Journal of Genetics and Genomics

Mycorrhizal fungi enhance plant resistance to environmental stresses: from mechanisms to applications

Jing Wang, Mengwei Wei, Ertao Wang

2025, 52(3): 273-275. doi: 10.1016/j.jgg.2025.01.013

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Genetic and molecular mechanisms underlying nitrogen use efficiency in maize

Jianfang Li, Huairong Cao, Shuxin Li, Xiaonan Dong, Zheng Zhao, Zhongtao Jia, Lixing Yuan

2025, 52(3): 276-286. doi: 10.1016/j.jgg.2024.10.007

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Nitrogen (N) is vital for crop growth and yield, impacting food quality. However, excessive use of N fertilizers leads to high agricultural costs and environmental challenges. This review offers a thorough synthesis of the genetic and molecular regulation of N uptake, assimilation, and remobilization in maize, emphasizing the role of key genes and metabolic pathways in enhancing N use efficiency (NUE). We summarize the genetic regulators of N transports for nitrate (NO₃^-) and ammonium (NH₄⁺) that contribute to efficient N uptake and transportation. We further discuss the molecular mechanisms by which root system development adapts to N distribution and how N influences root system development and growth. Given the advancements in high-throughput microbiome studies, we delve into the impact of rhizosphere microorganisms on NUE and the complex plant–microbe interactions that regulate maize NUE. Additionally, we conclude with intricate regulatory mechanisms of N assimilation and remobilization in maize, involving key enzymes, transcription factors, and amino acid transporters. We also scrutinize the known N signaling perception and transduction mechanisms in maize. This review underscores the challenges in improving maize NUE and advocates for an integrative research approach that leverages genetic diversity and synthetic biology, paving the way for sustainable agriculture.

Phosphorus acquisition, translocation, and redistribution in maize

Hui-Ling Guo, Meng-Zhi Tian, Xian Ri, Yi-Fang Chen

2025, 52(3): 287-296. doi: 10.1016/j.jgg.2024.09.018

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Phosphorus (P) is an essential nutrient for crop growth, making it important for maintaining food security as the global population continues to increase. Plants acquire P primarily via the uptake of inorganic phosphate (Pi) in soil through their roots. Pi, which is usually sequestered in soils, is not easily absorbed by plants and represses plant growth. Plants have developed a series of mechanisms to cope with P deficiency. Moreover, P fertilizer applications are critical for maximizing crop yield. Maize is a major cereal crop cultivated worldwide. Increasing its P-use efficiency is important for optimizing maize production. Over the past two decades, considerable progresses have been achieved in studies aimed at adapting maize varieties to changes in environmental P supply. Here, we present an overview of the morphological, physiological, and molecular mechanisms involved in P acquisition, translocation, and redistribution in maize and combine the advances in Arabidopsis and rice, to better elucidate the progress of P nutrition. Additionally, we summarize the correlation between P and abiotic stress responses. Clarifying the mechanisms relevant to improving P absorption and use in maize can guide future research on sustainable agriculture.

Metal ion transport in maize: survival in a variable stress environment

Kangqi Wang, Ziqi Wu, Man Zhang, Xueyao Lu, Jinsheng Lai, Meiling Zhang, Yi Wang

2025, 52(3): 297-306. doi: 10.1016/j.jgg.2025.01.005

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Maize (Zea mays) is the most widely cultivated crop in the world. Maize production is closely linked to the extensive uptake and utilization of various mineral nutrients. Potassium (K), calcium (Ca), and magnesium (Mg) are essential metallic macronutrients for plant growth and development. Sodium (Na) is an essential micronutrient for some C₄ and CAM plants. Several metallic micronutrients like iron (Fe), manganese (Mn), and zinc (Zn) serve as enzyme components or co-factors in plant cells. Maize has to face the combined ion stress conditions in the natural environment. The limited availability of these nutrients in soils restricts maize production. In saline land, excessive Na could inhibit the uptake of mineral elements. Additionally, aluminum (Al) and heavy metals cadmium (Cd) and lead (Pb) in soils are toxic to maize and pose a threat to food security. Thus, plants must evolve complex mechanisms to increase nutrient uptake and utilization while restraining harmful elements. This review summarizes the research progress on the uptake and transport of metal ions in maize, highlights the regulation mechanism of metal ion transporters under stress conditions, and discusses the future challenges for the improvement of maize with high nutrient utilization efficiency (NUE).

Epigenetic variation in maize agronomical traits for breeding and trait improvement

Daolei Zhang, Yujun Gan, Liang Le, Li Pu

2025, 52(3): 307-318. doi: 10.1016/j.jgg.2024.01.006

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Epigenetics-mediated breeding (epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.

