgi membrane 7 1.02×10-2
细胞组分
Cellular component		 GO:0004601 过氧化物酶活性 Peroxidase activity 7 2.83×10-5
GO:0005576 细胞外区域 Extracellular region 12 3.23×10-5
GO:0048046 质外体 Apoplast 6 2.96×10-4
GO:0005667 转录调节复合物 Transcription regulator complex 2 1.21×10-3
分子功能
Molecular function		 GO:0020037 血红素结合 Heme binding 12 4.82×10-5
GO:0052716 对苯二酚﹕氧氧化还原酶活性 Hydroquinone﹕oxygen oxidoreductase activity 4 7.60×10-5
GO:0015293 同向转运体活性 Symporter activity 4 3.15×10-3
GO:0008194 UDP-糖基转移酶活性 UDP-glycosyltransferase activity 6 4.10×10-3
GO:0071702 有机物质运输 Organic substance transport 2 4.49×10-3
GO:0005504 脂肪酸结合 Fatty acid binding 2 8.30×10-3

Table 6

KEGG pathway with significantly enriched differential proteins"

分类
Category		 通路编号
Path number		 途径
Pathway		 差异蛋白数量
DEPs number		 校正后P值
Corrected P-value
代谢
Metabolism		 ko00940 苯丙烷生物合成 Phenylpropanoid biosynthesis 9 1.44×10-4
ko00999 多种植物次生代谢物的生物合成
Biosynthesis of various plant secondary metabolites		 5 8.52×10-3
ko00561 甘油酯代谢 Glycerolipid metabolism 5 4.34×10-2
ko00908 玉米素生物合成 Zeatin biosynthesis 1 1.86×10-1
基因信息处理
Genetic information processing		 ko03410 碱基切除修复 Base excision repair 3 4.96×10-2
ko03030 DNA复制 DNA replication 4 1.54×10-2

Fig. 9

GO enrichment bar chart of differentially expressed proteins and genes"

Fig. 10

GO enrichment analysis of differentially expressed proteins co-upregulated and co-downregulated with differentially expressed genes A: The GO enrichment analysis of differentially expressed proteins co-upregulated with differentially expressed genes; B: The GO enrichment analysis of differentially expressed proteins co-down-regulated with differentially expressed genes"

Fig. 11

KEGG enrichment bubble plots of differentially expressed proteins and genes"

Table 7

Functional association analysis of differentially expressed proteins and differentially expressed genes"

分类
Category		 通路编号
Path number		 途径
Pathway		 差异蛋白数量
DEPs number		 差异基因数量
DEGs number
代谢
Metabolism		 ko04075 植物激素信号转导 Plant hormone signal transduction 4 9
ko00940 苯丙烷生物合成 Phenylpropanoid biosynthesis 9 8
ko00040 戊糖和葡糖醛酸相互转化 Pentose and glucuronate interconversions 2 12
ko00999 多种植物次生代谢产物的生物合成
Biosynthesis of various plant secondary metabolites		 5 3
ko00908 玉米素生物合成 Zeatin biosynthesis 1 7

Fig. 12

KEGG enrichment bar chart of differentially expressed proteins and genes and KEGG enrichment analysis heat map under common trend A: The KEGG enrichment analysis of differentially expressed genes and differentially expressed proteins; B: The KEGG enrichment analysis of differentially expressed genes and differentially expressed proteins"

Table 8

Association analysis of differentially expressed genes and proteins related to calyx abscission in Korla Xiangli"

通路名称
Path name		 蛋白质编号
Protein ID		 蛋白质名称
Protein name		 基因编号
Gene ID		 基因名称
Gene name		 上/下调
Up/Down
植物激素信号转导
Plant hormone signal transduction		 Psin05G015600 乙烯响应转录因子
Ethylene-responsive transcription factor		 上调Up
-- Psin03G014400 吲哚-3-乙酸O-甲基转移酶Indole-3-acetate O-methyltransferase 上调Up
苯丙烷生物合成
Phenylpropane biosynthesis		 GWHPDTVS001290-protein 过氧化物酶 Peroxidase Psin01G012900 过氧化物酶 Peroxidase 上调Up
GWHPDTVS022442-protein 过氧化物酶 Peroxidase Psin03G003950 过氧化物酶 Peroxidase 上调Up
GWHPDTVS004740-protein 过氧化物酶 Peroxidase Psin12G002990 过氧化物酶 Peroxidase 上调Up
Psin01G002910 过氧化物酶 Peroxidase 上调Up
戊糖和葡糖醛酸
互转化
Pentose and glucuronate interconversions		 Psin01G014890 果胶酯酶 Pectinesterase 上调Up
GWHPDTVS009649-protein 果胶裂解酶 Pectate lyase Psin10G013480 果胶裂解酶 Pectate lyase 上调Up
GWHPDTVS006230-protein 多聚半乳糖醛酸酶
Polygalacturonase		 Psin02G000220 多聚半乳糖醛酸酶
Polygalacturonase		 上调Up
Psin03G018850 多聚半乳糖醛酸酶 Polygalacturonase 上调Up

Fig. 13

Diagram of the ethylene signaling pathway in plant hormone signal transduction A: Partial schematic diagram of metabolic pathways based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene expression data. At the transcriptional or protein level, the up-regulated enzymes were shown in red; B: Heat maps of differentially expressed genes or proteins; C: The transcriptional abundance of differentially expressed genes in metabolic pathways. The same as below"

Fig. 14

Cell wall metabolic diagram in the pathway of Pentose and glucuronate interconversions"

Fig. 15

The biosynthetic pathway of phenylpropanoids"

Fig. 16

Verification of gene expression levels by qRT-PCR * indicates significant difference at P≤0.05, and ** indicates extremely significant difference at P≤0.01"

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