基于RNA-seq的大麦苗期抗旱相关基因的挖掘与分析

doi:10.6048/j.issn.1001-4330.2024.05.005

新疆农业科学 ›› 2024, Vol. 61 ›› Issue (5): 1077-1084.DOI: 10.6048/j.issn.1001-4330.2024.05.005

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于RNA-seq的大麦苗期抗旱相关基因的挖掘与分析

鞠乐¹^,²(), 齐军仓¹(), 牛银亭², 石培春¹, 宋瑞娇¹, 宋凌宇¹, 阴志刚², 陈培育², 强学兰³

1.石河子大学农学院,新疆石河子 832003
2.南阳市农业科学院,河南南阳 473000
3.宛城区农业农村局,河南南阳 473000

收稿日期:2023-10-25 出版日期:2024-05-20 发布日期:2024-07-09
通信作者: 齐军仓( 1971-),男,陕西宝鸡人,教授,硕士生/博士生导师,研究方向为大麦遗传育种与栽培,(E-mail)shzqjc@qq.com
作者简介:鞠乐(1987-),女,河南邓州人,助理研究员,研究方向为杂粮遗传育种与栽培,(E-mail)695112004@qq.com
基金资助:
财政部和农业农村部:国家现代农业产业技术体系项目(CARS-05-19B);国家自然科学基金项目(32360456)

RNA-seq-based mining and analysis of drought-related genes in barley seedlings

JU Le¹^,²(), QI Juncang¹(), NIU Yinting², SHI Peichun¹, SONG Ruijiao¹, SONG Lingyu¹, YIN Zhigang², CHEN Peiyu², QIANG Xuelan³

1. College of Agriculture, Shihezi University, Shihezi Xinjiang 832003, China
2. Academy of Agricultural Sciences, Nanyang City, Nanyan Henan 473000, China
3. Bureau of Agriculture and Rural Development, Wancheng District, Nanyang Henan 473000, China

Received:2023-10-25 Published:2024-05-20 Online:2024-07-09
Correspondence author: QI Juncang ( 1971-), male, from Baoji, Shaanxi, professor, doctoral supervisor,research direction: Genetic breeding and cultivation techniques of barley, (E-mail)shzqjc@qq.com
Supported by:
The Earmarked Fund for Modern Agro-industry Technology Research System(CARS-05-19B);National Natural Science Foundation of China(32360456)

摘要/Abstract

摘要：

【目的】挖掘与分析大麦苗期抗旱相关基因,为研究大麦分子抗旱机制和选育抗旱大麦品种提供理论支撑。【方法】以啤酒大麦品种新啤6号为材料,应用转录组测序RNA-seq技术对干旱胁迫前后大麦苗期倒二叶叶片进行转录组测序,并采用实时荧光定量 RT-PCR 方法进行功能基因验证。【结果】(1)干旱胁迫前后新啤6号倒二叶中3 835个差异表达基因,主要为编码ABC转运蛋白、核糖体蛋白、转录因子、脱水素、过氧化物酶、蛋白质磷酸酶等的基因。(2)DEG主要富集在淀粉和蔗糖代谢、转运蛋白、植物激素信号转导、伴侣和折叠催化剂、氨基糖和核苷酸糖的代谢、苯丙氨酸代谢、牛磺酸和次牛磺酸代谢、过氧化物酶体等途径。【结论】大麦干旱胁迫前后基因表达差异显著(其中上调基因1 592个,下调基因2 243个)。

关键词: 大麦; 干旱胁迫; 转录组; 基因挖掘

Abstract:

