高温胁迫下陆地棉转录组差异性分析

doi:10.6048/j.issn.1001-4330.2023.11.003

新疆农业科学 ›› 2023, Vol. 60 ›› Issue (11): 2618-2626.DOI: 10.6048/j.issn.1001-4330.2023.11.003

• 作物遗传育种·种质资源·分子遗传学·土壤肥料 • 上一篇下一篇

高温胁迫下陆地棉转录组差异性分析

王辉¹(), 董永梅²^,³, 郭伟锋¹, 曹新川¹, 郭金成¹, 谢宗铭²^,³(), 何良荣¹()

1.塔里木大学农学院,新疆阿拉尔 843300
2.新疆农垦科学院棉花研究所,新疆石河子 832000
3.作物种质创新与基因资源利用兵团重点实验室,新疆石河子 832000

收稿日期:2023-01-30 出版日期:2023-11-20 发布日期:2023-12-07
通信作者: 何良荣(1970-),女,湖北人,博士,教授,研究方向为棉花种质资源的研究与利用,(E-mail)hlrzky@163.com;谢宗铭(1971-),男,甘肃人,博士,研究员,研究方向为棉花种质资源保存与分子育种,(E-mail)xiezmchy@163.com
作者简介:王辉(1993-),男,河南荥阳人,硕士研究生,研究方向为作物种质资源研究与创新,(E-mail)347488940@qq.com
基金资助:
新疆生产建设兵团农业科技创新工程专项(NCG202224);国家自然科学基金项目“GhCIPK6调控棉花耐热胁迫机理研究”(31550010)

Analysis of the difference of transcription groups of upland cotton under heat stress

WANG Hui¹(), DONG Yongmei²^,³, GUO Weifeng¹, CAO Xinchuan¹, GUO Jincheng¹, XIE Zongming²^,³(), HE Liangrong¹()

1. College of Agronomy, Tarim University, Alar Xinjiang 843300, China
2. Cotton Research Institute, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi Xinjiang 832000, China
3. Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization,Shihezi Xinjiang 832000, China

Received:2023-01-30 Online:2023-11-20 Published:2023-12-07
Correspondence author: HE Liangrong (1970-), female, native place: Hubei, Doctor, professor, research field: research and innovation of crop germplasm resources, (E-mail)hlrzky@163.com;XIE Zongming(1971-),male, native place: Gansu, Doctor, research fellow, research field: cotton germplasm resources and molecular breeding,( E-mail) xiezmchy@163.com
Supported by:
Xinjiang Production and Construction Corps Agricultural Science and Technology Innovation Project(NCG202224);National Natural Science Foundation of China " Regulation mechanism of heat stress is studied in GhCIPK6 in cotton"(31550010)

摘要/Abstract

摘要：

【目的】 研究陆地棉高温胁迫下关键基因的响应,比较基因表达差异,为揭示陆地棉高温胁迫响应的分子机制提供参考。【方法】 利用RNA-Seq对正常温度(26℃)和高温胁迫(42℃)的陆地棉品系YZ1进行转录组测序和数据分析。【结果】 在WN4/WH4,WN12/WH12,WN24/WH24,WN48/WH48共鉴定出383个共有上调基因和234个共有下调基因。将差异基因按GO功能分类,主要富集到上调差异基因和下调差异基因20个类别;差异基因显著富集到类黄酮生物合成途径、苯丙烷代谢、昼夜节律-植物、内质网加工等通路;鉴定出39个转录因子,主要是WRKY和MYB两大家族;Gohir.A08G104100是高温胁迫主要的基因,对植物的耐热性至关重要,Gohir.D08G033300是质体类异戊二烯生物合成的限制酶,对叶绿体发育至关重要。2个差异基因在整个时期表达量差异倍数较为显著。【结论】 高温胁迫和正常温度下在不同时间段,陆地棉的基因转录表达差异。

关键词: RNA-Seq; 陆地棉; 高温胁迫; 差异表达; 代谢通路

Abstract:

【Objective】 To explore the response of key genes to heat stress and compare the differences of gene expression.【Methods】 RNA-Seq was used to sequence and analyze the transcriptome of YZ1 unde²r normal(26℃)and high temperature stress(42℃).【Results】 Gohir.A08G10410A total of 383 up-regulated genes and 234 down regulated genes were identified in WN4/WH4, WN12/WH12, WN24/WH24 and WN48/WH48. According to GO function, the differential genes were mainly enriched into 20 categories, namely, up-regulated differential genes and down-regulated differential genes. According to KEGG function analysis, the differential genes were significantly enriched in flavonoid biosynthesis pathway, phenylalanine metabolism, circadian rhythm-plant and endoplasmic reticulum processing and other pathways. 39 transcription factors were identified, mainly belonging to WRKY and MYB families; Combined with gene annotation, it was found that the expression levels of these two genes were significantly different in the whole period. Gohir.A08G104100 was the main gene of heat stress, which was crucial to the heat tolerance of plants, while Gohir. D08G033300 was a limiting enzyme for plastid isoprene biosynthesis and was critical for chloroplast development.【Conclusion】 Through comparative transcriptome analysis, the difference of gene transcription expression between upland cotton under high temperature stress and normal temperature is compared.

