甘蔗CLC基因家族鉴定与表达分析

doi:10.3724/SP.J.1006.2026.54105

作物学报 ›› 2026, Vol. 52 ›› Issue (3): 722-734.doi: 10.3724/SP.J.1006.2026.54105

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

甘蔗CLC基因家族鉴定与表达分析

杨宗桃¹^,²(), 杨婷¹^,², 王禹童¹^,², 艾静¹^,², 李燕烨¹^,², 刘家勇¹^,², 邓军¹^,², 赵勇¹^,²^,^*(), 张跃彬¹^,²

¹热带作物生物育种全国重点实验室, 云南昆明 650000
²云南省农业科学院甘蔗研究所, 云南开远 661699

收稿日期:2025-09-01 接受日期:2025-11-18 出版日期:2026-03-12 网络出版日期:2025-12-03
通讯作者: *赵勇, E-mail: 18087395132@163.com
作者简介:E-mail: fafuyangzongtao@163.com
基金资助:
云南省科技厅科技计划农业联合专项(202301BD070001-213);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-17);云南种子种业联合实验室项目(202205AR070001-13);云南省农业科学院科研预研项目(2024KYZX-02);“兴滇英才支持计划”云岭学者专项(XDYC-YLXZ-2022-0038)

Identification and expression analysis of the CLC gene family in sugarcane

Yang Zong-Tao¹^,²(), Yang Ting¹^,², Wang Yu-Tong¹^,², Ai Jing¹^,², Li Yan-Ye¹^,², Liu Jia-Yong¹^,², Deng Jun¹^,², Zhao Yong¹^,²^,^*(), Zhang Yue-Bin¹^,²

¹National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650000, Yunnan, China
²Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan 661699, Yunnan, China

Received:2025-09-01 Accepted:2025-11-18 Published:2026-03-12 Published online:2025-12-03
Contact: *赵勇, E-mail: 18087395132@163.com
Supported by:
Yunnan Provincial Department of Science and Technology Science and Technology Plan Agricultural Joint Special Project(202301BD070001-213);China Agriculture Research System of MOF and MARA(CARS-17);Yunnan Seed Industry Joint Laboratory Project(202205AR070001-13);Pre-research Project of Yunnan Academy of Agricultural Sciences(2024KYZX-02);Project of Supporting Talents in Xingdian-Yunling Scholars Special Project(XDYC-YLXZ-2022-0038)

摘要/Abstract

摘要：

氯离子通道(chloride channel, CLC)基因家族在植物液泡硝酸盐储存过程中发挥关键作用, 但其在复杂基因组作物甘蔗中尚未被系统鉴定。本研究基于割手密(Saccharum spontaneum)基因组数据, 鉴定出29个SsCLC基因, 分布于21条染色体上, 可分为6个亚族(Group a、Group c、Group d、Group e、Group f和Group g)。基因结构和motif分析表明该家族成员较为保守。共线性分析显示, SsCLC基因家族主要通过全基因组/片段复制事件扩增, 并受到纯化选择。启动子顺式作用元件分析表明, SsCLC富含激素响应(50.00%)、生长发育(42.86%)及胁迫响应(7.14%)等相关元件。以割手密82-1及其3个杂交后代为材料, 农艺性状调查显示杂交后代在茎径、叶长、锤度、鲜重和干重上均显著优于亲本; 转录组与qRT-PCR分析发现, 75.86%的SsCLC基因(22/29)在杂交种根中表达上调。本研究首次系统鉴定了SsCLC基因家族, 揭示了其在杂交种根中普遍上调的表达模式与优良农艺性状密切相关, 为解析甘蔗“高贵化”过程中的氮素高效利用机制提供了重要基因资源。

关键词: 甘蔗, CLC基因家族, 转录组学, 表达分析, 氮素

Abstract:

The chloride channel (CLC) gene family plays a crucial role in nitrate storage within plant vacuoles. However, its characteristics remain largely unexplored in the complex genome of sugarcane. In this study, we systematically identified 29 CLC genes (SsCLCs) from the Saccharum spontaneum genome. These SsCLCs were distributed across 21 chromosomes and phylogenetically classified into six subgroups (Groups a, c, d, e, f, and g). The gene family exhibited conserved structures and motif compositions. Genomic collinearity analysis indicated that the expansion of SsCLC was mainly driven by whole-genome or segmental duplication events under strong purifying selection. Promoter analysis revealed a high abundance of cis-acting elements associated with hormone responses (50.00%), growth and development (42.86%), and stress responses (7.14%). Furthermore, in a comparison between S. spontaneum Yunnan 82-1 and its three hybrid progenies, the hybrids exhibited significant improvements in key agronomic traits, including stalk diameter, leaf length, brix, fresh weight, and dry weight. Consistently, transcriptome and qRT-PCR analyses showed that 75.86% (22 out of 29) of the SsCLC genes were upregulated in the roots of the hybrids. This study presents the first comprehensive genomic characterization of the SsCLC gene family and highlights its potential role in improving nitrogen use efficiency during sugarcane nobilization through root-specific gene upregulation, thereby offering valuable genetic resources for breeding nitrogen-efficient sugarcane cultivars.

