卷叶木薯及其突变体叶片的比较转录组分析

doi:10.3724/SP.J.1006.2024.34168

作物学报 ›› 2024, Vol. 50 ›› Issue (8): 2143-2156.doi: 10.3724/SP.J.1006.2024.34168

• 研究简报 • 上一篇

卷叶木薯及其突变体叶片的比较转录组分析

肖明昆¹(), 严炜¹^,²^,^*(), 宋记明¹^,²(), 张林辉¹^,², 刘倩¹, 段春芳¹^,², 李月仙¹^,², 姜太玲¹^,², 沈绍斌¹^,², 周迎春¹, 沈正松¹^,², 熊贤坤¹, 罗鑫¹, 白丽娜¹, 刘光华³^,^*()

¹云南省农业科学院热带亚热带经济作物研究所, 云南保山 678000
²热带作物生物育种全国重点实验室, 云南昆明 650205
³云南省农业科学院国际农业研究所, 云南昆明 650205

收稿日期:2023-10-15 接受日期:2024-04-01 出版日期:2024-08-12 网络出版日期:2024-04-24
通讯作者: * 严炜, E-mail: rjsyw@yaas.org.cn;刘光华, E-mail: rjslgh@vip.126.com
作者简介:肖明昆, E-mail: nkyxmk@163.com;
宋记明, E-mail: 821427168@qq.com
^** 同等贡献
基金资助:
兴滇英才支持计划项目——云南优良饲草品种选育及产业化关键技术集成示范和财政部和农业农村部国家现代农业产业技术体系建设专项(木薯-保山综合试验站);兴滇英才支持计划项目——云南优良饲草品种选育及产业化关键技术集成示范和财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-11-YNLGH)

Comparative transcriptome profiling of leaf in curled-leaf cassava and its mutant

XIAO Ming-Kun¹(), YAN Wei¹^,²^,^*(), SONG Ji-Ming¹^,²(), ZHANG Lin-Hui¹^,², LIU Qian¹, DUAN Chun-Fang¹^,², LI Yue-Xian¹^,², JIANG Tai-Ling¹^,², SHEN Shao-Bin¹^,², ZHOU Ying-Chun¹, SHEN Zheng-Song¹^,², XIONG Xian-Kun¹, LUO Xin¹, BAI Li-Na¹, LIU Guang-Hua³^,^*()

¹Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan 678000, Yunnan, China
²National Key Laboratory of Tropical Crop Breeding, Kunming 650205, Yunnan, China
³International Agricultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, Yunnan, China

Received:2023-10-15 Accepted:2024-04-01 Published:2024-08-12 Published online:2024-04-24
Contact: * E-mail: rjsyw@yaas.org.cn;E-mail: rjslgh@vip.126.com
About author:^** Contributed equally to this work
Supported by:
Xingdian Talent Support Plan Project: Integrated Demonstration of Key Technologies for the Breeding and Industrialization of Excellent Forage Varieties in Yunnan, and the China Agriculture Research System of MOF and MARA (Cassava-Comprehensive Experimental Station Project);Xingdian Talent Support Plan Project: Integrated Demonstration of Key Technologies for the Breeding and Industrialization of Excellent Forage Varieties in Yunnan, and the China Agriculture Research System of MOF and MARA(CARS-11-YNLGH)

摘要/Abstract

摘要：

为解析卷叶木薯叶片异常发育的分子调控机制及代谢通路, 以正常卷叶木薯叶片(JY)、突变株展叶叶片(ZY)和突变株卷叶叶片(BJ)为试验材料, 基于转录组测序(RNA-seq)数据进行生物信息学分析。DESeq差异分析结果显示, ZY vs BJ、JY vs ZY、JY vs BJ分别有327 (255个上调, 72个下调)、1085 (337个上调, 748个下调)、689 (381个上调, 308个下调)个DEGs, 有19个DEGs是3个比较组共同表达的。GO功能分析显示, DEGs在刺激反应、膜的组成部分、跨膜转运蛋白活性等途径差异显著。KEGG富集分析显示, DEGs在苯丙素的生物合成、植物激素信号转导、内质网中的蛋白加工等通路较为活跃。进一步对变异展叶与同株的卷叶和其他植株正常卷叶的DEGs分析发现集中富集到苯丙素的生物合成途径、淀粉和蔗糖代谢、植物激素信号转导, 这可能是展叶突变体形成的关键因子。展叶与卷叶差异基因的主要KEGG代谢通路有9条, 重要差异基因有9个。对不同类型叶片显微分析发现突变后的展叶木薯上表皮细胞层数增加、海绵组织结构变得疏松、维管束细胞减少。研究结果为进一步理解木薯叶片异常发育的分子机制提供了理论指导, 为木薯遗传改良、种质创新挖掘提供基因资源和改良策略。

