藜麦CqPHD-finger基因家族成员鉴定及表达分析

doi:10.11733/j.issn.1007-0435.2026.08.005

草地学报 ›› 2026, Vol. 34 ›› Issue (8): 2793-2813.DOI: 10.11733/j.issn.1007-0435.2026.08.005

• 研究论文 • 上一篇

藜麦CqPHD-finger基因家族成员鉴定及表达分析

张帅¹, 董陈文华¹, 林春¹, 林艳¹, 熊艳娥¹, 杨燕¹, 刘正杰^1,2

1. 云南农业大学农学与生物技术学院, 云南昆明 650201;
2. 云南省作物生产与智慧农业重点实验室, 云南昆明 650201

收稿日期:2026-02-04 修回日期:2026-04-29 发布日期:2026-08-04
通讯作者: 杨燕,E-mail:2013045@ynau.edu.cn;刘正杰,E-mail:1153734659@qq.com
作者简介:张帅(2000-),男,回族,吉林吉林人,硕士研究生,主要从事基因挖掘与功能研究;E-mail:2236391576@qq.com
基金资助:
国家自然科学基金（32260482）；云南省农业联合专项面上项目（202501BD070001-049）；兴滇英才支持计划青年人才项目（XDYC-QNRC-2023-0409）资助

Identification and Expression Analysis of CqPHD-finger Gene Family Members in Quinoa

ZHANG Shuai¹, DONG Chen-wen-hua¹, LIN Chun¹, LIN Yan¹, XIONG Yan-e¹, YANG Yan¹, LIU Zheng-jie^1,2

1. College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan Province 650201, China;
2. The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan Province 650201, China

Received:2026-02-04 Revised:2026-04-29 Published:2026-08-04

摘要/Abstract

摘要： 为解析藜麦（Chenopodium quinoa Willd.）PHD-finger家族在发育与逆境适应中的潜在作用，本研究以藜麦参考基因组及多来源转录组数据为基础，开展全基因组鉴定、染色体定位、系统发育、基因结构、保守基序、顺式元件、复制事件及表达分析，并结合qRT-PCR进行验证。共鉴定出69个CqPHD-finger成员，这些成员不均匀分布于18条染色体，主要由片段复制驱动扩张，可划分为13个亚组，其启动子富含光信号、激素和逆境响应元件。group9与非生物胁迫响应相关蛋白聚类紧密，group10与绒毡层/花粉发育相关蛋白聚类显著。表达分析显示，该家族在分生组织、花器官和成熟籽粒中具有组织特异性，在高温、干旱及长日照下响应明显。qRT-PCR表明CqPHD-finger29，CqPHD-finger66，CqPHD-finger30和CqPHD-finger23均呈现显著的日照响应特性，提示其可能参与藜麦光周期依赖的开花调控。该研究为解析PHD-finger基因家族在藜麦生殖发育、逆境应答和光周期响应中的功能提供了理论依据。

关键词: 藜麦, PHD-finger, 转录因子, 生物信息学, 基因家族

Abstract: To elucidate the potential roles of the quinoa PHD-finger gene family in development and stress adaptation， this study was conducted based on the reference genome of quinoa （Chenopodium quinoa Willd.） and transcriptomic datasets from multiple sources. Genome-wide identification， chromosomal localization， phylogenetic analysis， gene structure characterization， conserved motif analysis， cis-acting element prediction， duplication event analysis， and expression profiling were performed， followed by validation using qRT-PCR. A total of 69 CqPHD-finger members were identified and found to be unevenly distributed across 18 chromosomes. The expansion of this gene family was mainly driven by segmental duplication. Phylogenetic analysis classified these members into 13 subgroups， and their promoters were enriched in cis-acting elements associated with light signaling， hormone responses， and stress responses. Members of group 9 clustered closely with proteins related to abiotic stress responses， whereas members of group 10 showed a close phylogenetic relationship with proteins involved in tapetum and pollen development. Expression analysis revealed that this gene family exhibited tissue-specific expression patterns in meristems， floral organs， and mature seeds， and showed pronounced responses to high temperature， drought， and long-day conditions. qRT-PCR analysis demonstrated that CqPHD-finger29， CqPHD-finger66， CqPHD-finger30， and CqPHD-finger23 exhibited significant photoperiod responsiveness， suggesting that they might participate in the regulation of photoperiod-dependent flowering in quinoa. This study provides a theoretical basis for further elucidating the functions of the PHD-finger gene family in quinoa reproductive development， stress responses， and photoperiodic regulation.

