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

doi:10.11733/j.issn.1007-0435.2026.08.005

Acta Agrestia Sinica ›› 2026, Vol. 34 ›› Issue (8): 2793-2813.DOI: 10.11733/j.issn.1007-0435.2026.08.005

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

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

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

Abstract

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

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

CLC Number:

S519

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.

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.

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

藜麦CqPHD-finger基因家族成员鉴定及表达分析

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