关键词: 木薯, 转录组分析, 突变, 差异基因表达

Abstract:

The objective of this study is to elucidate the molecular regulatory mechanisms and metabolic pathways underlying the abnormal development in the leaf of curled-leaf cassava. Normal curled cassava leaf (JY), mutant expanded leaf (ZY), and mutant curled leaf (BJ) were used as the experimental materials, and bioinformatics analysis was conducted based on transcriptome sequencing (RNA-seq) data. DESeq differential analysis showed that there were 327 (255 up-regulated, 72 down-regulated) DEGs for ZY vs BJ, 1085 (337 up-regulated, 748 down-regulated) DEGs for JY vs ZY, and 689 (381 up-regulated, 308 down-regulated) DEGs for JY vs BJ, and 19 DEGs were co-expressed by three comparative groups. GO functional analysis showed that DEGs had significant differences in the pathways of stimulus response, components of membranes, and transmembrane transporter protein activity. KEGG enrichment analysis indicated that the DEGs were more active in pathways such as phenylpropanoid biosynthesis, phytohormone signaling, and protein processing in the endoplasmic reticulum. Further analysis of the DEGs in the mutated leaf expansion, curled leaves of the same plant, and normal curled leaves of other plants, demonstrated that the DEGs were concentrated in the phenylpropanoid biosynthesis pathways, starch and sucrose metabolism, and plant hormone signal transduction, which may be the key factors causing leaf expansion mutants. There were 9 main KEGG metabolic pathways and 9 important differentially expressed genes involved in leaf expansion and leaf curling. Microscopic analysis of different types of leaf revealed an increase in the number of epidermal cell layers, a loosening of sponge tissue structure, and a decrease in vascular bundle cells in mutated expanded cassava. The results of this study provide theoretical guidance for further understanding the molecular mechanisms underlying the abnormal development of cassava leaf, as well as genetic resources and improvement strategies for cassava genetic improvement and germplasm innovation.

Key words: cassava, transcriptome analysis, mutation, differential gene expression

肖明昆, 严炜, 宋记明, 张林辉, 刘倩, 段春芳, 李月仙, 姜太玲, 沈绍斌, 周迎春, 沈正松, 熊贤坤, 罗鑫, 白丽娜, 刘光华. 卷叶木薯及其突变体叶片的比较转录组分析[J]. 作物学报, 2024, 50(8): 2143-2156.

XIAO Ming-Kun, YAN Wei, SONG Ji-Ming, ZHANG Lin-Hui, LIU Qian, DUAN Chun-Fang, LI Yue-Xian, JIANG Tai-Ling, SHEN Shao-Bin, ZHOU Ying-Chun, SHEN Zheng-Song, XIONG Xian-Kun, LUO Xin, BAI Li-Na, LIU Guang-Hua. Comparative transcriptome profiling of leaf in curled-leaf cassava and its mutant[J]. Acta Agronomica Sinica, 2024, 50(8): 2143-2156.

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名称 Name	株高 Plant height (cm)	主茎粗 Stem diameter (mm)	地上鲜重 Aboveground fresh weight (kg)	鲜薯个数 Number of fresh cassava	单株产量 Yield per plant (kg)	鲜薯内皮/外皮/薯肉颜色 Cassava inner skin color/exterior skin color/flesh color
BJ	220.80±10.71 a	24.18±1.30 a	1.70±0.55 a	10.0±2.36 a	1.54±0.69 a	白色/红褐色/白色 White/reddish brown/white
ZY	278.60±16.57 b	28.16±4.20 a	2.46±0.71 a	12.2±3.27 a	2.66±0.73 b	白色/红褐色/白色 White/reddish brown/white
JY	257.40±11.85 c	24.06±4.96 a	1.92±0.61 a	10.0±3.32 a	2.02±0.31 ab	白色/红褐色/白色 White/reddish brown/white

样品名 Sample name	原始Reads总数 Total number of original Reads	碱基总数 Base total	过滤后Reads总数 Total number of Reads after filtering (%)	比对上参考基因组的Reads总数 Total number of Reads for the reference genome on the comparison (%)	Phred>20的百分比Q20 (%)	Phred>30的百分比Q30 (%)
BJ1	48,631,342	7,294,701,300	42,424,940 (87.24%)	39,417,519 (92.91%)	97.98	94.44
BJ2	48,954,268	7,343,140,200	43,028,526 (87.9%)	40,024,972 (93.02%)	97.88	94.15
BJ3	46,016,900	6,902,535,000	40,829,784 (88.73%)	37,826,541 (92.64%)	98.03	94.51
JY1	56,255,460	8,438,319,000	49,247,380 (87.54%)	46,094,300 (93.60%)	98.01	94.48
JY2	48,692,404	7,303,860,600	43,869,232 (90.09%)	40,496,556 (92.31%)	97.96	94.37
JY3	53,605,768	8,040,865,200	47,008,274 (87.69%)	43,423,863 (92.37%)	98.01	94.49
ZY1	55,114,316	8,267,147,400	48,942,778 (88.80%)	45,888,649 (93.76%)	97.96	94.37
ZY2	48,301,582	7,245,237,300	41,856,280 (86.66%)	39,058,323 (93.32%)	97.92	94.30
ZY3	50,036,022	7,505,403,300	44,199,486 (88.34%)	40,576,149 (91.80%)	97.90	94.26

