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作物学报 ›› 2026, Vol. 52 ›› Issue (6): 1728-1742.doi: 10.3724/SP.J.1006.2026.52036

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

两系不育系水稻幼苗根系响应盐胁迫的转录因子调控网络鉴定

邹仪妹1,2(), 徐敏1, 汪海洋1, 姚辉1, 王加峰3, 刘浩2,*(), 任代胜1,*()   

  1. 1 安徽袁粮水稻产业有限公司, 安徽合肥 231131
    2 广东省农作物遗传改良重点实验室 / 广东省农业科学院作物研究所, 广东广州 510640
    3 国家植物航天育种工程技术研究中心 / 华南农业大学, 广东广州 510642
  • 收稿日期:2025-09-22 接受日期:2026-03-16 出版日期:2026-06-12 网络出版日期:2026-03-27
  • 通讯作者: * 刘浩, E-mail: liuhao2054@stu.scau.edu.cn; 任代胜, E-mail: rendaisheng@163.com
  • 作者简介:邹仪妹, E-mail: zouyimei1106@163.com
  • 基金资助:
    安徽袁粮水稻产业有限公司

Analysis of transcription factor regulatory networks in two-line male sterile rice seedling roots in response to salt stress

Zou Yi-Mei1,2(), Xu Min1, Wang Hai-Yang1, Yao Hui1, Wang Jia-Feng3, Liu Hao2,*(), Ren Dai-Sheng1,*()   

  1. 1 Anhui Yuanliang Rice Industry Co., Ltd., Hefei 231131, Anhui, China
    2 Guangdong Key Laboratory of Crop Genetic Improvement / Institute of Crop Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
    3 National Engineering Research Center of Plant Space Breeding / South China Agricultural University, Guangzhou 510642, Guangdong, China
  • Received:2025-09-22 Accepted:2026-03-16 Published:2026-06-12 Published online:2026-03-27
  • Contact: * Liu Hao, E-mail: liuhao2054@stu.scau.edu.cn; Ren Dai-Sheng, E-mail: rendaisheng@163.com
  • Supported by:
    Anhui Yuanliang Rice Industry Co., Ltd.

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摘要：

为全面解析水稻幼苗根系响应盐胁迫的转录因子调控网络, 本研究以经3个不同浓度NaCl溶液(0、0.25%、0.50%)处理1周的水稻不育系华兴166S幼苗根系为研究对象, 开展了表型数据测定。通过转录组测序技术分析基因表达特征, 共检测到30,378个基因, 其中, 26,315个为显著差异表达基因。对差异基因的生物学代谢通路富集分析发现, 在3个NaCl处理浓度下, 差异基因均显著富集于次生代谢分支通路。基于差异基因谱, 本研究进一步筛选出326个差异表达转录因子, 构建了包含88个转录因子的核心互作网络。功能富集分析表明, 核心网络涉及植物激素信号转导、植物MAPK信号通路、植物昼夜节律等途径。此外, 荧光定量PCR鉴定发现, 盐胁迫后, WRKY转录因子家族中的10个基因在水稻根系中表现特异高表达。本研究基于3个不同浓度NaCl胁迫处理的转录组测序数据, 构建了水稻幼苗根系的基因表达谱与转录因子核心互作网络, 为探究水稻幼苗根系响应盐胁迫的分子调控机制提供了理论参考。

关键词: 水稻, 根, 盐胁迫, 转录组测序, 转录因子

Abstract:

