核桃内果皮硬化期生长素动态变化及差异表达基因分析

doi:10.16420/j.issn.0513-353x.2020-0438

园艺学报 ›› 2021, Vol. 48 ›› Issue (3): 487-504.doi: 10.16420/j.issn.0513-353x.2020-0438

核桃内果皮硬化期生长素动态变化及差异表达基因分析

鱼尚奇¹^,²^,⁴, 张锐²^,³^,⁴^,^*(), 郭众仲¹^,², 宋岩²^,³, 付嘉智²^,³, 武鹏雨²^,³, 马治浩³

¹塔里木大学生命科学学院,新疆阿拉尔 843300
²新疆生产建设兵团塔里木盆地生物资源保护利用重点实验室,新疆阿拉尔 843300
³塔里木大学植物科学学院,新疆阿拉尔 843300
⁴南疆特色果树高效优质栽培与深加工技术国家地方联合工程实验室,新疆阿拉尔 843300

收稿日期:2020-11-16 出版日期:2021-03-25 发布日期:2021-04-02
通讯作者: 张锐 E-mail:zhrgsh@163.com
基金资助:
新疆生产兵团南疆重点产业创新发展支撑计划项目(2017DB006);国家自然科学基金项目(31260469);研究生科研创新项目(TDGRI201716);大学生创新创业训练计划项目(201910757017)

Dynamic Changes of Auxin and Analysis of Differentially Expressed Genes in Walnut Endocarp During Hardening

YU Shangqi¹^,²^,⁴, ZHANG Rui²^,³^,⁴^,^*(), GUO Zhongzhong¹^,², SONG Yan²^,³, FU Jiazhi²^,³, WU Pengyu²^,³, MA Zhihao³

¹College of Life Science,Tarim University,Alar,Xinjiang 843300,China
²Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin,Alar,Xinjiang 843300,China
³College of Plant Science and Technology,Tarim University,Alar,Xinjiang 843300,China
⁴The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in South Xinjiang,Alar,Xinjiang 843300,China

Received:2020-11-16 Online:2021-03-25 Published:2021-04-02
Contact: ZHANG Rui E-mail:zhrgsh@163.com

摘要/Abstract

摘要：

为研究核桃内果皮硬化主要涉及的生物过程及生长素在硬化过程中的作用,以‘新露’核桃为研究试材,形态学观察及木质素沉积分析表明,内果皮硬化与其表面维管束分布具有密切关系,靠近维管组织附近的内果皮硬化先于远离维管的区域。IAA含量在内果皮硬化过程中呈V字形变化;IAA在5个时期平均含量最高（16.467 ng·g^-1）,约为IBA、ICA和ME-IAA总和的6.8倍。木质素合成中间代谢物分析显示,木质素单体对香豆醇在内果皮硬化区的含量是未硬化区的16倍,芥子醇在内果皮硬化区的含量极高,但在未硬化区未检测到存在,且随着硬化进程这两种物质在内果皮硬化区的含量总体呈上升趋势。转录组与蛋白组关联分析获得了内果皮硬化相关的差异表达基因369条,在转录水平和蛋白质水平同时存在差异的基因关联结果较好,相关系数最低为0.48124;但差异表达基因整体关联结果较差,相关系数最高为0.22112。利用Metascape构建了差异表达基因显著富集的前20个生物学功能之间的关系网络,发现内果皮硬化主要涉及苯丙烷类代谢、氧胁迫响应、细胞壁组织与生物合成和氨基糖与核酸糖代谢4个生物过程。荧光定量结果表明,AUX/IAA基因JrIAA9、JrIAA16和JrIAA27的表达量变化趋势与IAA含量的基本一致。由此推测生长素IAA在内果皮硬化过程中发挥着重要调控作用,这对后续开展露仁发生机理研究具有重要参考意义。

关键词: 核桃, 生长素, 内果皮, 转录组, 蛋白组, 关联分析, 木质素

Abstract:

