Yuxin Xie

Chinese Academy of Agricultural Sciences

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Junjie Fu

Chinese Academy of Agricultural Sciences

Hongwei Zhang

Institute of Crop Sciences

Riliang Gu

China Agricultural University

Jiawen Lu

Institute of Crop Sciences

Jie Zhang

Southwest Hospital

Yu Cui

Xi'an Jiaotong University

Sihan Zhen

Institute of Crop Sciences

Xuemei Du

China Agricultural University

Huiqin Guo

Chinese Academy of Medical Sciences & Peking Union Medical College

Yunjun Liu

Institute of Crop Sciences

Cooperative Institutions

Chinese Academy of Agricultural Sciences

Institute of Crop Sciences

Chinese Academy of Sciences

China Agricultural University

Ministry of Agriculture and Rural Affairs

University of Chinese Academy of Sciences

Shanghai Jiao Tong University

Sichuan Agricultural University

Sun Yat-sen University

Huazhong Agricultural University

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Acute heat stress alters the expression of genes and proteins associated with the unfolded protein response pathway in the liver of broilers

British Poultry Science (2021)

Qixiang Miao X Y Yuxin Xie L. Chen Xiangfang Tang

1. The aim of this study was to explore the effects of acute heat stress on serum hormone levels and the expression of genes and proteins related to the unfolded protein response (UPR) pathway and apoptotic process in the liver of broilers.2. A total of 144 Arbor Acres broilers (35-d-old) were randomly allocated to 4 different environmental-controlled chambers for acute heat exposure. The temperature of the 4 environmental chambers was adjusted to 26°C (control), 29°C, 32°C, and 35°C within 1 h, respectively. The blood and liver samples were collected after 6 h of constant heat exposure at set temperatures.3. The results showed that 6 h of acute heat stress increased serum hormone levels and up-regulated the expression of heat shock protein. The endoplasmic reticulum (ER) stress markers, GRP78 and GRP94, in the liver of broilers were significantly upregulated at the mRNA and protein levels. The PERK, IRE1, and XBP1 genes, which are involved in the unfolded protein response signalling, were significantly up-regulated at the mRNA levels. However, other pro-apoptotic genes showed no significant changes in the liver of broiler chickens in all groups except for upregulation of the anti-apoptotic gene BCL-xl.4. The results suggested that broilers have tolerance to acute heat stress to a certain extent. The UPR activation can alleviate ER stress and further prevent apoptosis in the liver of broilers under short-term exposure to high ambient temperatures.

XBP1

10.1080/00071668.2021.1969644

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Exploration of Response Mechanisms in the Gills of Pacific Oyster (Crassostrea gigas) to Cadmium Exposure through Integrative Metabolomic and Transcriptomic Analyses

Animals (2024)

Luyao Dong Yanan Sun Muyang Chu Yuxin Xie Pinyi Wang

Marine mollusks, including oysters, are highly tolerant to high levels of cadmium (Cd), but the molecular mechanisms underlying their molecular response to acute Cd exposure remain unclear. In this study, the Pacific oyster Crassostrea gigas was used as a biological model, exposed to acute Cd stress for 96 h. Transcriptomic analyses of their gills were performed, and metabolomic analyses further validated these results. In our study, a total of 111 differentially expressed metabolites (DEMs) and 2108 differentially expressed genes (DEGs) were identified under acute Cd exposure. Further analyses revealed alterations in key genes and metabolic pathways associated with heavy metal stress response. Cd exposure triggered physiological and metabolic responses in oysters, including enhanced oxidative stress and disturbances in energy metabolism, and these changes revealed the biological response of oysters to acute Cd stress. Moreover, oysters could effectively enhance the tolerance and detoxification ability to acute Cd exposure through activating ABC transporters, enhancing glutathione metabolism and sulfur relay system in gill cells, and regulating energy metabolism. This study reveals the molecular mechanism of acute Cd stress in oysters and explores the molecular mechanism of high tolerance to Cd in oysters by using combined metabolomics and transcriptome analysis.

