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Epigenetics in the modern era of crop improvements

Science China Life Sciences 2025年

作者： Yan Xue Xiaofeng Cao Xiangsong Chen Xian Deng Xingwang Deng Yong Ding Aiwu Dong Chengguo Duan Xiaofeng Fang Lei Gong Zhizhong Gong Xiaofeng Gu Chongsheng He Hang He Shengbo He Xinjian He Yan He Yuehui He Guifang Jia Danhua Jiang Jianjun Jiang Jinsheng Lai Zhaobo Lang Chenlong Li Qing Li Xingwang Li Bao Liu Bing Liu Xiao Luo Yijun Qi Weiqiang Qian Guodong Ren Qingxin Song Xianwei Song Zhixi Tian Jiawei Wang Yuan Wang Liang Wu Zhe Wu Rui Xia Jun Xiao Lin Xu Zhengyi Xu Wenhao Yan Hongchun Yang Jixian Zhai Yijing Zhang Yusheng Zhao Xuehua Zhong Daoxiu Zhou Ming Zhou Yue Zhou Bo Zhu Jiankang Zhu Qikun Liu College of Life Sciences Institute of Life Science and Green Development Hebei University Biotechnology Research Institute Chinese Academy of Agricultural Sciences College of Biology Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan Engineering and Technology Research Center of Hybrid Rapeseed Hunan University Institute of Advanced Agricultural Sciences School of Advanced Agricultural Sciences Peking University State Key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural University National Institute of Biological Sciences Key laboratory of Seed Innovation Institute of Genetics and Developmental Biology Chinese Academy of Sciences School of Advanced Agricultural Sciences Peking-Tsinghua Center for Life Sciences Peking University Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University Key laboratory of Seed Innovation State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences State Key laboratory of Wheat Improvement Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in Weifang State Key laboratory of Crop Stress Adaptation and Improvement School of Life Sciences Henan University State Key laboratory of Maize Bio-breeding National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University Frontiers Science Center for Molecular Design breeding China Agricultural University Center for Crop Functional Genomics and Molecular breeding China Agricultural University Sanya Institute of China Agricultural University Hainan Yazhou Bay Seed laboratory Institute of Advan

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades,our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

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Reversing anther thermotolerance by manipulating the cis-elements in the promoter of a high-temperature upregulated gene Casein Kinase I in upland cotton

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Science China Life Sciences 2025年

作者： Yanlong Li Yinuo Fu Yaoyao Li Rui Zhang Jing Yang Huanhuan Ma Ling Min Xianlong Zhang National Key laboratory of Crop genetic Improvement Huazhong Agricultural University

High temperature (HT) stress causes male sterility,leading to reduced upland cotton ***,we identified a key gene,Casein Kinase I (GhCKI),that negatively regulates male fertility in upland cotton under ***,conventional genetic manipulations of GhCKI would result in male sterility,hindering its utilization in breeding ***,we engineered quantitative variation for anther thermotolerance-related traits in upland cotton by creating weak promoter alleles of GhCKI genes,using CRISPR/Cas9 and CRISPR/Cpf1genome ***,we screened and identified two new upland cotton plant lines exhibiting a HT-tolerant phenotype with edited GhCKI promoters,and characterized their corresponding heat-tolerant allelic *** research revealed that the primary reason for the HT tolerance of the GhCKI promoter editing mutants is that the trans-acting factors GhMYB73 and GhMYB4,which positively regulate GhCKI expression under HT,failed to bind and activate the expression of ***,our study not only provides a rapid strategy to generate new beneficial alleles but also offers novel germplasm resources and molecular insights for crop HT tolerance breeding.

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Discovery of microchromosomes in wheat and their special behavior in meiosis

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Chinese Science Bulletin 1997年第24期42卷 2084-2087页

作者： XU Qi, YU Ling, TIAN Zengrong, ZHU Jianfeng, LI Bin and LI Zhensheng laboratory of plant genetic engineering and breeding of shaanxi province, Northwestern Institute of Botany, Chinese Academy of Sciences, Yangling, shaanxi 712100, China 2. State Key laboratory of plant Cell and Chromosome engineering, Institute of genetics, Chinese Academy of Sciences, Beijing 100101, China laboratory of plant genetic engineering and breeding of shaanxi province Northwestern Institute of Botany Chinese Academy of Sciences Yangling Shaanxi China State Key laboratory of plant Cell and Chromosome engineering Institute of Genetics Chinese Academy of Sciences Beijing China

THERE are 42 chromosomes in common wheat (Triticum aestivum L). The extra microchro-mosomes were discovered in alloplasmic lines of common wheat with cytoplasms of Ae. muti-ca, Secale cereale, Elytrigia elongatum and Agropyron glaucum. The microchromo-somes were discovered in amphiploid of Triticum aestivum-Secale cereale (DDRR) too.

关键词： wheat microchromosomes behavior in meiosis.