Key words: RNA-Seq; Gossypium hirsutum; heat stress; differential expression; metabolic pathway

中图分类号:

S562

王辉, 董永梅, 郭伟锋, 曹新川, 郭金成, 谢宗铭, 何良荣. 高温胁迫下陆地棉转录组差异性分析[J]. 新疆农业科学, 2023, 60(11): 2618-2626.

WANG Hui, DONG Yongmei, GUO Weifeng, CAO Xinchuan, GUO Jincheng, XIE Zongming, HE Liangrong. Analysis of the difference of transcription groups of upland cotton under heat stress[J]. Xinjiang Agricultural Sciences, 2023, 60(11): 2618-2626.

图/表 8

参考文献 31

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碱基质量值分值 Quality phred	不正确的碱基识别 Incorrect base identification	碱基正确识别率 Correct base recognition rate(%)
Q10	1/10	90
Q20	1/100	99
Q30	1/1000	99.90
Q40	1/10000	99.99

碱基质量值分值 Quality phred	不正确的碱基识别 Incorrect base identification	碱基正确识别率 Correct base recognition rate(%)
Q10	1/10	90
Q20	1/100	99
Q30	1/1000	99.90
Q40	1/10000	99.99

基因序号Gene_id	基因名称Gene name	描述Description	调控Regulation
Gohir.A11G135500	HSP15.7	15.7 k Da heat shock protein, peroxisomal	down
Gohir.A05G091600	HSP17.3-B	17.3 k Da class I heat shock protein	down
Gohir.D05G092500	HSP17.3-B	17.3 k Da class I heat shock protein	down
Gohir.D05G139900	HSP17.4B	17.4 k Da class ⅡI heat shock protein	down
Gohir.D06G084500	HSP17.6	17.6 k Da class Ⅱ heat shock protein	down
Gohir.D07G106100	HSP18.5-C	18.5 k Da class I heat shock protein	down
Gohir.A08G104100	HSP22	Small heat shock protein, chloro-plastic	down
Gohir.D05G127000	HSP26.5	26.5 k Da heat shock protein, mitochondrial	down
Gohir.D05G096900	HSP70	Heat shock cognate 70 k Da protein	down
Gohir.A13G234100	HSP70	Heat shock 70 k Da protein	down
Gohir.D13G239700	HSP70	Heat shock 70 k Da protein	down
Gohir.D09G208200	HSP70-7	Heat shock 70 k Da protein 7, chloro-plastic	down
Gohir.D09G212600	HSP70-7	Heat shock 70 k Da protein 7, chloro-plastic	down
Gohir.A12G254100	HSP83A	Heat shock protein 83	down
Gohir.D08G135400	HSP83A	Heat shock protein 83	down
Gohir.D03G148100	HSP83A	Heat shock protein 83	down
Gohir.D12G256400	HSP83A	Heat shock protein 83	down

基因序号Gene_id	基因名称Gene name	描述Description	调控Regulation
Gohir.A11G135500	HSP15.7	15.7 k Da heat shock protein, peroxisomal	down
Gohir.A05G091600	HSP17.3-B	17.3 k Da class I heat shock protein	down
Gohir.D05G092500	HSP17.3-B	17.3 k Da class I heat shock protein	down
Gohir.D05G139900	HSP17.4B	17.4 k Da class ⅡI heat shock protein	down
Gohir.D06G084500	HSP17.6	17.6 k Da class Ⅱ heat shock protein	down
Gohir.D07G106100	HSP18.5-C	18.5 k Da class I heat shock protein	down
Gohir.A08G104100	HSP22	Small heat shock protein, chloro-plastic	down
Gohir.D05G127000	HSP26.5	26.5 k Da heat shock protein, mitochondrial	down
Gohir.D05G096900	HSP70	Heat shock cognate 70 k Da protein	down
Gohir.A13G234100	HSP70	Heat shock 70 k Da protein	down
Gohir.D13G239700	HSP70	Heat shock 70 k Da protein	down
Gohir.D09G208200	HSP70-7	Heat shock 70 k Da protein 7, chloro-plastic	down
Gohir.D09G212600	HSP70-7	Heat shock 70 k Da protein 7, chloro-plastic	down
Gohir.A12G254100	HSP83A	Heat shock protein 83	down
Gohir.D08G135400	HSP83A	Heat shock protein 83	down
Gohir.D03G148100	HSP83A	Heat shock protein 83	down
Gohir.D12G256400	HSP83A	Heat shock protein 83	down