Pacific oyster

CADMIUM EXPOSURE

10.3390/ani14162318

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GWAS-based population genetic analysis identifies bZIP29 as a heterotic gene in maize

Plant Communications (2025)

Yuehua Zhang Riliang Gu Xinxin Miao Renate Schmidt Zhenxiang Xu

Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding. We analyzed plant height (PH), ear height (EH), and transcriptomic data from a maize hybrid population. GWAS identified that dominance effects of QTL play a significant role in hybrid traits and mid-parent heterosis. By integrating GWAS, expression GWAS (eGWAS) analysis, and module eGWAS, six candidate heterotic genes underlying six QTL were prioritized, including one QTL spanned the bZIP29 gene. In the hybrid population, bZIP29 exhibited additive expression and dominance effects for both traits and mid-parent heterosis, with its favorable allele correlating positively with PH and EH. bZIP29 demonstrated dominance or over-dominance patterns in the hybrids derived from crosses between transgenic and wildtype lines, contingent upon its expression. tsCUT&Tag assay revealed that bZIP29 protein bound directly to a gene regulated by its associated eQTL and six genes within expression modules governed by their meQTL. Regulatory networks involving bZIP29 were more extensive in hybrid sub-populations compared to the parental population. This study offers insights into key heterotic genes and networks underpinning the robust growth of hybrid maize.

Genome-wide Association Study

10.1016/j.xplc.2025.101289

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Tensor decomposition reveals trans-regulated gene modules in maize drought response

Journal of genetics and genomics/Journal of Genetics and Genomics (2024)

Jiawen Lu Yuxin Xie Chunhui Li Jinliang Yang Junjie Fu

10.1016/j.jgg.2024.10.011

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Genome‐wide expression quantitative trait locus analysis reveals silk‐preferential gene regulatory network in maize

Physiologia Plantarum (2024)

Xiaoli Wang Jiawen Lu Mingfang Han Zheyuan Wang Hongwei Zhang

Abstract Silk of maize ( Zea mays L. ) contains diverse metabolites with complicated structures and functions, making it a great challenge to explore the mechanisms of metabolic regulation. Genome‐wide identification of silk‐preferential genes and investigation of their expression regulation provide an opportunity to reveal the regulatory networks of metabolism. Here, we applied the expression quantitative trait locus (eQTL) mapping on a maize natural population to explore the regulation of gene expression in unpollinated silk of maize. We obtained 3,985 silk‐preferential genes that were specifically or preferentially expressed in silk using our population. Silk‐preferential genes showed more obvious expression variations compared with broadly expressed genes that were ubiquitously expressed in most tissues. We found that trans ‐eQTL regulation played a more important role for silk‐preferential genes compared to the broadly expressed genes. The relationship between 38 transcription factors and 85 target genes, including silk‐preferential genes, were detected. Finally, we constructed a transcriptional regulatory network around the silk‐preferential gene Bx10 , which was proposed to be associated with response to abiotic stress and biotic stress. Taken together, this study deepened our understanding of transcriptome variation in maize silk and the expression regulation of silk‐preferential genes, enhancing the investigation of regulatory networks on metabolic pathways.

Gene regulatory network

10.1111/ppl.14386

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Fine-Tuning Quantitative Trait Loci Identified in Immortalized F2 Population Are Essential for Genomic Prediction of Hybrid Performance in Maize

Agriculture (2024)

Pingxi Wang Xingye Ma Xining Jin Xiang‐Yuan Wu Xiaoxiang Zhang

Maize breeding is greatly affected by hybrid vigor, a phenomenon that hybrids exhibit superior performance than parental lines. The immortalized F2 population (IMF2) is ideal for the genetic dissection and prediction of hybrid performance. Here, in this study, we conducted the QTL mapping and genomic prediction of six traits related to plant architecture using an IMF2 population. Broad-sense heritability of these traits ranged from 0.85 to 0.94. Analysis of genetic effects showed that additive variance was the main contributor to phenotypic variations. The mapping of quantitative trait loci (QTLs) revealed 10 to 16 QTLs (including pleiotropic loci and epistatic QTLs) for the six traits. Additionally, we identified 15 fine-tuning QTLs for plant height (PH). For genomic prediction (GP), the model of additive and dominance (AD) exhibited higher prediction accuracy than those fitting general combining ability (GCA) and its combination with special combining ability (SCA) effects for all tested traits. And adding the epistasis (E) effect into the AD model did not significantly increase its prediction accuracy. Moreover, the identified 15 fine-tuning QTLs of PH, which exerted large genomic prediction effects, were verified by the marker effect of GP. Our results not only provide an approach for the fine-mapping of fine-tuning QTLs but also serve as references for GP breeding in crops.