Decoding maize meristems maintenance and differentiation: integrating single-cell and spatial omics

Bin Li, Wenhao Liu, Jie Xu, Xuxu Huang, Long Yang, Fang Xu

2025, 52(3): 319-333. doi: 10.1016/j.jgg.2025.01.012

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All plant organs are derived from stem cell-containing meristems. In maize, the shoot apical meristem (SAM) is responsible for generating all above-ground structures, including the male and female inflorescence meristems (IMs), which give rise to tassel and ear, respectively. Forward and reverse genetic studies on maize meristem mutants have driven forward our fundamental understanding of meristem maintenance and differentiation mechanisms. However, the high genetic redundancy of the maize genome has impeded progress in functional genomics. This review comprehensively summarizes recent advancements in understanding maize meristem development, with a focus on the integration of single-cell and spatial technologies. We discuss the mechanisms governing stem cell maintenance and differentiation in SAM and IM, emphasizing the roles of gene regulatory networks, hormonal pathways, and cellular omics insights into stress responses and adaptation. Future directions include cross-species comparisons, multi-omics integration, and the application of these technologies to precision breeding and stress adaptation research, with the ultimate goal of translating our understanding of meristem into the development of higher yield varieties.

ZmL75 is required for colonization by arbuscular mycorrhizal fungi and for saline–alkali tolerance in maize

Jie Liu, Boming Yang, Xunji Chen, Tengfei Zhang, Huairen Zhang, Yimo Du, Qian Zhao, Zhaogui Zhang, Darun Cai, Juan Liu, Huabang Chen, Li Zhao

2025, 52(3): 334-345. doi: 10.1016/j.jgg.2024.12.015

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Saline–alkali soil severely reduces the productivity of crops, including maize (Zea mays). Although several genes associated with saline–alkali tolerance have been identified in maize, the underlying regulatory mechanism remains elusive. Here, we report a direct link between colonization by arbuscular mycorrhizal fungi (AMF) and saline–alkali tolerance in maize. We identify s75, a natural maize mutant that cannot survive under moderate saline–alkali soil conditions or establish AM symbioses. The saline–alkali hypersensitive phenotype of s75 is caused by a 1340-bp deletion in Zm00001d033915, designated as ZmL75. This gene encodes a glycerol-3-phosphate acyltransferase localized in the endoplasmic reticulum, and is responsible for AMF colonization. ZmL75 expression levels in roots correspond with the root length colonization (RLC) rate during early vegetative development. Notably, the s75 mutant line shows a complete loss of AMF colonization, along with alterations in the diversity and structure of its root fungal microbiota. Conversely, overexpression of ZmL75 increases the RLC rate and enhances tolerance to saline–alkali soil conditions. These results suggest that ZmL75 is required for symbiosis with AMF, which directly improves saline–alkali tolerance. Our findings provide insights into maize–AMF interactions and offer a potential strategy for maize improvement.

ZmGolS1 underlies natural variation of raffinose content and salt tolerance in maize

Xiaoyan Liang, Pan Yin, Fenrong Li, Yibo Cao, Caifu Jiang

2025, 52(3): 346-355. doi: 10.1016/j.jgg.2024.12.013

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Salt stress significantly inhibits crop growth and development, and mitigating this can enhance salt tolerance in various crops. Previous studies have shown that regulating saccharide biosynthesis is a key aspect of plant salt tolerance; however, the underlying molecular mechanisms remain largely unexplored. In this study, we demonstrate that overexpression of a salt-inducible galactinol synthase gene, ZmGolS1, alleviates salt-induced growth inhibition, likely by promoting raffinose synthesis. Additionally, we show that natural variation in ZmGolS1 transcript levels contributes to the diversity of raffinose content and salt tolerance in maize. We further reveal that ZmRR18, a type-B response regulator transcription factor, binds to the AATC element in the promoter of ZmGolS1, with this binding increases the transcript levels of ZmGolS1 under salt conditions. Moreover, a single nucleotide polymorphism (termed SNP-302T) within the ZmGolS1 promoter significantly reduces its binding affinity for ZmRR18, resulting in decreased ZmGolS1 expression and diminished raffinose content, ultimately leading to a salt-hypersensitive phenotype. Collectively, our findings reveal the molecular mechanisms by which the ZmRR18-ZmGolS1 module enhances raffinose biosynthesis, thereby promoting maize growth under salt conditions. This research provides important insights into salt tolerance mechanisms associated with saccharide biosynthesis and identifies valuable genetic loci for breeding salt-tolerant maize varieties.

