利用基因芯片分析比较Giza75和SG747纤维发育差异表达基因

doi:10.6048/j.issn.1001-4330.2022.06.002

新疆农业科学 ›› 2022, Vol. 59 ›› Issue (6): 1312-1330.DOI: 10.6048/j.issn.1001-4330.2022.06.002

• 作物道传育种·耕作栽培·生理生化 • 上一篇下一篇

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

收稿日期:2021-09-26 出版日期:2022-06-20 发布日期:2022-07-07
通信作者: 于霁雯(1978-),女,河南安阳人,研究员,博士,研究方向为棉花分子育种,(E-mail) yujw666@hotmail.com;
吴嫚(1980-),女,河南安阳人,副研究员,博士,研究方向为棉花分子育种,(E-mail) wuman2004@163.com
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)

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 Published:2022-06-20 Online:2022-07-07
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)

摘要/Abstract

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

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

中图分类号:

S562

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.

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.

图/表 6

参考文献 34

[1]	Wendel J F, Brubaker C, Alvarez I, et al. Evolution and natural history of the cotton genus[J]. In: Paterson AP (ed.) Genetics and Genomics of Cotton, 2009, 3-22.
[2]	Bowman D T, Gutierrez O A. Sources of fiber strength in the U.S. upland cotton crop from 1980 to 2000[J]. The Journal of Cotton Science, 2003, 7:164-169.
[3]	Sajid M, Ahmad R I, Muhammad A R, et al. Role of SNPs in determining QTLs for major traits in cotton[J]. Journal of Cotton Research, 2019, 2:5. DOI URL
[4]	Ma L L, Su Y, Nie H S, et al. QTL and genetic analysis controlling fiber quality traits using paternal back cross population in upland cotton[J]. Journal of Cotton Research, 2020, 3:22. DOI URL
[5]	Deng X Y, Gong J W, Liu A Y, et al. QTL mapping for fiber quality and yield related traits across multiple generations in segregating population of CCRI 70[J]. Journal of Cotton Research, 2019, 2:13. DOI URL
[6]	Tu L L, Zhang X L, Liang S G, et al. Genes expression analyses of sea-island cotton (Gossypium barbadense L.) during fiber development[J]. Plant Cell Reports, 2007, 26(8):1309-1320. PMID
[7]	Wu M, Zhang L Y, Li X L, et al. A comparative transciptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population[J]. Molecular Genetics and Genomics, 2016, 291(4):1749-1767. DOI URL
[8]	Alabady M S, Youn E, Wilkins T A. Double feature selection and cluster analyses in mining of microarray data from cotton[J]. BMC Genomics, 2008, 9:295. DOI PMID
[9]	Wu M, Li L Y, Liu G Y, et al. Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton[J]. Molecular Biology Reports, 2019, 46(1):1199-1212. DOI URL
[10]	Qin Y M, Zhu Y X. How cotton fibers elongate: a tale of linear cell-growth mode[J]. Current Opinion in Plant Biology, 2011, 14(1):106-11. DOI URL
[11]	Liu C X, Li Z F, Dou L L, et al. A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development[J]. Journal of Cotton Research, 2020, 3:26. DOI URL
[12]	Chen F, Guo Y J, Chen L, et al. Global identification of genes associated with xylan biosynthesis in cotton fiber[J]. Journal of Cotton Research, 2020, 3:25. DOI URL
[13]	Yu J W, Zhang K, Li S Y, et al. Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population[J]. Theoretical and Applied Genetics, 2013, 126(1): 275-287. DOI URL
[14]	蒋建雄, 张天真. 利用CTAB/酸酚法提取棉花组织总RNA[J]. 棉花学报, 2003, 15(3):166-167.
	JIANG Jiangxiong, ZHANG Tianzhen. Extraction of total RNA in cotton tissues with CTAB-acidic phenolic method[J]. Cotton Science, 2003, 15(3):166-167
[15]	李龙云, 于霁雯, 翟红红, 等. 利用基因芯片技术筛选棉纤维伸长相关基因[J]. 作物学报, 2011, 37(1):95-104.
	LI Longyun, YU Jiwen, ZHAI Honghong, et al. Identification of fiber length related genes using cotton oligonucleotide microarrays[J]. Acta Agronomica Sinica, 2011, 37(1): 95-104. DOI URL
[16]	吴嫚, 李龙云, 裴文锋, 等. 利用马克隆值差异显著的BILs鉴定棉纤维品质相关基因[J]. 棉花学报, 2020, 32(1):52-62.