In order to study the hardening of the walnut endocarp,which mainly involves the biological process and the role of auxin in the hardening process,the‘Xinlu’walnut was used as the research material. There is a close relationship between walnut endocarp hardening and distribution of vascular bundles on the walnut endocarp surface by morphological observation and lignin deposition analysis;The hardening of walnut endocarp near the vascular tissue is earlier than that away from the vascular tissue. The content of IAA showed a V-shaped change in the hardening of the endocarp. The average content of IAA was the highest than others during the five stages,16.467 ng·g^-1,which was about 6.8 times of the sum of IBA,ICA and ME-IAA. The analysis of intermediate metabolites of lignin synthesis showed that the content of p-coumaryl alcohol of lignin monomer in the hardening area of the endocarp was 16 times of the unhardening area. The content of sinapyl alcohol in the hardening area of the walnut endocarp was extremely high,but it was not detected in the unhardening area,and the content of these two substances in the hardening area of the walnut endocarp showed an overall upward trend with the hardening process. Through transcriptome and proteome correlation analysis,369 differentially expressed genes related to endocarp hardening were obtained. The correlation result of genes that are differentially expressed at both the transcription and protein levels is good,with the lowest correlation coefficient of 0.48124,but the correlation result of all differentially expressed genes is poor,with the highest correlation coefficient of 0.22112. Using Metascape to construct a network of relationships among the top 20 biological functions that are significantly enriched by differentially expressed genes,it is found that four biological processes,namely Phenylpropanoid metabolic process,Response to oxidative stress,Cell wall organization or biogenesis,Amino sugar and nucleotide sugar metabolism were mainly involved in endocarp hardening mainly involve. The fluorescence quantitative results showed that the expression changes trend of AUX/IAA genes JrIAA9,JrIAA16 and JrIAA27 were basically consistent with that of IAA content. It is speculated that IAA plays an important regulatory role in the process of walnut endocarp hardening,and it is of great significance to carry out the research on the mechanism of Bared-nut later.

Key words: walnut, auxin, endocarp, transcriptome, proteome, correlation analysis, lignin

中图分类号:

S664.1

鱼尚奇, 张锐, 郭众仲, 宋岩, 付嘉智, 武鹏雨, 马治浩. 核桃内果皮硬化期生长素动态变化及差异表达基因分析[J]. 园艺学报, 2021, 48(3): 487-504.

YU Shangqi, ZHANG Rui, GUO Zhongzhong, SONG Yan, FU Jiazhi, WU Pengyu, MA Zhihao. Dynamic Changes of Auxin and Analysis of Differentially Expressed Genes in Walnut Endocarp During Hardening[J]. Acta Horticulturae Sinica, 2021, 48(3): 487-504.

图/表 12

表1 qRT-PCR 定量分析引物

Table 1 The primers of qRT-PCR

引物名称	引物序列（5′-3′）	长度/bp	退火温度/℃
Primer name	Primer sequence	Length	Annealing temperature
JrIAA9-F	TCTGGGTTCATCAGCAGCACG	21	59.52
JrIAA9-R	TGCGATGCTGTCCTCAAGGT	20	57.45
JrIAA16-F	AGTGCTTGACCGCACAGGTT	20	57.45
JrIAA16-R	TGCTTGTAGGCGATGTGCCA	20	57.45
JrIAA27-F	GCTAGCACCAAGGGCAATGGA	21	59.52
JrIAA27-R	AGGGAAAGGGTGGGGCCTAAT	21	59.52
JrPAL1-F	ACAACCGGCTTCCGGTACTCCT	22	61.40
JrPAL1-R	AACGGCAACGGCAACGGCAA	20	59.50
Jr4CL1-F	ACTGTGCGTATTGCCGCTGT	20	59.52
Jr4CL1-R	TCGCCAAGACAATCGGTGGA	20	57.45
JrC4H1-F	GTTAGCCCTGTTTGTAGCCGC	21	57.45
JrC4H1-R	TTGGCCATGTCGGTGAGGTT	20	57.45
JrC3H1-F	TTGCACGTGATCCGGCAGT	19	57.32
JrC3H1-R	TGGTGCAGTAGGTGAGCAAGC	21	59.52
JrF5H1-F	TTCACAGGCTTGCCGATGCT	20	57.45
JrF5H1-R	ACATGGCCTTCGCTCACTACG	21	59.52
JrCAD1-F	ACAACACGACCTCTGCTTGTTA	22	55.81
JrCAD1-R	CGTTGTGGATGTTGCTGGAAGT	22	57.67
JrCCR1-F	TTCTGCAGCGCGGTTACACT	20	57.45
JrCCR1-R	TCACAGCCCTGAATAGCAGCA	21	57.57
JrCOMT1-F	TCTTCTCAGATCCTCGCCCGTGTC	24	62.98
JrCOMT1-R	TTCTCTCGGAGTCGGAGTCGTTGG	24	62.98
JrCCOAOMT1-F	AGCGGTATTCGGGGGTTTGGT	21	59.52
JrCCOAOMT1-R	CGTCGTGGCGCCTCCTGATG	20	63.60
JrPER1-F	TGCTTCGCTGCTGCTGGACTCAA	23	61.33
JrPER1-R	TCCCACCGCAACAATGCCATCTCT	24	61.28
JrLACC1-F	AGCTGACAGTTGTGGGTGCGGATG	24	62.98
JrLACC1-R	AGAATGGCGGTGGTGGTGGTGTTG	24	62.98
JrLTPG1-F	TGCGGTGGTGTTGGTCGCAA	20	59.50
JrLTPG1-R	AGCAACTGCTGGGTGCTTCG	20	59.50