【Objective】To excavate the genes related to drought resistance in the hope of providing theoretical support for analyzing the molecular drought resistance mechanism of barley and guiding the drought resistance breeding of barley.【Methods】Taking New beer No.6 as the test material, we applied transcriptome sequencing RNA-seq technology to sequence the inverted bilobed leaves of barley seedlings before and after drought stress, and real-time fluorescence quantitative RT-PCR was used to verify the functional genes.【Results】(1) In this study, 3835 differentially expressed genes were detected in the inverted bilobed of New beer 6 before and after drought stress by using RNA-seq, mainly genes encoded by ABC transporter proteins, ribosomal proteins, transcription factors, dehydrins, peroxidases, protein phosphatases, etc.The results showed that DEG was mainly enriched in starch and sucrose metabolism, transporter proteins, plant hormone signaling transduction, and protein phosphatases.(2) By KEGG metabolic pathway enrichment analysis, DEGs were mainly enriched in starch and sucrose metabolism, transporter proteins, phytohormone signaling, chaperones and folding catalysts, aminosugar and ribosugar metabolism, phenylalanine metabolism, taurine and hyposulphite metabolism, peroxisomes and other pathways.【Conclusion】Significant differences are shown in gene expression before and after drought stress in barley.The results of this study have laid the foundation for the excavation of key drought-resistant genes and for further analysis of drought-resistant mechanisms in barley(1592 up-regulated genes and 2243 down-regulated genes).

Key words: barley; drought stress; transcriptome; gene mining

中图分类号:

S512.3

鞠乐, 齐军仓, 牛银亭, 石培春, 宋瑞娇, 宋凌宇, 阴志刚, 陈培育, 强学兰. 基于RNA-seq的大麦苗期抗旱相关基因的挖掘与分析[J]. 新疆农业科学, 2024, 61(5): 1077-1084.

JU Le, QI Juncang, NIU Yinting, SHI Peichun, SONG Ruijiao, SONG Lingyu, YIN Zhigang, CHEN Peiyu, QIANG Xuelan. RNA-seq-based mining and analysis of drought-related genes in barley seedlings[J]. Xinjiang Agricultural Sciences, 2024, 61(5): 1077-1084.

图/表 6

参考文献 28

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基因ID Gene ID	正向引物Forward primer	反向引物Reverse primer
HG0227420.1	TCACTGTTGTATCGGTTTTGTATCA	GTAGTAGCTCTTGCCTCTTAATCATTT
HG0720280.1	AGGAGAGGCTACTACGGGATGT	TTAAAGTCGACGTTGTTGAGGG
HG0464400.1	GTACGTCACGGGGAGGGC	ATCACACATACACATCGGCTAAAGT
HG0330150.1	GGGATTTCTTGGCTAAGGTGTC	CCGTGATGATGTGAGTGGTTG
HG0333810.1	CTGTCTACCGTGTTATCGCTCG	AACTTTTGCCCTCATTTTTCATT

基因ID Gene ID	正向引物Forward primer	反向引物Reverse primer
HG0227420.1	TCACTGTTGTATCGGTTTTGTATCA	GTAGTAGCTCTTGCCTCTTAATCATTT
HG0720280.1	AGGAGAGGCTACTACGGGATGT	TTAAAGTCGACGTTGTTGAGGG
HG0464400.1	GTACGTCACGGGGAGGGC	ATCACACATACACATCGGCTAAAGT
HG0330150.1	GGGATTTCTTGGCTAAGGTGTC	CCGTGATGATGTGAGTGGTTG
HG0333810.1	CTGTCTACCGTGTTATCGCTCG	AACTTTTGCCCTCATTTTTCATT

