Comparative Analysis of Gene Expression between Giza 75 and SG 747 Using Cotton Oligonucleotide Microarrays during Fiber Development

doi:10.6048/j.issn.1001-4330.2022.06.002

Xinjiang Agricultural Sciences ›› 2022, Vol. 59 ›› Issue (6): 1312-1330.DOI: 10.6048/j.issn.1001-4330.2022.06.002

• Crop Genetics and Breeding·Cultivation Physiology·Physiology and Biochemistry • Previous Articles Next Articles

Comparative Analysis of Gene Expression between Giza 75 and SG 747 Using Cotton Oligonucleotide Microarrays during Fiber Development

SONG Jikun¹^,²(), XIN Yue¹, LI Longyun¹, LIU Guoyuan¹, PEI Wenfeng¹^,², MA Jianjiang¹, QU Yanying², YU Jiwen¹^,²(), WU Man¹()

1. Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology/Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Anyang Henan 455000 China
2. Research Centre of Cotton Engineering, Ministry of Education and Rural Affairs / College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052 China

Received:2021-09-26 Online:2022-06-20 Published:2022-07-07
Correspondence author: YU Jiwen, WU Man
Supported by:
Natural Science Foundation of Xinjiang Uygur Autonomous Region of China(2020D01A135);Natural Science Foundation of Xinjiang Uygur Autonomous Region of China(2021D0113113);Agricultural Science and Technology Innovation Program Project of CAAS;Basic Scientific R &D Program of Public Welfare Research Institutions of China(1610162021043)

利用基因芯片分析比较Giza75和SG747纤维发育差异表达基因

宋吉坤¹^,²(), 辛玥¹, 李龙云¹, 刘国元¹, 裴文锋¹^,², 马建江¹, 曲延英², 于霁雯¹^,²(), 吴嫚¹()

1.中国农业科学院棉花研究所/棉花生物学国家重点实验室,河南安阳 455000
2.新疆农业大学农学院/教育部棉花工程研究中心,乌鲁木齐 830052

通讯作者: 于霁雯,吴嫚
作者简介:宋吉坤(1995-),男,山东青岛人,博士研究生,研究方向为棉花分子育种,(E-mail) sjkow513@163.com
基金资助:
新疆维吾尔自治区自然科学基金(2020D01A135);新疆维吾尔自治区自然科学基金(2021D0113113);中国农业科学院科技创新工程;中央级公益性科研院所基本科研业务费专项(1610162021043)

Abstract

Abstract:

【Objective】 High-throughput gene chip analysis is performed using upland cotton with wide adaptability and high yield and sea island cotton with excellent fiber quality, aiming to screen and identify key genes involved in cotton fiber development. 【Methods】 The upland cotton SG747 (Gossypium hirsutum L.) and Egyptian cotton Giza75 (G. barbadense L.) were used as experimental materials. The Affymetrix Cotton Gene Chip was then used to perform a transcriptome analysis in developing fibers (10 Days after anthesis, DPA). 【Results】 The 3,905 transcripts obtained showed 2-fold or higher levels of expression changes between the two materials. Clustering analysis of these DE genes by Clusters of Orthologous Groups database was performed, which revealed that many genes were related to general function prediction (17.80%), translation, ribosomal structure and biogenesis (16.82%), posttranslational modification (14.32%). According to qRT-PCR analysis, it was speculated that Gra.2198.1.A1_at positively regulated cotton fiber development and Gra.85.1.S1_at, Ghi.249.1.A1_at, Ghi.8448.1.S1_x_at negatively regulated cotton fiber development, and the above genes might be involved in the development of cotton fiber. 【Conclusion】 We screened and identified four key candidate genes related to fiber development by using upland cotton and sea island cotton gene chips combined with qRT-PCR.

Key words: Gossypium barbadense; Gossypium hirsutum; fiber quality; affymetrix microarray; differentially expressed genes

摘要：

【目的】 利用适应性广、产量高的陆地棉和纤维品质优异的海岛棉进行高通量基因芯片比较分析,筛选和鉴定棉纤维发育相关的关键基因。【方法】 以SG747(Gossypium hirsutum L.)和Giza75(Gossypium barbadense L.)为材料,利用Affymetrix公司的棉花寡聚核苷酸基因芯片对其开花后10 d(10 days after anthesis, 10 DPA)的棉纤维进行表达谱分析。【结果】 材料Giza75和SG747共筛选到3 905个差异表达基因,其中功能预测基因占比17.80%,翻译、核糖体结构相关基因占比16.82%,翻译后修饰占比14.32%。Gra.2198.1.A1_at正向调控棉纤维发育过程,Gra.85.1.S1_at、Ghi.249.1.A1_at和Ghi.8448.1.S1_x_at负向调控棉纤维发育过程,可能参与了棉纤维发育过程。【结论】 利用陆地棉和海岛棉基因芯片并结合qRT-PCR筛选和鉴定到4个纤维发育相关的关键候选基因。

关键词: 海岛棉, 陆地棉, 棉纤维品质, 基因芯片, 差异表达基因

CLC Number:

S562

SONG Jikun, XIN Yue, LI Longyun, LIU Guoyuan, PEI Wenfeng, MA Jianjiang, QU Yanying, YU Jiwen, WU Man. Comparative Analysis of Gene Expression between Giza 75 and SG 747 Using Cotton Oligonucleotide Microarrays during Fiber Development[J]. Xinjiang Agricultural Sciences, 2022, 59(6): 1312-1330.

宋吉坤, 辛玥, 李龙云, 刘国元, 裴文锋, 马建江, 曲延英, 于霁雯, 吴嫚. 利用基因芯片分析比较Giza75和SG747纤维发育差异表达基因[J]. 新疆农业科学, 2022, 59(6): 1312-1330.