Key words: sugarcane, CLC gene family, transcriptomics, expression analysis, nitrogen

杨宗桃, 杨婷, 王禹童, 艾静, 李燕烨, 刘家勇, 邓军, 赵勇, 张跃彬. 甘蔗CLC基因家族鉴定与表达分析[J]. 作物学报, 2026, 52(3): 722-734.

Yang Zong-Tao, Yang Ting, Wang Yu-Tong, Ai Jing, Li Yan-Ye, Liu Jia-Yong, Deng Jun, Zhao Yong, Zhang Yue-Bin. Identification and expression analysis of the CLC gene family in sugarcane[J]. Acta Agronomica Sinica, 2026, 52(3): 722-734.

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链接本文: https://zwxb.chinacrops.org/CN/10.3724/SP.J.1006.2026.54105

https://zwxb.chinacrops.org/CN/Y2026/V52/I3/722

图/表 11

附表1

图1

附表2

SsCLC蛋白基本信息"

基因名称 Gene name	基因 ID Gene ID	染色体定位 Chr. localization		相对分子量Molecular weight (kD)	等电点pI	不稳定系数 Instability index	脂肪指数 Aliphatic index	疏水性 Grand average of hydropathicity	亚细胞定位预测 Subcellular localization
SsCLC-a1	Sspon.08G0019260-3D	Chr. 8D	801	87.85	6.38	45.48	106.99	0.282	质膜 Plasma membrane
SsCLC-a2	Sspon.08G0019260-2C	Chr. 8C	754	82.90	9.16	40.23	115.86	0.475	质膜 Plasma membrane
SsCLC-a3	Sspon.08G0019260-1B	Chr. 8B	778	85.07	9.16	39.23	109.58	0.368	质膜 Plasma membrane
SsCLC-c1	Sspon.04G0009220-1A	Chr. 4A	716	76.98	6.83	34.86	100.54	0.335	质膜 Plasma membrane
SsCLC-c2	Sspon.04G0009220-3C	Chr. 4C	750	80.76	6.98	36.64	99.11	0.288	质膜 Plasma membrane
SsCLC-c3	Sspon.04G0009220-2B	Chr. 5B	723	78.29	5.91	38.76	104.83	0.360	质膜 Plasma membrane
SsCLC-c4	Sspon.04G0009220-4D	Chr. 5D	730	78.53	6.20	38.99	102.90	0.360	质膜 Plasma membrane
SsCLC-c5	Sspon.04G0009220-1P	Chr. 5A	689	74.38	6.65	42.03	99.70	0.276	质膜 Plasma membrane
SsCLC-c6	Sspon.04G0009220-2P	Chr. 5C	600	64.57	6.09	40.55	95.98	0.241	质膜 Plasma membrane
SsCLC-c7	Sspon.03G0029010-1B	Chr. 3B	1240	132.22	8.36	32.67	106.15	0.461	质膜 Plasma membrane
SsCLC-c8	Sspon.03G0029010-3D	Chr. 3D	730	77.95	8.49	34.21	105.79	0.448	质膜 Plasma membrane
SsCLC-d1	Sspon.01G0025410-2B	Chr. 1B	829	91.61	8.78	39.12	99.79	0.111	质膜 Plasma membrane
SsCLC-d2	Sspon.01G0025410-3C	Chr. 1C	740	81.33	7.89	37.67	102.09	0.253	质膜 Plasma membrane
SsCLC-d3	Sspon.01G0025410-1A	Chr. 1A	796	87.41	8.39	37.50	103.09	0.256	质膜 Plasma membrane
SsCLC-d4	Sspon.01G0025410-1P	Chr. 1A	410	44.29	7.09	30.49	97.78	0.340	质膜 Plasma membrane
SsCLC-e1	Sspon.03G0004960-1A	Chr. 3A	725	77.67	6.32	52.27	98.10	0.186	质膜 Plasma membrane
SsCLC-e2	Sspon.03G0004960-2B	Chr. 3B	779	83.88	6.60	51.03	94.67	0.089	叶绿体, 质膜 Chloroplast, plasma membrane
SsCLC-f1	Sspon.04G0004760-4D	Chr. 4D	352	36.98	7.65	48.36	89.38	0.017	线粒体, 叶绿体, 质膜 Mitochondrial, chloroplast, plasma membrane
SsCLC-f2	Sspon.04G0004760-1A	Chr. 4A	803	85.43	7.57	42.60	96.14	0.049	质膜 Plasma membrane
SsCLC-f3	Sspon.04G0004760-2B	Chr. 4B	771	82.09	6.98	40.19	98.37	0.129	质膜 Plasma membrane
SsCLC-f4	Sspon.06G0000980-3C	Chr. 6C	630	67.82	6.35	42.54	100.48	0.181	质膜 Plasma membrane
SsCLC-f5	Sspon.06G0000980-2B	Chr. 6B	752	79.97	6.07	43.51	97.71	0.116	质膜 Plasma membrane
SsCLC-f6	Sspon.06G0000980-1A	Chr. 6A	720	76.41	6.06	44.55	94.89	0.063	叶绿体, 质膜 Chloroplast, plasma membrane
SsCLC-f7	Sspon.06G0000980-4D	Chr. 6D	676	71.74	5.97	44.08	93.28	−0.008	线粒体, 叶绿体, 质膜 Mitochondrial, chloroplast, plasma membrane
SsCLC-g1	Sspon.04G0016160-2B	Chr. 4B	796	86.56	8.89	44.05	106.04	0.340	质膜 Plasma membrane
SsCLC-g3	Sspon.05G0022270-2C	Chr. 5C	815	88.48	8.51	39.87	103.36	0.314	质膜 Plasma membrane
SsCLC-g4	Sspon.05G0022270-1B	Chr. 5B	815	88.50	8.58	39.86	103.13	0.313	质膜 Plasma membrane
SsCLC-g5	Sspon.05G0022270-3D	Chr. 5D	814	88.42	8.58	39.66	103.13	0.306	质膜 Plasma membrane