To comprehensively elucidate the transcription factor regulatory network underlying salt-stress responses in rice seedling roots, we used the rice male sterile line Huaxing 166S as material, treated seedling roots with three NaCl concentrations (0, 0.25%, and 0.50%) for one week and recorded phenotypic data. RNA-seq was then used to characterize gene expression patterns, detecting 30,378 genes, of which 26,315 were identified as significantly differentially expressed genes (DEGs). Pathway enrichment analysis showed that, across all three NaCl treatments, DEGs were significantly enriched in secondary metabolism-related pathways. Based on the DEG dataset, we further identified 326 differentially expressed transcription factors and constructed a core interaction network comprising 88 transcription factors. Functional enrichment analysis indicated that this core network was mainly involved in plant hormone signal transduction, the plant MAPK signaling pathway, and the plant circadian rhythm pathway. In addition, quantitative real-time PCR (qPCR) validation showed that, following salt stress, 10 WRKY family genes were specifically highly expressed in rice roots. Together, these transcriptome data across three NaCl concentrations define the gene expression landscape and a core transcription factor interaction network in rice seedling roots, providing a basis for dissecting the molecular regulatory mechanisms of rice root responses to salt stress.

Key words: rice, root, salt stress, transcriptome sequencing, transcription factor

图1

水稻华兴166S经不同NaCl溶液处理1周的表型数据统计 A: 水稻华兴166S经3种浓度NaCl溶液处理1周的表型图; B: 水稻的表型数据图, 包括主根长、侧根长、地上部长度、叶鞘长、叶宽以及叶长。数字代表平均数, 不同圆点代表独立观察的样本数值。星号表示通过单因素方差分析与其他处理相比具有显著性; ns表示差异不显著; *、**、***、****分别表示在0.05、0.01、0.001和0.0001水平差异显著。CK: H2O处理; NCL1: 0.25% NaCl处理; NCL2: 0.50% NaCl处理。比例尺: 1 cm。"

表1

测序原始数据质量统计分析"

样本Sample 原始数据Raw date 有效数据Clean date ≥ Q20 (%) ≥ Q30 (%) 总基因组比对
Total mapped (%)		 单基因组比对
Unique mapped (%)
CK 43,275,807 43,243,773 6,377,082,790 (98.74%) 6,254,517,192 (96.84%) 16,002,536 (37.06%) 15,636,570 (36.21%)
NCL1 48,472,627 48,406,191 7,075,855,425 (98.36%) 6,886,617,516 (95.73%) 32,750,575 (67.80%) 31,956,882 (66.16%)
NCL2 48,042,298 47,985,791 7,016,035,857 (98.37%) 6,834,873,942 (95.83%) 20,215,178 (42.24%) 19,754,634 (41.27%)

表2

样本皮尔逊系数统计"

样本Sample CK1 CK2 CK3 NCL1-1 NCL1-2 NCL1-3 NCL2-1 NCL2-2 NCL2-3
CK1 1.0000 0.9988 0.9966 0.9571 0.9563 0.9589 0.8132 0.8361 0.8439
CK2 0.9988 1.0000 0.9980 0.9563 0.9554 0.9580 0.8140 0.8365 0.8442
CK3 0.9966 0.9980 1.0000 0.9534 0.9525 0.9544 0.8092 0.8307 0.8375
NCL1-1 0.9571 0.9563 0.9534 1.0000 0.9975 0.9980 0.8794 0.9069 0.9114
NCL1-2 0.9563 0.9554 0.9525 0.9975 1.0000 0.9989 0.8756 0.9012 0.9064
NCL1-3 0.9589 0.9580 0.9544 0.9980 0.9989 1.0000 0.8765 0.9033 0.9092
NCL2-1 0.8132 0.8140 0.8092 0.8794 0.8756 0.8765 1.0000 0.9868 0.9883
NCL2-2 0.8361 0.8365 0.8307 0.9069 0.9012 0.9033 0.9868 1.0000 0.9962
NCL2-3 0.8439 0.8442 0.8375 0.9114 0.9064 0.9092 0.9883 0.9962 1.0000

图2

华兴166S经不同浓度NaCl溶液处理后样本转录组数据相关性系数鉴定 A: 转录组测序程序流程图; B: 比对参考区域统计图; C: 样本主成分分析; D: 基因表达量小提琴图; E: 样本相关性热图。CK: 清水对照样本; NCL1: 0.25% NaCl处理样本; NCL2: 0.50% NaCl处理样本。"