Figures/Tables 6

References 34

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探针编号 Probe Set	NCBI 登录号 Accessionnumber	基因名称 Gene Name	引物序列 Sequence	引物长度 Length (bp)
__	AY305737	Actin9	-F5’-ATCCTCCGTCTTGACCTTG -3’	19
__	AY305737	Actin9	-R5’-TGTCCGTCAGGCAACTCAT-3’	19
Ghi.8448.1.S1_x_at	AF521240.1	GhXu-142 βTUB1	-F5’-TAACTATGTCGGCACTTC -3’	18
Ghi.8448.1.S1_x_at	AF521240.1	GhXu-142 βTUB1	-R5’-AATCAATTCAGCTCCTTC -3’	18
Gra.2198.1.A1_at	CO100609	GhSAHH	-F5’-CAGCTCCCAGATCCGTCTTC -3’	20
Gra.2198.1.A1_at	CO100609	GhSAHH	-R5’-CACCAACTAATCTCTCCCTCATCC -3’	24
Gra.85.1.S1_at	CO097359	GhCESA4	-F5’- GTAACCATAAGGCATGTCCAAAATG-3’	25
Gra.85.1.S1_at	CO097359	GhCESA4	-R5’- AGAAAAGGTGGGAATGAACGAA-3’	22
Ghi.249.1.A1_at	DQ204496.1	GhAlpha-expansin 2	-F5’-CCCCTGTATGAAGAAAGGAGGA -3’	22
			-R5’-AACATCTCCAGCACCACCAAC -3’	21
			-R5’-CGAAGTTGTTGGCAGCGTCT -3’	20

探针编号 Probe Set	NCBI 登录号 Accessionnumber	基因名称 Gene Name	引物序列 Sequence	引物长度 Length (bp)
__	AY305737	Actin9	-F5’-ATCCTCCGTCTTGACCTTG -3’	19
__	AY305737	Actin9	-R5’-TGTCCGTCAGGCAACTCAT-3’	19
Ghi.8448.1.S1_x_at	AF521240.1	GhXu-142 βTUB1	-F5’-TAACTATGTCGGCACTTC -3’	18
Ghi.8448.1.S1_x_at	AF521240.1	GhXu-142 βTUB1	-R5’-AATCAATTCAGCTCCTTC -3’	18
Gra.2198.1.A1_at	CO100609	GhSAHH	-F5’-CAGCTCCCAGATCCGTCTTC -3’	20
Gra.2198.1.A1_at	CO100609	GhSAHH	-R5’-CACCAACTAATCTCTCCCTCATCC -3’	24
Gra.85.1.S1_at	CO097359	GhCESA4	-F5’- GTAACCATAAGGCATGTCCAAAATG-3’	25
Gra.85.1.S1_at	CO097359	GhCESA4	-R5’- AGAAAAGGTGGGAATGAACGAA-3’	22
Ghi.249.1.A1_at	DQ204496.1	GhAlpha-expansin 2	-F5’-CCCCTGTATGAAGAAAGGAGGA -3’	22
			-R5’-AACATCTCCAGCACCACCAAC -3’	21
			-R5’-CGAAGTTGTTGGCAGCGTCT -3’	20

性状 Trait	基因型Genetype		T测验T test
性状 Trait	Giza75	SG7474	T Stat	P(T≤T)双尾 P(T≤t) two- tailed
纤维长度 Fiber Length (mm)	34.090 0	29.201 7	10.433 0	0.000 0	^**
整齐度指数 Uniformity index(%)	86.066 7	84.666 7	2.613 8	0.028 1	^*
马克隆值 Micronair value	4.565 0	5.621 7	-3.038 0	0.028 8	^*
伸长率 Fiber Elongation rate(%)	5.750 0	6.416 7	-1.913 0	0.092 1
纤维强度 Fiber Strength (cN/tex)	40.391 3	27.693 3	8.487 3	0.000 0	^**
籽棉产量 Seed Yield (kg/667m²)	70.947 5	191.813 8	-4.838 0	0.000 7	^**
皮棉产量 Lint Yield (kg/667m²)	26.677 5	78.272 5	-5.397 7	0.000 2	^**
衣分 Lint Percentage (%)	36.926 3	41.707 5	-4.312 8	0.000 8	^**
铃重 Boll Weight (g)	3.617 5	6.007 5	-10.792 4	0.000 0	^**

性状 Trait	基因型Genetype		T测验T test
性状 Trait	Giza75	SG7474	T Stat	P(T≤T)双尾 P(T≤t) two- tailed
纤维长度 Fiber Length (mm)	34.090 0	29.201 7	10.433 0	0.000 0	^**
整齐度指数 Uniformity index(%)	86.066 7	84.666 7	2.613 8	0.028 1	^*
马克隆值 Micronair value	4.565 0	5.621 7	-3.038 0	0.028 8	^*
伸长率 Fiber Elongation rate(%)	5.750 0	6.416 7	-1.913 0	0.092 1
纤维强度 Fiber Strength (cN/tex)	40.391 3	27.693 3	8.487 3	0.000 0	^**
籽棉产量 Seed Yield (kg/667m²)	70.947 5	191.813 8	-4.838 0	0.000 7	^**
皮棉产量 Lint Yield (kg/667m²)	26.677 5	78.272 5	-5.397 7	0.000 2	^**
衣分 Lint Percentage (%)	36.926 3	41.707 5	-4.312 8	0.000 8	^**
铃重 Boll Weight (g)	3.617 5	6.007 5	-10.792 4	0.000 0	^**

Comparative Analysis of Gene Expression between Giza 75 and SG 747 Using Cotton Oligonucleotide Microarrays during Fiber Development

利用基因芯片分析比较Giza75和SG747纤维发育差异表达基因

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