Trait

Genomic Selection

10.3390/agriculture14030340

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Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize

Theoretical and Applied Genetics (2023)

Jiawen Lu Sihan Zhen Jie Zhang Yuxin Xie Cheng He

Intergenic region

10.1007/s00122-023-04293-2

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cis‐Regulatory variation affecting gene expression contributes to the improvement of maize kernel size

The Plant Journal (2022)

Yongxiang Li Jiawen Lu Cheng He Xun Wu Yu Cui

SUMMARY cis ‐Regulatory variations contribute to trait evolution and adaptation during crop domestication and improvement. As the most important harvested organ in maize ( Zea mays L.), kernel size has undergone intensive selection for size. However, the associations between maize kernel size and cis ‐regulatory variations remain unclear. We chose two independent association populations to dissect the genetic architecture of maize kernel size together with transcriptomic and genotypic data. The resulting phenotypes reflected a strong influence of population structure on kernel size. Compared with genome‐wide association studies (GWASs), which accounted for population structure and relatedness, GWAS based on a naïve or simple linear model revealed additional associated single‐nucleotide polymorphisms significantly involved in the conserved pathways controlling seed size in plants. Regulation analyses through expression quantitative trait locus mapping revealed that cis ‐regulatory variations likely control kernel size by fine‐tuning the expression of proximal genes, among which ZmKL1 (GRMZM2G098305) was transgenically validated. We also proved that the pyramiding of the favorable cis‐ regulatory variations has contributed to the improvement of maize kernel size. Collectively, our results demonstrate that cis ‐regulatory variations, together with their regulatory genes, provide excellent targets for future maize improvement.

Genetic architecture

Association mapping

Trait

Kernel (algebra)

Genetic Association

10.1111/tpj.15910

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Performance evaluation and feasibility study on reuse of reclaimed epoxy asphalt pavement (REAP)

Construction and Building Materials (2024)

Yitong Min Yuheng Zhang Zhendong Qian Hancheng Zhang Bangyan Hu

Asphalt pavement

10.1016/j.conbuildmat.2024.138653

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Small kernel 501 (smk501) encodes the RUBylation activating enzyme E1 subunit ECR1 (E1 C‐TERMINAL RELATED 1) and is essential for multiple aspects of cellular events during kernel development in maize

New Phytologist (2021)

Quanquan Chen Jie Zhang Jie Wang Yuxin Xie Yu Cui

Summary RUBylation plays essential roles in plant growth and development through regulating Cullin‐RING ubiquitin E3 ligase (CRL) activities and the CRL‐mediated protein degradations. However, the function of RUBylation in regulating kernel development remains unclear. Through genetic and molecular analyses of a small kernel 501 ( smk501 ) mutant in maize ( Zea mays ), we cloned the smk501 gene, revealed its molecular function, and defined its roles in RUBylation pathway and seed development. Smk501 encodes a RUBylation activating enzyme E1 subunit ZmECR1 (E1 C‐TERMINAL RELATED 1) protein. Destruction in RUBylation by smk501 mutation resulted in less embryo and endosperm cell number and smaller kernel size. The transcriptome and proteome profiling, hormone evaluation and cell proliferation observation revealed that disturbing ZmECR1 expression mainly affects pathways on hormone signal transduction, cell cycle progression and starch accumulation during kernel development. In addition, mutant in zmaxr1 (Auxin resistant 1), another RUB E1 subunit, also showed similar defects in kernel development. Double mutation of zmecr1 and zmaxr1 lead to empty pericarp kernel phenotype. RUBylation is a novel regulatory pathway affecting maize kernel development, majorly through its functions in modifying multiple cellular progresses.

Cullin

10.1111/nph.17354

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Citations (9)