Key words: Quinoa, PHD-finger, Transcription factor, Bioinformatics, Gene family

中图分类号:

S519

张帅, 董陈文华, 林春, 林艳, 熊艳娥, 杨燕, 刘正杰. 藜麦CqPHD-finger基因家族成员鉴定及表达分析[J]. 草地学报, 2026, 34(8): 2793-2813.

ZHANG Shuai, DONG Chen-wen-hua, LIN Chun, LIN Yan, XIONG Yan-e, YANG Yan, LIU Zheng-jie. Identification and Expression Analysis of CqPHD-finger Gene Family Members in Quinoa[J]. Acta Agrestia Sinica, 2026, 34(8): 2793-2813.

参考文献

[1] TAKATSUJI H. Zinc-finger transcription factors in plants[J]. Cellular and Molecular Life Sciences CMLS，1998，54（6）：582-596
[2] SCHINDLER U，BECKMANN H，CASHMORE A R. HAT3.1，a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region[J]. The Plant Journal，1993，4（1）：137-150
[3] YANG J K，SHEN Y，CAI X X，et al. Genome-wide identification and expression patterns analysis of the PHD family protein in Glycine max[J]. Crops，2019（3）：55-65杨珺凯，沈阳，才晓溪，等. 大豆PHD家族蛋白的全基因组鉴定及表达特征分析[J]. 作物杂志，2019（3）：55-65
[4] YANG P Y，CUI J H，REN G Z，et al. Identification，classification and expression characteristics of sorghum PHD-finger gene family[J]. Journal of Mountain Agriculture and Biology，2020，39（4）：10-20杨溥原，崔江慧，任根增，等. 高粱PHD-Finger基因家族的鉴定、分类及表达特征分析[J]. 山地农业生物学报，2020，39（4）：10-20
[5] LIU M L，LI W J，ZHENG X L，et al. Genome-wide identification and expression analysis of the PHD finger gene family in pea （Pisum sativum）[J]. Plants，2024，13（11）：1489
[6] JUNG W J，JEONG J H，YOON J S，et al. Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time[J]. Plant Cell Reports，2024，43（6）：142
[7] LI X B，ZHANG J W. Structure and function of zinc finger proteins in eucaryon[J]. Chinese Journal of Biochemistry and Molecular Biology，2009，25（3）：206-211李晓波，张俊武. 真核生物中锌指蛋白的结构与功能[J]. 中国生物化学与分子生物学报，2009，25（3）：206-211
[8] WANG Y L. Functional study of soybean PHD-finger transcription factor GmPHD3 in high temperature and humidity stress[D]. Nanjing：Nanjing Agricultural University，2020：71-72王依隆. 大豆PHD-finger转录因子GmPHD3参与高温高湿等胁迫的功能研究[D]. 南京：南京农业大学，2020：71-72
[9] FENG Y，LIU Q P，XUE Q Z. Comparative phylogenetic analysis of the rice and Arabidopsis PHD-finger proteins[J]. Acta Genetica Sinica，2004，31（11）：1284-1293冯英，刘庆坡，薛庆中. 水稻与拟南芥PHDfinger蛋白的系统分析[J]. 遗传学报，2004，31（11）：1284-1293
[10] QUAN W L，CHAN Z L，WEI P W，et al. PHD finger proteins function in plant development and abiotic stress responses： an overview[J]. Frontiers in Plant Science，2023，14：1297607
[11] BIENZ M. The PHD finger，a nuclear protein-interaction domain[J]. Trends in Biochemical Sciences，2006，31（1）：35-40
[12] QIN M Y，LUO W B，ZHENG Y，et al. Genome-wide identification and expression analysis of the PHD-finger gene family in Solanum tuberosum[J]. PLoS One，2019，14（12）：e0226964
[13] YANG C Y，VIZCAY-BARRENA G，CONNER K，et al. MALE STERILITY1 is required for tapetal development and pollen wall biosynthesis[J]. The Plant Cell，2007，19（11）：3530-3548
[14] FU D L，DUNBAR M，DUBCOVSKY J. Wheat VIN3-like PHD finger genes are up-regulated by vernalization[J]. Molecular Genetics and Genomics，2007，277（3）：301-313