LG1 promotes preligule band formation through directly activating ZmPIN1 genes in maize

Zhuojun Zhong, Minhao Yao, Yingying Cao, Dexin Kong, Baobao Wang, Yanli Wang, Rongxin Shen, Haiyang Wang, Qing Liu

2025, 52(3): 356-366. doi: 10.1016/j.jgg.2025.01.014

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Increasing plant density is an effective strategy for enhancing crop yield per unit land area. A key architectural trait for crops adapting to high planting density is a smaller leaf angle (LA). Previous studies have demonstrated that LG1, a SQUAMOSA BINDING PROTEIN (SBP) transcription factor, plays a critical role in LA establishment. However, the molecular mechanisms underlying the regulation of LG1 on LA formation remain largely unclear. In this study, we conduct comparative RNA-seq analysis of the preligule band (PLB) region of wild type and lg1 mutant leaves. Gene Ontology (GO) term enrichment analysis reveals enrichment of phytohormone pathways and transcription factors, including three auxin transporter genes ZmPIN1a, ZmPIN1b, and ZmPIN1c. Further molecular experiments demonstrate that LG1 can directly bind to the promoter region of these auxin transporter genes and activate their transcription. We also show that double and triple mutants of these ZmPINs genes exhibit varying degrees of auricle size reduction and thus decreased LA. On the contrary, overexpression of ZmPIN1a causes larger auricle and LA. Taken together, our findings establish a functional link between LG1 and auxin transport in regulating PLB formation and provide valuable targets for genetic improvement of LA for breeding high-density tolerant maize cultivars.

Genetic variations in ZmEREB179 are associated with waterlogging tolerance in maize

Kun Liang, Chenxu Zhao, Jing Wang, Xueqing Zheng, Feng Yu, Fazhan Qiu

2025, 52(3): 367-378. doi: 10.1016/j.jgg.2024.04.005

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Maize (Zea mays) is highly susceptible to waterlogging stress, which reduces both the yield and quality of this important crop. However, the molecular mechanism governing waterlogging tolerance is poorly understood. In this study, we identify a waterlogging- and ethylene-inducible gene ZmEREB179 that encodes an ethylene response factor (ERF) localized in the nucleus. Overexpression of ZmEREB179 in maize increases the sensitivity to waterlogging stress. Conversely, the zmereb179 knockout mutants are more tolerant to waterlogging, suggesting that ZmEREB179 functions as a negative regulator of waterlogging tolerance. A transcriptome analysis of the ZmEREB179-overexpressing plants reveals that the ERF-type transcription factor modulates the expression of various stress-related genes, including ZmEREB180. We find that ZmEREB179 directly targets the ZmEREB180 promoter and represses its expression. Notably, the analysis of a panel of 220 maize inbred lines reveals that genetic variations in the ZmEREB179 promoter (Hap2) are highly associated with waterlogging resistance. The functional association of Hap2 with waterlogging resistance is tightly co-segregated in two F₂ segregating populations, highlighting its potential applications in breeding programs. Our findings shed light on the involvement of the transcriptional cascade of ERF genes in regulating plant-waterlogging tolerance.

PPR21 is involved in the splicing of nad2 introns via interacting with PPR-SMR1 and SPR2 and is essential to maize seed development

Yan-Zhuo Yang, Xin-Yuan Liu, Song Gao, Shu-Guang Zhang, Bao-Cai Tan

2025, 52(3): 379-387. doi: 10.1016/j.jgg.2024.08.010

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Pentatricopeptide repeat (PPR) proteins are a large group of eukaryote-specific RNA-binding proteins that play pivotal roles in plant organelle gene expression. Here, we report the function of PPR21 in mitochondrial intron splicing and its role in maize kernel development. PPR21 is a typical P-type PPR protein targeted to mitochondria. The ppr21 mutants are arrested in embryogenesis and endosperm development, leading to embryo lethality. Null mutations of PPR21 reduce the splicing efficiency of nad2 intron 1, 2, and 4 and impair the assembly and activity of mitochondrial complex I. Previous studies show that the P-type PPR protein EMP12 is required for the splicing of identical introns. However, our protein interaction analyses reveal that PPR21 does not interact with EMP12. Instead, both PPR21 and EMP12 interact with the small MutS-related (SMR) domain-containing PPR protein 1 (PPR-SMR1) and the short P-type PPR protein 2 (SPR2). PPR-SMR1 interacts with SPR2, and both proteins are required for the splicing of many introns in mitochondria, including nad2 intron 1, 2, and 4. These results suggest that a PPR21–(PPR-SMR1/SPR2)–EMP12 complex is involved in the splicing of nad2 introns in maize mitochondria.