突变类型 Mutation type	ZY突变基因数量 Number of ZY mutated genes	占ZY突变基因数量 Percentage of the number of ZY mutated genes (%)	BJ突变基因数量 Number of BJ mutated genes	占BJ突变基因数量 Percentage of the number of BJ mutated genes (%)	JY突变基因数量 Number of JY mutated genes	占JY突变基因数量 Percentage of the number of JY mutated genes (%)
同义单核苷酸突变Synonymous SNV	43,071	51.32	43,602	51.26	44,439	50.89
非同义单核苷酸突变 Non synonymous SNV	39,678	47.28	40,291	47.37	41,641	47.69
非移码替换 Non frameshift substitution	591	0.70	587	0.69	608	0.70
未知类型 Unknown	194	0.23	187	0.22	233	0.27
移码替换 Frameshift substitution	170	0.20	172	0.20	182	0.21
终止密码子增加 Stopgain	167	0.20	164	0.19	171	0.20

路径ID Pathway ID	条目 Term	数量Number
路径ID Pathway ID	条目 Term	ZY vs BJ	JY vs ZY
mesc00360	苯丙氨酸代谢 Phenylalanine metabolism	2	6
mesc00460	氰胺酸代谢 Cyanoamino acid metabolism	3	8
mesc00480	谷胱甘肽代谢 Glutathione metabolism	3	7
mesc00500	淀粉和蔗糖代谢 Starch and sucrose metabolism	7	12
mesc00592	α-亚麻酸代谢 Alpha-Linolenic acid metabolism	5	7
mesc00904	二萜类化合物的生物合成 Diterpenoid biosynthesis	2	5
mesc00940	苯丙素类化合物的生物合成 Phenylpropanoid biosynthesis	9	22
mesc00941	类黄酮的生物合成 Flavonoid biosynthesis	2	6
mesc04075	植物激素信号转导 Plant hormone signal transduction	5	12

基因ID	基因长度 Gene length	上调出现频数 Frequency of gene up-regulation	下调出现频数Frequency of gene downregulation	描述 Description	条目 Term
LOC110625143	1706	3	3	β-葡萄糖苷酶12 [木薯] XP_021626382.1 beta-glucosidase 12-like [Manihot esculenta]	苯丙素类化合物的生物合成 Phenylpropanoid biosynthesis α-亚麻酸代谢 Starch and sucrose metabolism 谷胱甘肽代谢 Cyanoamino acid metabolism
LOC110619850	1880	3	3	木薯亚麻苦甙水解酶 AAB22162.1 linamarase [Manihot esculenta]
LOC122724051	1849	3	3	木薯亚麻苦甙水解酶 AAB22162.1 linamarase [Manihot esculenta]
LOC110603741	1879	3	0	β-葡萄糖苷酶45 [木薯] XP_021597319.1 beta-glucosidase 45 [Manihot esculenta]
LOC110618460	1829	3	0	β-葡萄糖苷酶24-样异构体 X2 [木薯] XP_021617285.1 beta-glucosidase 24-like isoform X2 [Manihot esculenta]
LOC110618773	1768	3	0	β-葡萄糖苷酶24-样异构体 X1 [木薯] XP_021617701.1 beta-glucosidase 24-like isoform X1 [Manihot esculenta]
LOC110615840	2048	0	3	β-葡萄糖苷酶11 [木薯] XP_021613689.1 beta-glucosidase 11-like [Manihot esculenta]
LOC110625014	2363	2	2	PLA:苯丙氨酸氨解酶G4 [木薯] PLA: phenylalanine ammonia-lyase G4-like [Manihot esculenta]	苯丙氨酸代谢 Phenylalanine metabolism 类黄酮的生物合成 Flavonoid biosynthesis
LOC110618581	1657	2	2	肌酸合成酶[木薯] XP_021617435.1 vinorine synthase-like [Manihot esculenta]

卷叶木薯及其突变体叶片的比较转录组分析

Comparative transcriptome profiling of leaf in curled-leaf cassava and its mutant

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