[15] KIM D H，SUNG S. The binding specificity of the PHD-finger domain of VIN3 moderates vernalization response[J]. Plant Physiology，2017，173（2）：1258-1268
[16] THU S W，RAI K M，SANDHU D，et al. Mutation in a PHD-finger protein MS4 causes male sterility in soybean[J]. BMC Plant Biology，2019，19（1）：378
[17] MOHAN V，BOROVSKY Y，KAMARA I，et al. CaVIL1，a plant homeodomain gene that promotes flowering in pepper[J]. Theoretical and Applied Genetics，2018，131（12）：2639-2649
[18] LEE W Y，LEE D，CHUNG W I，et al. Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2via plant homeodomain fingers[J]. The Plant Journal，2009，58（3）：511-524
[19] WU T，PI E X，TSAI S N，et al. GmPHD5 acts as an important regulator for crosstalk between histone H3K4 di-methylation and H3K14 acetylation in response to salinity stress in soybean[J]. BMC Plant Biology，2011，11（1）：178
[20] TANAKA N，URAGUCHI S，KAJIKAWA M，et al. A rice PHD-finger protein OsTITANIA，is a growth regulator that functions through elevating expression of transporter genes for multiple metals[J]. The Plant Journal，2018，96（5）：997-1006
[21] WEI W，HUANG J，HAO Y J，et al. Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants[J]. PLoS One，2009，4（9）：e7209
[22] LIU Y. Overexpression of a kind of transcription factor，OSPHD1，can enhance stress tolerance in rice[D]. Hefei：Anhui Agricultural University，2010：42-43刘雨. 转录因子OSPHD1的过表达提高水稻耐逆性的研究[D]. 合肥：安徽农业大学，2010：42-43
[23] QUAN W L，LIU X，WANG L H，et al. Ectopic expression of Medicago truncatula homeodomain finger protein，MtPHD6，enhances drought tolerance in Arabidopsis[J]. BMC Genomics，2019，20（1）：982
[24] WEI W，ZHANG Y Q，TAO J J，et al. The Alfin-like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis[J]. The Plant Journal，2015，81（6）：871-883
[25] SONG Y，GAO J，YANG F X，et al. Molecular Evolutionary Analysis of the Alfin-Like Protein Family in Arabidopsis lyrata，Arabidopsis thaliana，and Thellungiella Halophila[J]. PLoS One，2013，8（7）：e66838
[26] HARIADI Y，MARANDON K，TIAN Y，et al. Ionic and osmotic relations in quinoa （Chenopodium quinoa Willd.） plants grown at various salinity levels[J]. Journal of Experimental Botany，2011，62（1）：185-193
[27] DAKHILI S，ABDOLALIZADEH L，HOSSEINI S M，et al. Quinoa protein： Composition，structure and functional properties[J]. Food Chemistry，2019，299：125161
[28] MALDONADO-TAIPE N，REY E，TESTER M，et al. Leaf and shoot apical meristem transcriptomes of quinoa （Chenopodium quinoa Willd.） in response to photoperiod and plant development[J]. Plant，Cell & Environment，2024，47（6）：2027-2043
[29] WU Q，BAI X，LUO Y M，et al. Identification of the global diurnal rhythmic transcripts，transcription factors and time-of-day specific cis elements in Chenopodium quinoa[J]. BMC Plant Biology，2023，23（1）：96
[30] ZHANG Y M，LIN C，LIU Z J，et al. Cloning and functional analysis of CqAMSlike in Chenopodium quinoa[J]. Acta Agriculturae Boreali-occidentalis Sinica，2024，33（4）：683-694张玉敏，林春，刘正杰，等. 藜麦CqAMSlike基因的克隆与功能分析[J]. 西北农业学报，2024，33（4）：683-694