图1 盛花后不同天数的核桃内果皮发育的动态变化 A ~ D:‘纸皮’核桃盛花后37、44、66和80 d内果皮木质素的积累变化。E ~ J:‘新露’核桃盛花后50、57、64、71、78和85 d内果皮木质素的积累变化。K ~ L:‘新露’核桃成熟前内果皮形态。M ~ P:‘新露’核桃子房壁细胞形态。Q ~ S:‘新露’核桃成熟后内果皮形态。Te:种皮;Co:子叶;Ex:外果皮;Me:中果皮;En:内果皮;Pu:未硬化区;Sc:硬化区;Va:维管束;Iwo:子房内壁;Mwo:子房中壁;Owo:子房外壁。

Fig. 1 Dynamic changes of endocarp development of walnut in different days after florescence A-D:Changes of lignin accumulation in endocarp of the‘Zhipi’walnut during 37,44,66 and 80 days after florescence. E-J:Changes of lignin accumulation in endocarp of the‘Xinlu’walnut during 50,57,64,71,78 and 85 days after florescence. K-L:The form of endocarp of the‘Xinlu’walnut before ripening. M-P:The cell form of ovary wall of the‘Xinlu’walnut. Q-S:The form of endocarp of the‘Xinlu’walnut after ripening. Te:Testa;Co:Cotyledon;Ex:Exocarp;Me:Mesocarp;En:Endocarp;Pu:Pulpy;Sc:Sclerotic;Va:Vascular bundle;Iwo:Inner wall of ovary;Mwo:Middle wall of ovary;Owo:Outer wall of ovary.

图2 ‘新露’核桃内果皮内源激素含量小写字母表示同一种内源生长素在不同时期在5%水平差异显著。

Fig. 2 Endogenous hormone levels in endocarp of‘Xinlu’walnut Lower case letters indicate that the same endogenous auxin has significant difference at the 5% level.

图3 木质素代谢通路和木质素合成中间代谢产物变化示意图示意图中X代表其他物质,箭头代表代谢物生成的上下游关系。A:肉桂酸;B:L-苯丙氨酸;C:4-香豆酸;D:咖啡酸;E:阿魏酸;F:芥子酸;G:香豆醛; H:咖啡醛;I:松柏醛;J:芥子醛;K:对香豆醇;L:咖啡醇;M:松柏醇;N:芥子醇。“*”表示同一时期内果皮两个区域代谢物含量差异显著,“**”表示同一时期内果皮两个区域代谢物含量差异极显著。下同。

Fig. 3 Changes of intermediate metabolites of lignin synthesis and schematic diagram of the lignin metabolism pathway X is for something else,and the arrows represent the upstream and downstream relationships of metabolite production.A:Cinnamic acid;B:L-Phenylalanine;C:p-Coumaric acid;D:Caffeic acid;E:Ferulic acid;F:Sinapic acid;G:p-Coumaraldehyde;H:Caffeyl aldehyde;I:4-Hydroxy-3-methoxycinnamaldehyde;J:Sinapinaldehyde; K:p-Coumaryl alcohol;L:Caffeyl alcohol;M:Coniferyl alcohol;N:Sinapyl alcohol; “*”means that the content of metabolite is significantly different between the two regions of endocarp during the same period, and“**”means that the content of metabolite is extremely significanly different between the two regions of endocarp during the same period. The same below.