附表2

图2

图3

图4

图5

图6

图7

图8

图9

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基因名称 Gene name	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)
SsCLC-a1	AGCTTATGCACTGGGAGCTG	ATGACGAGGTGATGTTGCCT
SsCLC-a2	CAACTCCGGCAACTTCAAGC	AAGATGAGCAGCGAGTCGAG
SsCLC-a3	TCTTGGCTCTTGCGTCTCAT	GCCAGTCGTGCTTGAACAGA
SsCLC-c1	AATGTCACTGGCAAAAGCGG	ATTCTCAGTGCGTCTGGTGT
SsCLC-c2	TTGCGGTGGTATTGAAGGGG	ACATGATCAATCCACCTTTCCCA
SsCLC-c3	CCATGAACACCACCTCCCAG	TGCTGTGAAGTACTCGTAGTCG
SsCLC-c4	CCTCGACTACGAGTACTTCAC	GCAGCAGCAGGTGCTATGTA
SsCLC-c5	CGACTACGAGTACTTCACAGC	AGGTGCTATGTAAGCGCAGA
SsCLC-c6	GCCTCGACTACGAGTACTTCAC	AGGTGCTATGTAAGCGCAGA
SsCLC-c7	GGTCGGTGAAGTGGGAGAAGG	ATGCATACTCGTAATCGAGGCT
SsCLC-c8	GCGGGACGATGCGGATGAC	TTGGCGATGAGCAGCACGAG
SsCLC-d1	CCATCGAGAGCCTCGACTAC	CCAGCTCGTTCAATTTGCCA
SsCLC-d2	GCGGACGGCGAGTTCTTAT	GACGTAGTAGGGCACCCAGA
SsCLC-d3	CTAAATGGCGGCGAACGCAT	CAGTAGTGGCAGCACAAAGG
SsCLC-d4	CTAAATGGCGGCGAACGCAT	CATGGGCTGCATTTCCTCAG
SsCLC-e1	AGAAAAGATGGCTCCCTCCG	GAGGGCTCCGATCGCTCA
SsCLC-e2	GAGAAAAGACGGCTCCCTCC	CCGTGAATCGTGATTTGGGC
SsCLC-f1	TCACCTCCATTTACGACTGC	AGAACAGTTACCAGCAGCAGA
SsCLC-f2	TTCGTCGTTCCTCGGTTCTG	GTTCGGTGCTGGTCTACTCG
SsCLC-f3	GGATACTGCTGATCCCGGTG	GTTGATTCGTTGCCTCTGCC
SsCLC-f4	AAACGTGGTGCTGGCCGTAG	CCACCGCTCAAGCTCTTCCC
SsCLC-f5	CTCGTCGGCTGCCTCCTTG	TGCCTGCCCATGCCCATTC
SsCLC-f6	CGTCGGCTGCCTCCTTGG	TGCCTGCCCATGCCCATTC
SsCLC-f7	GCCAGTCACCTCGCCATCG	TCCGCCAGTCGTGCTTGAAC
SsCLC-g1	GCGGTGCCACAAGGAGTACG	GGCGATGGTGTCCTGCTTCC
SsCLC-g2	ACCTGCTGGTGCTGCTCAAG	AGTCCTCCGCCTGGAACCTC
SsCLC-g3	TCTCCTCCGGCTCGTCCTTC	TGGTGTTGGAGTGCGTGTGG
SsCLC-g4	GGCCACATCCTGCGCTACG	CCGAGGTTGGCGACGAAGC
SsCLC-g5	TCTCCTCCGGCTCGTCCTTC	TGGTGTTGGAGTGCGTGTGG
25s-RNA1	ATAACCGCATCAGGTCTCCAAG	CCTCAGAGCCAATCCTTTTCC

甘蔗CLC基因家族鉴定与表达分析

Identification and expression analysis of the CLC gene family in sugarcane

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