基因编号 Gene ID	基因注释 Gene annotation	差异倍数 logFC	显著性 P value
HORVU.MOREX.r3.1HG0008130	可能为肉桂醇脱氢酶5	8.53	1.96E-07
HORVU.MOREX.r3.1HG0041720	极长链醛脱碳酶GL1-5	9.96	5.34E-07
HORVU.MOREX.r3.1HG0082800	可能为异天冬氨酸肽酶/ l -天冬酰胺酶2	9.40	0.0013
HORVU.MOREX.r3.2HG0139380	异柠檬酸裂合酶	10.33	6.10E-07
HORVU.MOREX.r3.2HG0170930	22.0 kDa热休克蛋白	11.13	3.99E-16
HORVU.MOREX.r3.2HG0195920	泛素- 40s核糖体蛋白S27a-1	9.35	1.03E-08
HORVU.MOREX.r3.3HG0286930	BURP结构域蛋白RD22	8.54	8.95E-07
HORVU.MOREX.r3.3HG0286980	可能的WRKY转录因子56	10.06	1.94E-05
HORVU.MOREX.r3.3HG0325680	丝氨酸脱羧酶1	11.65	7.56E-13
HORVU.MOREX.r3.4HG0386330	ABC转运蛋白G家族成员5	11.16	7.68E-07
HORVU.MOREX.r3.5HG0481950	叶绿体低分子质量早期光诱导蛋白HV90	9.06	5.10E-12
HORVU.MOREX.r3.6HG0622760	脱水素DHN4	14.24	8.48E-07
HORVU.MOREX.r3.6HG0622770	脱水素DHN3	15.66	2.39E-11
HORVU.MOREX.r3.7HG0666580	叶绿体ATP依赖性锌金属蛋白酶FTSH 6	13.64	1.32E-07
HORVU.MOREX.r3.1HG0010600	色氨酸脱羧酶1	-12.52	1.53E-06
HORVU.MOREX.r3.2HG0112630	过氧化物酶1	-10.23	4.46E-08
HORVU.MOREX.r3.2HG0112720	过氧化物酶2	-10.62	9.72E-22
HORVU.MOREX.r3.2HG0117260	蛋白质HEADING DATE 3A	-11.38	2.44E-16
HORVU.MOREX.r3.3HG0227850	AP2/ERF和B3结构域蛋白	-10.82	7.05E-19
HORVU.MOREX.r3.3HG0276230	磷脂酶A1-II 3	-10.78	6.26E-23
HORVU.MOREX.r3.3HG0318390	LRR受体激酶BAK1	-8.15	1.43E-16
HORVU.MOREX.r3.4HG0399940	转氨酶ALD1同源物	-8.56	9.99E-06
HORVU.MOREX.r3.4HG0408430	乙烯应答转录因子ERF096	-9.72	1.10E-10
HORVU.MOREX.r3.5HG0479070	转录因子MYB20	-10.31	4.43E-22
HORVU.MOREX.r3.5HG0514340	转录因子JUNGBRUNNEN 1	-10.74	2.81E-16
HORVU.MOREX.r3.5HG0528610	细胞数目调控因子10	-8.29	1.66E-08
HORVU.MOREX.r3.7HG0659450	羟基肉桂酰转移酶4	-11.43	1.35E-13