表2 转录组与蛋白组关联统计

Table 2 Association statistics of transcriptome and proteome

比对组 Group name	关联水平 Type of correlations	蛋白质数量 Number of proteins	基因数量 Number of genes	关联数量 Number of correlations
57 d-VS-71 d	鉴定Identification	6 776	75 654	6 751
	定量Quantitative	6 765	75 654	6 740
	差异表达Differentially expressed	545	8 339	110
57 d-VS-85 d	鉴定 Identification	6 776	76 053	6 756
	定量Quantitative	6 770	76 053	6 750
	差异表达Differentially expressed	1 260	9 985	300

图4 比对组（57 d-VS-71 d和57 d-VS-85 d）差异表达基因富集分析条形图代表差异基因富集条目,颜色代表P值。P值越小表示富集的条目越可靠,即-Log10(P)值越大表示富集的条目越可靠。A1:M00138黄酮和花葵素的生物合成;A2:ath00520:氨基糖和核苷酸糖代谢;A3:GO:0044036:细胞壁大分子物质代谢过程;A4:GO:0009408:对热的响应;A5:GO:0019751:多元醇代谢过程;A6:GO:0017144:药物代谢过程;A7:GO:0016052:碳水化合物分解过程;A8:GO:0006979:对氧化应激的响应;A9:GO:0010038:对金属离子的响应;B1:ath00940:苯丙烷类生物合成;B2:GO:0046686:对镉离子的响应;B3:GO:0017144:药物代谢过程;B4:ath00360:苯丙氨酸代谢;B5:GO:0009266:对温度刺激的响应;B6:GO:0071554:细胞壁组织或生物发生;B7:ath01230:氨基酸的生物合成;B8:GO:0006826:铁离子转运;B9:GO:0051186:辅助因子代谢过程;B10:GO:0009226:核苷酸糖生物合成过程;B11:GO:0009636:对有毒物质的响应;B12:ath00500:淀粉和蔗糖代谢;B13:GO:0006575:细胞修饰氨基酸代谢过程;B14:GO:0009072:芳香族氨基酸家族代谢过程;B15:GO:0006457:蛋白质折叠;B16:M00002:糖酵解相关;B17:ath00960:莨菪烷,哌啶和吡啶生物合成;B18:GO:0042133:神经递质代谢过程;B19:GO:0018298:蛋白质-嗜铬细胞连锁;B20:GO:0010431:种子成熟。

Fig. 4 Enrichment analysis of differentially expressed genes in comparison group（57 d-VS-71 d and 57 d-VS-85 d） Bar graph of enriched terms across input gene lists, colored by p-values. The smaller the p value is,the more reliable the enriched item is,i.e. the larger the -log10 (p) value is, the more reliable the enriched item is. A1:M00138:Flavonoid biosynthesis, naringenin => pelargonidin;A2:ath00520:Amino sugar and nucleotide sugar metabolism;A3:GO:0044036:Cell wall macromolecule metabolic process;A4:GO:0009408:Response to heat;A5:GO:0019751:Polyol metabolic process;A6:GO:0017144:Drug metabolic process;A7:GO:0016052:Carbohydrate catabolic process;A8:GO:0006979:Response to oxidative stress;A9:GO:0010038:Response to metal ion;B1:ath00940:Phenylpropanoid biosynthesis;B2:GO:0046686:Response to cadmium ion;B3:GO:0017144:Drug metabolic process;B4:ath00360:Phenylalanine metabolism;B5:GO:0009266:Response to temperature stimulus;B6:GO:0071554:Cell wall organization or biogenesis;B7:ath01230:Biosynthesis of amino acids;B8:GO:0006826:Iron ion transport;B9:GO:0051186:Cofactor metabolic process;B10:GO:0009226:Nucleotide-sugar biosynthetic process;B11:GO:0009636:Response to toxic substance;B12:ath00500:Starch and sucrose metabolism;B13:GO:0006575:Cellular modified amino acid metabolic process;B14:GO:0009072:Aromatic amino acid family metabolic process;B15:GO:0006457:Protein folding;B16:M00002:Glycolysis, core module involving three-carbon compounds;B17:ath00960:Tropane, piperidine and pyridine alkaloid biosynthesis;B18:GO:0042133:Neurotransmitter metabolic process;B19:GO:0018298:Protein-chromophore linkage. B20:GO:0010431:Seed maturation.

表 3 差异表达基因mRNA表达量和蛋白表达量之间的相关系数

Table 3 Correlation coefficient between mRNA expression and protein expression of the differentially expressed genes

比对组	亚组类型	斯皮尔曼相关系数（R）
Group name	Type of subgroup	Spearman correlation coefficient
57 d-VS-71 d	DEPs_DEGs	0.481 24
	DEPs_DEGs_Same Trend	0.802 57
	DEPs_DEGs_Opposite	-0.821 57
	DEPs_NDEGs	0.020 74
	NDEPs_DEGs	0.123 15
	NDEPs_NDEGs	0.045 00
	ALL	0.073 99
57 d-VS-85 d	DEPs_DEGs	0.700 65
	DEPs_DEGs_Same Trend	0.833 35
	DEPs_DEGs_Opposite	-0.573 34
	DEPs_NDEGs	0.225 70
	NDEPs_DEGs	0.356 13
	NDEPs_NDEGs	0.085 44
	ALL	0.221 12