	WU Man, LI Longyun, PEI Wenfeng, et al. Identification of differentially expressed genes in developing cotton fibers between two groups of backcross inbred lines differing in fiber Micronaire[J]. Cotton Science, 2020, 32(1):52-62.
[17]	Hu Y, Chen J D, Fang L, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton[J]. Nature Genetics, 2019, 51(4):739-748. DOI URL
[18]	Chee P, Draye X, Jiang C X, et al. Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. fiber elongation[J]. Theoretical and Applied Genetics, 2005, 111(4):757-763. DOI URL
[19]	李龙云. 利用基因芯片技术筛选棉纤维发育相关基因[D]. 杨凌: 西北农林科技大学, 2010.
	LI Longyun. Identification Of Fiber Quality Genes By Using Cotton Oligonucleotide Microarrays with Gene Expression Analysis[D]. Yangling: Northwest A&F University, 2010.
[20]	Sun Q, Cai Y F, Xie Y F, et al. Gene expression profiling during gland morphogenesis of a mutant and a glandless upland cotton[J]. Molecular Biology Reports, 2010, 37(7):3319-3325. DOI URL
[21]	佘义斌, 朱一超, 张天真, 等. 棉花腺苷高半胱氨酸水解酶cDNA的克隆、表达及染色体定位[J]. 作物学报, 2008, (6):958-964.
	SHE Yibin, ZHU Yichao, ZHANG Tianzhen, et al. Cloning, expression, and mapping of s-adenosyl-l-homocysteine hydrolase (GhSAHH) cDNA in cotton[J]. Acta Agronomica Sinica, 2008, 34(6):958-964. DOI URL
[22]	Li C H, Zhu Y Q, Meng Y L, et al. Isolation of genes preferentially expressed in cotton fibers by cDNA filter arrays and RT-PCR[J]. Plant Science, 2002, 163(6):1113-1120. DOI URL
[23]	Bach I. The LIM domain: regulation by association[J]. Mechanisms of Development, 2000, 91(1-2):5-17. PMID
[24]	Saxena I M, Brown R M. Cellulose synthases and related enzymes[J]. Current Opinion in Plant Biology, 2000, 3(6):523-31. PMID
[25]	武耀廷, 张恒木, 刘进元. 棉纤维细胞发育过程中纤维素的生物合成[J]. 棉花学报, 2003, 15(3):174-179.
	WU Yaoting, ZHANG Hengmu, LIU Jinyuan. Cellulose biosynthesis in developing cotton fibers[J]. Cotton Science, 2003, 15(3):174-179.
[26]	Zhang S J, Jiang Z X, Chen J, et al. The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton[J]. Molecular Genetics and Genomics, 2021, 296(2):355-368. DOI URL
[27]	Harmer S E, Oxford S J, Timmis J N. Characterization of six alpha-expansin genes in Gossypium hirsutum (upland cotton)[J]. Molecular Genetics and Genomics, 2002, 268(1):1-9. PMID
[28]	Wilkins T A, Arpat A, Sickler B. Cotton fiber genomics: developmental mechanisms[J]. Pflanzenschutz-Nachrichten Bayer, 2005, 1:119-139.
[29]	Gou J Y, Wang L J, Chen S P, et al. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis[J]. Cell Research, 2007, 17(5):422-34. DOI URL
[30]	Li Y, Tu L L, Pettolino F A, et al. GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring[J]. Plant Biotechnology Journal, 2016, 14(3):951-963. DOI URL
[31]	杨君, 马峙英, 王省芬. 棉花纤维品质改良相关基因研究进展[J]. 中国农业科学, 2016, 49(22):4310-4322,4469-4472.
	YANG Jun, MA Zhiying, WANG Xingfen. Progress in studies on genes related to fiber quality improvement of cotton[J]. Scientia Agricultura Sinica, 2016, 49(22):4310-4322,4469-4472.
[32]	Dixon D C, Seagull R W, Triplett B A. Changes in the accumulation of α- and β-tubulin isotypes during cotton fiber development[J]. Plant Physiology, 1994, 105(4):1347-1353. PMID
[33]	Li X B, Cai L, Cheng N H, et al. Molecular characterization of the cotton GhTUB1 gene that is preferentially expressed in fiber[J]. Plant Physiology, 2002, 130(2), 666-674. DOI URL
[34]	刘迪秋. 陆地棉纤维特异表达基因的克隆与表达研究[D]. 武汉: 华中农业大学, 2007.
	LIU Diqiu. Molecular cloning and expression analysis of the genes specifically expressed in fibers of Gossypium hirsutum[D]. Wuhan: Huazhong Agricultural University, 2007

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	^**

利用基因芯片分析比较Giza75和SG747纤维发育差异表达基因

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

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