图3

水稻华兴166S幼根总体表达基因的分析和鉴定 A: 全体基因表达量圈图; B: 全体基因K-means聚类图; C: 全部基因绘制的韦恩图; D: 各组别基因表达量。CK: 清水对照样本; NCL1: 0.25% NaCl处理样本; NCL2: 0.50% NaCl处理样本。"

图4

水稻华兴166S经不同浓度NaCl溶液处理幼根差异基因的鉴定 A: 差异基因统计图; B: 差异基因表达量圈图; C: 筛选出关键基因的韦恩图; D: 各组别特异基因的表达热量图; E: 关键521个基因的表达量热图; F: 3个不同浓度的KEGG通路富集气泡图。CK: 清水对照样本; NCL1: 0.25% NaCl处理样本; NCL2: 0.50% NaCl处理样本。"

图5

WGCNA分析 A: 基因聚类树与模块构建; B: 基因共表达模块与样品类型的相关性分析; C: WGCNA筛选的模块基因的表达量热图; D: KEGG富集条形图(前10条); E: 关键转录因子的表达量箱线图; F: WGCNA筛选的模块基因转录因子PPI网络图。CK: 清水对照样本; NCL1: 0.25% NaCl处理样本; NCL2: 0.50% NaCl处理样本。"

图6

筛选出水稻华兴166S不同NaCl浓度的关键转录因子 A: 关键转录因子PPI网络图; B: KEGG显著性气泡图; C: 转录因子表达量热图; D: 关键转录因子的共表达基因网络; E: 关键转录因子在根系中的表达量小提琴图和UMAP图。CK: 清水对照样本; NCL1: 0.25% NaCl处理样本; NCL2: 0.50% NaCl处理样本。"

表3

差异表达转录因子的表达倍数变化表"

基因名称
Gene name		 基因号
Gene ID		 CK vs NCL1 CK vs NCL2
OsWRKY10 LOC_Os01g09100 2.892,349,507,717,20 4.208,186,410,507,11
OsWRKY15 LOC_Os01g46800 2.077,620,897,122,47 2.906,407,199,711,59
OsWRKY21 LOC_Os01g60640 3.271,167,936,121,78 2.830,158,795,789,49
OsWRKY24 LOC_Os01g61080 3.716,990,240,352,99 2.224,369,246,044,20
OsWRKY71 LOC_Os02g08440 2.163,577,774,072,10 2.068,959,346,932,18
OsMYB30 LOC_Os02g41510 2.209,477,903,971,47 2.379,157,503,205,14
OsBIERF3 LOC_Os02g43790 2.452,243,431,892,17 2.290,418,257,659,48
OsZFP36 LOC_Os03g32230 3.214,718,493,451,03 3.741,474,139,238,18
OsBHLH6 LOC_Os04g23550 4.113,290,984,177,07 3.541,721,650,326,90
OsWRKY48 LOC_Os05g40060 3.468,591,617,922,77 2.346,527,848,519,60
OsWRKY58 LOC_Os05g45230 9.736,401,931,318,29 9.389,452,089,084,37
OsWRKY19 LOC_Os05g49620 2.896,985,368,520,98 3.927,360,850,031,74
OsAPG LOC_Os06g05550 2.465,663,572,348,81 -7.392,317,423,000,00
OsWRKY28 LOC_Os06g44010 3.796,956,052,941,55 3.897,143,066,085,37
OsNF-YA5 LOC_Os07g06470 -2.415,012,809,000,00 -3.507,174,423,000,00
OsERF87 LOC_Os09g39850 5.181,501,872,682,66 2.867,639,779,526,03
OsWRKY64 LOC_Os12g02450 2.926,988,648,318,06 2.971,751,818,621,09

图7

关键转录因子编码基因的qPCR验证 星号表示通过单因素方差分析与其他处理相比具有显著性。ns: 差异不显著; *、**、***、****分别表示在0.05、0.01、0.001和0.0001水平差异显著。CK: 清水对照样本; NCL1: 0.25% NaCl处理样本; NCL2: 0.50% NaCl处理样本。"

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