图6 核桃内果皮硬化相关功能网路图为显著富集排名前20个生物学功能簇的条目间的可视化关系网络图。为了作图方便,每个生物学功能簇中选取具有最佳P-value的条目,但条目数不超过15个。在20个生物学功能簇中,总条目数不超过250个。每一个节点代表一个条目,条目之间的成员相似度 > 0.3时,条目之间用线连接在一起。Pic1中不同颜色代表不同的生物学功能簇,同一生物学功能簇中的条目具有相同颜色。生物学功能簇的名称为在一个生物学功能簇中用具有最显著统计意义的条目的名称。Pic2中不同颜色代表条目的 P-value的转换值[Log10(P)],颜色越深表示条目显著性越高。A:苯丙烷类代谢过程;B:对氧化应激的响应;C:细胞壁组织或生物发生;D:对金属离子的响应;E:对温度刺激的响应;F:黄酮类化合物生物合成;G:黄酮及柚皮素合成;H:半纤维素代谢过程;I:氨基糖和核苷酸糖代谢;J:小分子物质生物合成过程;K:对有毒物质的响应;L:苯丙烷类分解代谢过程;M:S-腺苷甲硫氨酸生物合成过程;N:蛋白质的折叠;O:对缺水的响应;P:香豆素生物合成过程;Q:对紫外线的响应;R:淀粉和蔗糖代谢;S:细胞对有毒物质的响应;T:小分子物质分解过程。

Fig. 6 Network of the enriched function for hardening of walnut endocarp The picture shows the visual relationship network among the Terms of the clusters that were enriched the top 20 significantly. For the convenience of drawing,selected the Terms with the best P-value in each cluster,but the number of Term does not exceed 15. In 20 clusters,the total number of Term does not exceed 250. Each node represents a Term. When the member similarity between Term > 0.3,the Term is connected by edges. Different colors in Pic1 represent different clusters,and Term in the same cluster has the same color. The name of the cluster is the name of the term with the most significant statistical significance in a cluster. Different colors in Pic2 represent the conversion value of Term's P-value[Log10(P)]. The darker the color,the higher the significance of Term. A:Phenylpropanoid metabolic process;B:Response to oxidative stress;C:Cell wall organization or biogenesis;D:Response to metal ion;E:Response to temperature stimulus;F:Flavonoid biosynthesis;G:Flavanone biosynthesis,phenylalanine => naringenin;H:Hemicellulose metabolic process;I:Amino sugar and nucleotide sugar metabolism;J:Small molecule biosynthetic process;K:Response to toxic substance;L:Phenylpropanoid catabolic process;M:S-adenosylmethionine biosynthetic process;N:Protein folding;O:Response to water deprivation;P:Coumarin biosynthetic process;Q:Response to UV;R:Starch and sucrose metabolism;S:Cellular response to toxic substance;T:Small molecule catabolic process.

图7 核桃3个生长素响应基因保守基序（Motif 1 ~ Motif 10）

Fig. 7 Conserved motifs（Motif 1-Motif 10）of three auxin response genes in walnut

图8 核桃内果皮硬化期3个生长素相关基因的表达不同大写字母表示同一基因在不同时期在1%水平差异显著。

Fig. 8 Expression of three auxin related genes in walnut endocarp at sclerosis stage Different capital indicates there are significant difference in same gene at the 1% level in different periods.

图9 木质素合成途径相关的12个基因的表达 “*”表示同一时期内果皮两个区域基因表达差异显著,“**”表示同一时期内果皮两个区域基因表达差异极显著。

Fig. 9 Expression of 12 genes related to lignin synthesis pathway “*”means that the expression of gene is significant difference between the two regions of endocarp during the same period,and“**”means that the expression of gene is extremely significant difference between the two regions of endocarp during the same period.

图10 ‘新露’核桃内果皮硬化预测模型示意图

Fig. 10 Schematic diagram of possible‘Xinlu’walnut endocarp hardening model

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核桃内果皮硬化期生长素动态变化及差异表达基因分析

Dynamic Changes of Auxin and Analysis of Differentially Expressed Genes in Walnut Endocarp During Hardening

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核桃内果皮硬化期生长素动态变化及差异表达基因分析

Dynamic Changes of Auxin and Analysis of Differentially Expressed Genes in Walnut Endocarp During Hardening

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