An LRR-RLK protein modulates drought- and salt-stress responses in maize

Zhirui Yang, Chen Wang, Tengfei Zhu, Jiafan He, Yijie Wang, Shiping Yang, Yu Liu, Bochen Zhao, Chaohui Zhu, Shuqing Ye, Limei Chen, Shengxue Liu, Feng Qin

2025, 52(3): 388-399. doi: 10.1016/j.jgg.2024.10.016

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Maize (Zea mays), which is a vital source of food, feed, and energy feedstock globally, has significant potential for higher yields. However, environmental stress conditions, including drought and salt stress, severely restrict maize plant growth and development, leading to great yield losses. Leucine-rich repeat receptor-like kinases (LRR-RLKs) function in biotic and abiotic stress responses in the model plant Arabidopsis (Arabidopsis thaliana), but their roles in abiotic stress responses in maize are not entirely understood. In this study, we determine that the LRR-RLK ZmMIK2, a homolog of the Arabidopsis LRR-RK MALE DISCOVERER 1 (MDIS1)-INTERACTING RECEPTOR LIKE KINASE 2 (MIK2), functions in resistance to both drought and salt stress in maize. Zmmik2 plants exhibit enhanced resistance to both stresses, whereas overexpressing ZmMIK2 confers the opposite phenotypes. Furthermore, we identify C2-DOMAIN-CONTAINING PROTEIN 1 (ZmC2DP1), which interacts with the intracellular region of ZmMIK2. Notably, that region of ZmMIK2 mediates the phosphorylation of ZmC2DP1, likely by increasing its stability. Both ZmMIK2 and ZmC2DP1 are mainly expressed in roots. As with ZmMIK2, knockout of ZmC2DP1 enhances resistance to both drought and salt stress. We conclude that ZmMIK2–ZmC2DP1 acts as a negative regulatory module in maize drought- and salt-stress responses.

Time-course transcriptomic analysis reveals transcription factors involved in modulating nitrogen sensibility in maize

Mingliang Zhang, Yuancong Wang, Qi Wu, Yangming Sun, Chenxu Zhao, Min Ge, Ling Zhou, Tifu Zhang, Wei Zhang, Yiliang Qian, Long Ruan, Han Zhao

2025, 52(3): 400-410. doi: 10.1016/j.jgg.2024.09.021

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Nitrogen (N) serves both as a vital macronutrient and a signaling molecule for plants. Unveiling key regulators involved in N metabolism helps dissect the mechanisms underlying N metabolism, which is essential for developing maize with high N use efficiency. Two maize lines, B73 and Ki11, show differential chlorate and low-N tolerance. Time-course transcriptomic analysis reveals that the expression of N utilization genes (NUGs) in B73 and Ki11 have distinct responsive patterns to nitrate variation. By the coexpression networks, significant differences in the number of N response modules and regulatory networks of transcription factors (TFs) are revealed between B73 and Ki11. There are 23 unique TFs in B73 and 41 unique TFs in Ki11. MADS26 is a unique TF in the B73 N response network, with different expression levels and N response patterns in B73 and Ki11. Overexpression of MADS26 enhances the sensitivity to chlorate and the utilization of nitrate in maize, at least partially explaining the differential chlorate tolerance and low-N sensitivity between B73 and Ki11. The findings in this work provide unique insights and promising candidates for maize breeding to reduce unnecessary N overuse.

Maize transcription factor ZmEREB167 negatively regulates starch accumulation and kernel size

Xiangyu Qing, Jianrui Li, Zhen Lin, Wei Wang, Fei Yi, Jian Chen, Qiujie Liu, Weibin Song, Jinsheng Lai, Baojian Chen, Haiming Zhao, Zhijia Yang

2025, 52(3): 411-421. doi: 10.1016/j.jgg.2025.01.011

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Transcription factors play critical roles in the regulation of gene expression during maize kernel development. The maize endosperm, a large storage organ, accounting for nearly 90% of the dry weight of mature kernels, serves as the primary site for starch storage. In this study, we identify an endosperm-specific EREB gene, ZmEREB167, which encodes a nucleus-localized EREB protein. Knockout of ZmEREB167 significantly increases kernel size and weight, as well as starch and protein content, compared with the wild type. In situ hybridization experiments show that ZmEREB167 is highly expressed in the BETL as well as PED regions of maize kernels. Dual-luciferase assays show that ZmEREB167 exhibits transcriptionally repressor activity in maize protoplasts. Transcriptome analysis reveals that a large number of genes are up-regulated in the Zmereb167-C1 mutant compared with the wild type, including key genetic factors such as ZmMRP-1 and ZmMN1, as well as multiple transporters involved in maize endosperm development. Integration of RNA-seq and ChIP-seq results identify 68 target genes modulated by ZmEREB167. We find that ZmEREB167 directly targets OPAQUE2, ZmNRT1.1, ZmIAA12, ZmIAA19, and ZmbZIP20, repressing their expressions. Our study demonstrates that ZmEREB167 functions as a negative regulator in maize endosperm development and affects starch accumulation and kernel size.