[31] SANTHOSHI Y，ANJANA A B，ZALA H，et al. Comprehensive analysis of the NHX gene family and its regulation under salt and drought stress in quinoa （Chenopodium quinoa Willd.）[J]. Genes，2025，16（1）：70
[32] FU W C. Genome-wide identification and characterization of the AP2/ERF gene family in quinoa （Chenopodium quinoa） and their expression profiling during abiotic stress conditions[J]. Journal of Plant Growth Regulation，2024，43（4）：1118-1136
[33] MELGAR A E，RIZZO A J，MOYANO L，et al. Genome-wide identification and salt stress-expression analysis of the dehydrin gene family in Chenopodium quinoa[J]. Current Plant Biology，2024，38：100340
[34] CHEN Y Q，LIN Y F，ZHANG S B，et al. Genome-wide identification and characterization of the HAK gene family in quinoa （Chenopodium quinoa Willd.） and their expression profiles under saline and alkaline conditions[J]. Plants，2023，12（21）：3747
[35] LIN C，LIU Z J，DONG Y M，et al. Domesticated cultivation and genetic breeding of Chenopodium quinoa[J]. Hereditas，2019，41（11）：1009-1022林春，刘正杰，董玉梅，等. 藜麦的驯化栽培与遗传育种[J]. 遗传，2019，41（11）：1009-1022
[36] HORTON P，PARK K J，OBAYASHI T，et al. WoLF PSORT： protein localization predictor[J]. Nucleic Acids Research，2007，35：W585-W587
[37] ZHANG F，YANG Z N，ZHANG S. Genome-wide analysis of PHD-finger protein family in Arabidopsis thaliana[J]. Acta Botanica Yunnanica，2009，31（3）：227-238张帆，杨仲南，张森. 拟南芥PHD-finger蛋白家族的全基因组分析[J]. 云南植物研究，2009，31（3）：227-238
[38] FERGUSON A C，PEARCE S，BAND L R，et al. Biphasic regulation of the transcription factor ABORTED MICROSPORES （AMS） is essential for tapetum and pollen development in Arabidopsis[J]. New Phytologist，2017，213（2）：778-790
[39] SUNG S，AMASINO R M. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3[J]. Nature，2004，427（6970）：159-164
[40] SUNG S，SCHMITZ R J，AMASINO R M. A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis[J]. Genes & Development，2006，20（23）：3244-3248
[41] JIN J B，JIN Y H，LEE J，et al. The SUMO E3 ligase，AtSIZ1，regulates flowering by controlling a salicylic acid-mediated floral promotion pathway and through affects on FLC chromatin structure[J]. The Plant Journal，2008，53（3）：530-540
[42] MÜSSIG C，KAUSCHMANN A，CLOUSE S D，et al. The Arabidopsis PHD-finger protein SHL is required for proper development and fertility[J]. Molecular Genetics and Genomics，2000，264（4）：363-370
[43] LÓPEZ-GONZÁLEZ L，MOURIZ A，NARRO-DIEGO L，et al. Chromatin-dependent repression of the Arabidopsis Floral integrator genes involves plant specific PHD-containing proteins[J]. The Plant Cell，2014，26（10）：3922-3938
[44] WEI W，TAO J J，CHEN H W，et al. PHD6 recognizes histone code and LHP1 to improve salt tolerance in soybean[C]//Crop Science Society of China Soybean Professional Committee. Abstracts of the 10th National Soybean Symposium. Beijing： National Key Laboratory of Plant Genomics/Institute of Genetics and Developmental Biology，Chinese Academy of Sciences；University of Chinese Academy of Sciences，2017：100韦伟，陶建军，陈昊伟，等. PHD6识别组蛋白密码及LHP1从而提高大豆抗盐能[C]//中国作物学会大豆专业委员会.第十届全国大豆学术讨论会论文摘要集.北京：植物基因组学国家重点实验室/中国科学院遗传与发育生物学研究所；中国科学院大学，2017：100