基因编号 Gene ID	基因注释 Gene annotation	差异倍数 logFC	显著性 P value
HORVU.MOREX.r3.1HG0008130	可能为肉桂醇脱氢酶5	8.53	1.96E-07
HORVU.MOREX.r3.1HG0041720	极长链醛脱碳酶GL1-5	9.96	5.34E-07
HORVU.MOREX.r3.1HG0082800	可能为异天冬氨酸肽酶/ l -天冬酰胺酶2	9.40	0.0013
HORVU.MOREX.r3.2HG0139380	异柠檬酸裂合酶	10.33	6.10E-07
HORVU.MOREX.r3.2HG0170930	22.0 kDa热休克蛋白	11.13	3.99E-16
HORVU.MOREX.r3.2HG0195920	泛素- 40s核糖体蛋白S27a-1	9.35	1.03E-08
HORVU.MOREX.r3.3HG0286930	BURP结构域蛋白RD22	8.54	8.95E-07
HORVU.MOREX.r3.3HG0286980	可能的WRKY转录因子56	10.06	1.94E-05
HORVU.MOREX.r3.3HG0325680	丝氨酸脱羧酶1	11.65	7.56E-13
HORVU.MOREX.r3.4HG0386330	ABC转运蛋白G家族成员5	11.16	7.68E-07
HORVU.MOREX.r3.5HG0481950	叶绿体低分子质量早期光诱导蛋白HV90	9.06	5.10E-12
HORVU.MOREX.r3.6HG0622760	脱水素DHN4	14.24	8.48E-07
HORVU.MOREX.r3.6HG0622770	脱水素DHN3	15.66	2.39E-11
HORVU.MOREX.r3.7HG0666580	叶绿体ATP依赖性锌金属蛋白酶FTSH 6	13.64	1.32E-07
HORVU.MOREX.r3.1HG0010600	色氨酸脱羧酶1	-12.52	1.53E-06
HORVU.MOREX.r3.2HG0112630	过氧化物酶1	-10.23	4.46E-08
HORVU.MOREX.r3.2HG0112720	过氧化物酶2	-10.62	9.72E-22
HORVU.MOREX.r3.2HG0117260	蛋白质HEADING DATE 3A	-11.38	2.44E-16
HORVU.MOREX.r3.3HG0227850	AP2/ERF和B3结构域蛋白	-10.82	7.05E-19
HORVU.MOREX.r3.3HG0276230	磷脂酶A1-II 3	-10.78	6.26E-23
HORVU.MOREX.r3.3HG0318390	LRR受体激酶BAK1	-8.15	1.43E-16
HORVU.MOREX.r3.4HG0399940	转氨酶ALD1同源物	-8.56	9.99E-06
HORVU.MOREX.r3.4HG0408430	乙烯应答转录因子ERF096	-9.72	1.10E-10
HORVU.MOREX.r3.5HG0479070	转录因子MYB20	-10.31	4.43E-22
HORVU.MOREX.r3.5HG0514340	转录因子JUNGBRUNNEN 1	-10.74	2.81E-16
HORVU.MOREX.r3.5HG0528610	细胞数目调控因子10	-8.29	1.66E-08
HORVU.MOREX.r3.7HG0659450	羟基肉桂酰转移酶4	-11.43	1.35E-13

GO编号 GO ID	GO分类 GO term	矫正后的P值 P.adjust	GO编号 GO ID	GO分类 GO term	矫正后的P值 P.adjust
GO:0010200	对几丁质的反应	4.56E-10	GO:0071484	细胞对光照强度的反应	9.56E-06
GO:0009451	RNA修饰	2.27E-08	GO:0006952	防御反应	9.56E-06
GO:0009607	对生物刺激的反应	8.66E-07	GO:0006950	对胁迫的反应	1.76E-05
GO:1901700	对含氧化合物的反应	8.66E-07	GO:0010243	对有机氮化合物的反应	2.90E-05
GO:0043207	对外部生物刺激的反应	8.66E-07	GO:0009644	对高光照强度的反应	4.32E-05
GO:0010117	光保护	8.66E-07	GO:0010030	种子萌发的正向调节	5.33E-05
GO:0051707	对其他生物的反应	8.66E-07	GO:0090305	核酸磷酸二酯键水解	5.33E-05
GO:0070141	对紫外线A的反应	1.33E-06	GO:0042493	对药物的反应	6.22E-05
GO:0071492	细胞对紫外线A的反应	1.33E-06	GO:0001101	对酸化学物质的反应	6.22E-05
GO:0004519	内切酶活性	1.33E-06	GO:0010380	叶绿素生物合成过程的调节	6.22E-05
GO:0098542	对其他生物的防御反应	1.47E-06	GO:1901463	四吡咯生物合成过程的调控	6.22E-05
GO:0042742	对细菌的防御反应	3.52E-06	GO:0071490	细胞对远红外线的反应	8.41E-05
GO:0004518	核酸酶活性	3.72E-06	GO:0016788	水解酶活性,作用于酯键	9.30E-05
GO:0071491	细胞对红光的反应	4.76E-06	GO:0009620	对真菌的反应	9.74E-05
GO:0071486	细胞对高光照强度的反应	4.76E-06	GO:0009295	类核	9.77E-05

基于RNA-seq的大麦苗期抗旱相关基因的挖掘与分析

RNA-seq-based mining and analysis of drought-related genes in barley seedlings

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参考文献 28

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Metrics

基因编号Gene ID	相对表达量Relative expression
HG0227420.1	4.71
HG0720280.1	8.62
HG0464400.1	7.73
HG0330150.1	4.50
HG0333810.1	3.63

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