Tang Huaijun, Jing De, Liu Cheng, Xie Xiaoqing, Zhang Lei, Chen Xunji, Li Changyu
Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
Curr Issues Mol Biol. 2024 Jan 2;46(1):430-449. doi: 10.3390/cimb46010027.
As transcription factors derived from transposase, () and its homolog play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six genes (, , , , , and ) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in and , which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding.
作为源自转座酶的转录因子，（）及其同源物通过协调下游靶基因的表达，在光信号调节和各种应激反应中发挥关键作用。尽管对拟南芥和其他物种中的FAR1/FHY3家族进行了广泛研究，但迄今为止尚未对玉米中的这些基因进行全面研究。在本研究中，我们采用基因组挖掘方法在玉米自交系B73中鉴定出16个ZmFAR1基因，并根据它们的系统发育关系将其进一步分为五个亚组。本研究对ZmFAR1家族所有成员的预测多肽序列、分子量、等电点、染色体分布、基因结构、保守基序、亚细胞定位、系统发育关系和顺式调控元件进行了表征。此外，利用RNA测序分析了16个ZmFAR1基因的组织特异性表达，并通过qRT-qPCR在雌穗和雄穗中验证了它们在远红光条件下的表达模式。观察到的这些ZmFAR1基因高度的时空表达模式可能与其在不同光照条件下的特定功能能力有关。进一步分析表明，六个ZmFAR1基因（，，，，，和）对模拟遮荫处理有反应，并积极促进玉米雌穗的发育。通过整合表达数量性状位点（eQTL）分析和群体遗传学，我们在和中鉴定出潜在的因果变异，它们分别在调节穗行数和粒体积重方面起关键作用。总之，本研究代表了对玉米中ZmFAR1家族成员的首次鉴定和表征，揭示了现代玉米育种过程中与重要农艺性状改良相关的候选调控基因的功能变异。