The maize mTERF18 regulates transcriptional termination of the mitochondrial nad6 gene and is essential for kernel development

Zhengwei Guan, Yong Wang, Jun Yang

2025, 52(3): 422-431. doi: 10.1016/j.jgg.2025.01.001

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Mitochondria are semi-autonomous organelles present in eukaryotic cells, containing their own genome and transcriptional machinery. However, their functions are intricately linked to proteins encoded by the nuclear genome. Mitochondrial transcription termination factors (mTERFs) are nucleic acid-binding proteins involved in RNA splicing and transcription termination within plant mitochondria and chloroplasts. Despite their recognized importance, the specific roles of mTERF proteins in maize remain largely unexplored. Here, we clone and functionally characterize the maize mTERF18 gene. Our findings reveal that mTERF18 mutations lead to severely undifferentiated embryos, resulting in abortive phenotypes. Early kernel exhibits abnormal basal endosperm transfer layer and a significant reduction in both starch and protein accumulation in mterf18. We identify the mTERF18 gene through mapping-based cloning and validate this gene through allelic tests. mTERF18 is widely expressed across various maize tissues and encodes a highly conserved mitochondrial protein. Transcriptome data reveal that mTERF18 mutations disrupt transcriptional termination of the nad6 gene, leading to undetectable levels of Nad6 protein and reduced complex I assembly and activity. Furthermore, transmission electron microscopy observation of mterf18 endosperm uncover severe mitochondrial defects. Collectively, these findings highlight the critical role of mTERF18 in mitochondrial gene transcription termination and its pivotal impact on maize kernel development.

Natural variation of CT2 affects the embryo/kernel weight ratio in maize

Yumin Zhang, Sihan Zhen, Chunxia Zhang, Jie Zhang, Xiaoqing Shangguan, Jiawen Lu, Qingyu Wu, Lynnette M. A. Dirk, A. Bruce Downie, Guoying Wang, Tianyong Zhao, Junjie Fu

2025, 52(3): 432-440. doi: 10.1016/j.jgg.2024.09.012

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Embryo size is a critical trait determining not only grain yield but also the nutrition of the maize kernel. Up to the present, only a few genes have been characterized affecting the maize embryo/kernel ratio. Here, we identify 63 genes significantly associated with maize embryo/kernel weight ratio using a genome-wide association study (GWAS). The peak GWAS signal shows that the natural variation in Zea mays COMPACT PLANT2 (CT2), encoding the heterotrimeric G protein α subunit, is significantly associated with the Embryo/Kernel Weight Ratio (EKWR). Further analyses show that a missense mutation of CT2 increases its enzyme activity and associates with EKWR. The function of CT2 on affecting embryo/kernel weight ratio is further validated by the characterization of two ct2 mutants, for which EKWR is significantly decreased. Subsequently, the key downstream genes of CT2 are identified by combining the differential expression analysis of the ct2 mutant and quantitative trait transcript analysis in the GWAS population. In addition, the allele frequency spectrum shows that CT2 was under selective pressure during maize domestication. This study provides important genetic insights into the natural variation of maize embryo/kernel weight ratio, which could be applied in future maize breeding programs to improve grain yield and nutritional content.

Maize plastid terminal oxidase (ZmPTOX) regulates the color formation of leaf and kernel by modulating plastid development

Qiang Huang, Zhuofan Zhao, Xiaowei Liu, Xin Yuan, Ruiqing Zhao, Qunkai Niu, Chuan Li, Yusheng Liu, Danfeng Wang, Tao Yu, Hongyang Yi, Chengming Yang, Tingzhao Rong, Moju Cao

2025, 52(3): 441-445. doi: 10.1016/j.jgg.2024.05.008

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PURINE PERMEASE 4 regulates plant height in maize

Yuchen Huang, Yuehui Zhang, Xiaofeng Cai, Shui Wang

2025, 52(3): 446-448. doi: 10.1016/j.jgg.2024.04.012

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2025 Vol. 52, No. 3