记录号 Accession	项目 Term	输入基因数目 Input Gene Number	所有基因数目 All Gene Number	P值 P-value	Q值 Q-value
ko00941	Flavonoid biosynthesis	20 (14.60%)	81 (0.57%)	8.40E-25	2.90E-23
ko01110	Biosynthesis of secondary metabolites	62 (45.26%)	2,573 (18.15%)	5.40E-14	1.20E-12
ko00360	Phenylalanine metabolism	10 (7.30%)	104 (0.73%)	4.80E-09	5.50E-08
ko04915	Estrogen signaling pathway	9 (6.57%)	89 (0.63%)	1.40E-08	1.30E-07
ko01100	Metabolic pathways	76 (55.47%)	4,904 (34.59%)	1.70E-07	1.30E-06
ko04612	Antigen processing and presentation	10 (7.30%)	175 (1.23%)	1.00E-06	7.00E-06
ko04940	Type I diabetes mellitus	4 (2.92%)	24 (0.17%)	2.90E-06	1.80E-05
ko05134	Legionellosis	8 (5.84%)	145 (1.02%)	1.10E-05	6.00E-05
ko04621	NOD-like receptor signaling pathway	4 (2.92%)	32 (0.23%)	1.30E-05	6.30E-05
ko04141	Protein processing in endoplasmic reticulum	17 (12.41%)	593 (4.18%)	1.60E-05	7.30E-05
ko00072	Synthesis and degradation of ketone bodies	3 (2.19%)	17 (0.12%)	1.80E-05	7.30E-05
ko04712	Circadian rhythm-plant	7 (5.11%)	120 (0.85%)	2.10E-05	8.00E-05

高温胁迫下陆地棉转录组差异性分析

Analysis of the difference of transcription groups of upland cotton under heat stress

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参考文献 31

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Metrics

转录因子 TF	基因登录号 Gene_id	调控 Regulation	结构域 Domain	描述 Description	e-值 e_value
MYB	Gohir.D09G170800	up	PF00249	Myb-like DNA- binding domain	2.00E-30
	Gohir.A07G020200	up			5.20E-30
	Gohir.A13G099200	up			4.00E-30
	Gohir.A08G111000	up			9.30E-34
	Gohir.D12G116900	up			3.20E-33
	Gohir.A01G153200	up			5.90E-28
	Gohir.D01G146000	up			2.80E-30
	Gohir.D12G267100	down			7.40E-33
	Gohir.A06G082300	up			1.40E-36
WRKY	Gohir.D11G100800	up	PF03106	WRKY DNA- binding domain	5.40E-25
	Gohir.A12G119500	up			1.40E-26
	Gohir.A05G379600	up			2.70E-26
	Gohir.D07G143900	up			2.20E-24
	Gohir.D08G131700	up			3.70E-27
	Gohir.D10G011400	up			5.30E-27
	Gohir.A04G096000	up			1.70E-51
	Gohir.D06G103300	up			2.80E-25
	Gohir.D04G135800	up			2.00E-51
	Gohir.D12G236600	up			2.80E-26
	Gohir.D07G020700	up			8.40E-25
	Gohir.A07G138800	up			9.80E-25
	Gohir.A08G100100	up			9.50E-27
	Gohir.A12G235400	up			7.60E-27
ERF	Gohir.D08G130900	down	PF00847	AP2 domain	7.50E-13
ERF	Gohir.D13G069800	up	PF00847	AP2 domain	9.90E-09
NAC	Gohir.A01G001700	up	PF02365	No apical meristem (NAM) protein	7.90E-25
	Gohir.A12G035000	up			6.20E-26
	Gohir.D01G001300	up			3.10E-23
	Gohir.D03G003700	up			4.40E-26
bZIP	Gohir.D11G259400	down	PF00170	bZIP transcription factor	6.60E-13
bZIP	Gohir.A11G248500	down	PF00170	bZIP transcription factor	1.50E-13
MYB_related	Gohir.A01G075400	up	PF00249	Myb-like DNA- binding domain	9.00E-10
MYB_related	Gohir.D02G216000	up	PF00249	Myb-like DNA- binding domain	6.60E-06
Dof	Gohir.D12G068300	down	PF02701	Dof domain, zinc finger	7.30E-33
Dof	Gohir.D06G130200	up	PF02701	Dof domain, zinc finger	2.20E-31
HSF	Gohir.A07G012200	down	PF00447	HSF-type DNA-binding	6.50E-31
DBB	Gohir.A06G006200	up	PF00643	B-box zinc finger	1.70E-13
HB-other	Gohir.A08G236600	down	PF00046	Homeobox domain	3.50E-07
bHLH	Gohir.D05G002300	up	PF00010	Helix-loop-helix DNA-binding domain	1.40E-12

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