[45] HOU J J，FAN W W，MA R R，et al. MALE STERILITY 3 encodes a plant homeodomain-finger protein for male fertility in soybean[J]. Journal of Integrative Plant Biology，2022，64（5）：1076-1086
[46] ZHANG D L，MA S X，LIU Z X，et al. ZmABF4-ZmVIL2/ZmFIP37 module enhances drought tolerance in maize seedlings[J]. Plant，Cell & Environment，2024，47（9）：3605-3618
[47] AN X L，MA B，DUAN M J，et al. Molecular regulation of ZmMs7required for maize male fertility and development of a dominant male-sterility system in multiple species[J]. Proceedings of the National Academy of Sciences of the United States of America，2020，117（38）：23499-23509
[48] LI H，YUAN Z，VIZCAY-BARRENA G，et al. PERSISTENT TAPETAL CELL1 encodes a PHD-finger protein that is required for tapetal cell death and pollen development in rice[J]. Plant Physiology，2011，156（2）：615-630
[49] SUN M Z，JIA B W，YANG J K，et al. Genome-wide identification of the PHD-finger family genes and their responses to environmental stresses in Oryza sativa L[J]. International Journal of Molecular Sciences，2017，18（9）：2005
[50] CHOI S C，LEE S，KIM S R，et al. Trithorax group protein Oryza sativa trithorax1 controls flowering time in rice via interaction with early heading date3[J]. Plant Physiology，2014，164（3）：1326-1337
[51] MATSUBARA K，YAMANOUCHI U，NONOUE Y，et al. Ehd3，encoding a plant homeodomain finger-containing protein，is a critical promoter of rice flowering[J]. The Plant Journal，2011，66（4）：603-612
[52] YANG Z F，SUN L P，ZHANG P P，et al. TDR INTERACTING PROTEIN 3，encoding a PHD-finger transcription factor，regulates Ubisch bodies and pollen wall formation in rice[J]. The Plant Journal，2019，99（5）：844-861
[53] LI J Z，SHEN L，YANG S，et al. Cloning and expressional characterization of pepper CaPHD1 gene[J]. Chinese Journal of Tropical Crops，2016，37（4）：728-735李佳智，申磊，杨晟，等. 一个辣椒PHD-finger家族转录因子CaPHD1的克隆及其表达分析[J]. 热带作物学报，2016，37（4）：728-735
[54] JEONG K，CHOI D，LEE J. Fine mapping of the genic male-sterile ms₁ gene in Capsicum annuum L.[J]. Theoretical and Applied Genetics，2018，131（1）：183-191
[55] WU X L，TANG W W. Identification and evolutionary analysis of the PHD-finger transcription factor family in Chinese cabbage （Brassica rapa L.）[J]. Molecular Plant Breeding，2023，21（20）：6649-6658吴秀兰，唐文武. 白菜PHD-finger转录因子家族的鉴定及进化分析[J]. 分子植物育种，2023，21（20）：6649-6658
[56] FERNÁNDEZ GÓMEZ J，WILSON Z A. A barley PHD finger transcription factor that confers male sterility by affecting tapetal development[J]. Plant Biotechnology Journal，2014，12（6）：765-777
[57] JIA B C，WANG Y，ZHANG D L，et al. Screening of reference genes and analysis of gene expression under salt stress in Chenopodium quinoa[J]. Journal of Yantai University （Natural Science and Engineering Edition），2020，33（3）：283-288贾冰晨，王宇，张东亮，等. 藜麦内参基因筛选及盐胁迫相关基因表达分析[J]. 烟台大学学报（自然科学与工程版），2020，33（3）：283-288

藜麦CqPHD-finger基因家族成员鉴定及表达分析

Identification and Expression Analysis of CqPHD-finger Gene Family Members in Quinoa

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