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Development and characterization of a novel common wheat–Mexico Rye T1DL·1RS translocation line with stripe rust and powdery mildew resistance

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Journal of Integrative Agriculture 2023年第5期22卷 1291-1307页

作者： LI Jiao-jiao ZHAO Li Lü Bo-ya FU Yu ZHANG Shu-fa LIU Shu-hui YANG Qun-hui WU Jun LI Jia-chuang CHEN Xin-hong shaanxi Key laboratory of plant genetic engineering breeding College of AgronomyNorthwest A&F UniversityYangling 712100P.R.China

Rye(Secale cereale L., 2n=2x=14, RR) is a significant genetic resource for improving common wheat because of its resistance to multiple diseases and abiotic-stress tolerant traits. The 1RS chromosome from the German cultivated rye variety Petkus is critical in wheat breeding. However, its weakened disease resistance highlights the need to identify new resources. In the present study, a novel derived line called D27 was developed from common wheat and Mexico *** observations characterized the karyotype of D27 as 2n=42=21 Ⅱ. Genomic in situ hybridization indicated that a pair of whole-arm translocated Mexico Rye chromosomes were inherited typically in the mitotic and meiosis stages of D27. Experiments using fluorescence in situ hybridization(FISH) and gliadin electrophoresis showed that D27 lacked wheat 1DS chromosomes. They were replaced by 1RS chromosomes of Mexico Rye, supported by wheat simple-sequence repeat markers, rye sequence characterized amplified region markers, and wheat 40K SNP array *** wheat 1DS chromosomes could not be detected by molecular markers and wheat SNP array, but the presence of rye 1RS chromosomes was confirmed. Agronomic trait assessments indicated that D27 had a higher tiller number and enhanced stripe rust and powdery mildew resistance. In addition, dough properties analysis showed that replacing 1DS led to higher viscosity and lower dough elasticity in D27, which was beneficial for cake making. In conclusion, the novel cytogenetically stable common wheat–Mexico Rye T1DL·1RS translocation line D27 offers excellent potential as outstanding germplasm in wheat breeding programs focusing on disease resistance and yield improvement. Additionally,it can be valuable for researching the rye 1RS chromosome’s genetic diversity.

关键词： common wheat disease resistance dough properties rye translocation line

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Effect of cDNA fragments in different length derived from Potato Virus Y coat protein gene on the induction of RNA-mediated virus resistance

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Science China(Life Sciences) 2004年第4期47卷 382-388页

作者： ZHU Junhua ZHU Xiaoping WEN Fujiang BAI Qingrong ZHU Changxiang SONG Yunzhi laboratory of plant genetic engineering College of Plant ProtectionShandong Agricultural UniversityTaian 271018China

We have reported that cDNA derived from entire coat protein (CP) gene of potato virus Y (PVY) could induce resistance to PVY infection in transgenic tobacco plants, and the resistance was further demonstrated to be RNA-mediated rather than coat protein-mediated. In this study, we cloned cDNA fragments of 202 bp, 417 bp, and 603 bp in length derived from the 3′ end of the PVY CP gene, and the cDNA fragments were introduced into tobacco (var. NC89) plants via Agrobacterium-mediated transformation system. The results of resistance assay showed that the CP cDNA fragments of 417 bp and 603 bp could confer resistance of the trans-genic plants to PVY infection, but the fragment of 202 bp in length could not. Molecular analysis revealed that the resistance was RNA-mediated, which is believed to be a result of post-transcriptional gene silencing. The results indicate that the length of cDNA fragments needed for resistance induction was located somewhere between 202 bp and 417 bp from the 3′ end of PVY CP gene.

关键词： PVY partial length of CP gene fragments transgenic tobacco plants RNA-mediated resistance post-transcrip-tional gene silencing.

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Cloning,Localization and Expression Analysis of ZmHsf-like Gene in Zea mays

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Journal of Integrative Agriculture 2014年第6期13卷 1230-1238页

作者： LI Hui-cong LI Guo-liang LIU Zi-hui ZHANG Hong-mei ZHANG Yan-min GUO Xiu-lin Institute of genetics and Physiology Hebei Academy of Agriculture and Forestry Sciences/plant genetic engineering Center of Hebei province

Using homology cloning method, a heat shock transcription factor （Hsf） like gene, ZmHsf-like, was cloned from maize （Zea mays） leaves. Sequence analyses showed that the open reading frame （ORF） of the gene ZmHsf-like is 1 404 bp long, encoding 467 amino acids. The sequence of amino acids encoded by ZmHsf-like contains the most conserved and typical DNA-binding domain of Hsf family. By bombardment into onion epidermis, we ifrstly found that the ZmHsf-like was subcellular-located in nucleus. NucPred analysis revealed there is a classic NLS of KKRR peptide in protein. Real-time PCR showed that ZmHsf-like gene expressed in leaves, stems and roots of maize seedlings under normal growth conditions, and the highest expression level was in roots, lower in leaves and the lowest in stems. The ZmHsf-like gene expression could be up-regulated by heat shock, PEG, ABA, and H2O2 in different degrees, among which the heat shock and ABA worked more efifciently. Obvious differences of the peak value and its corresponding time point of ZmHsf-like gene expression were observed among treatments. Experiments with inhibitor further suggested that the up-regulation ZmHsf-like gene expression of heat shock was H2O2-dependent while the induction of ZmHsf-like with PEG did not depend on the existence of H2O2. These results pointed out that ZmHsf-like gene probably regulates responsive reactions to abiotic stresses especially heat shock and drought through different signal transduction pathways.

关键词： maize Hsf ZmHsf-like stress nuclear-localization

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Molecular identification of ω-secalin gene expression activity in a wheat 1B/1R translocation cultivar

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Journal of Integrative Agriculture 2016年第12期15卷 2712-2718页

作者： CHAI Jian-fang ZHANG Cui-mian MA Xiu-ying WANG Hai-bo Institute of genetics and Physiology Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province

ω-Secalin was an important factor influencing processing quality of wheat 1BL/1RS translocations. On the basis of four ω-secalin gene sequences cloned from Lankao 906 （a wheat cultivar with 1BL/1RS translocation） with putative transcription activity, a pair of primers with suitable restriction endonucleases added at their 5＂ ends were designed to amplify the mature protein-coding regions of the four genes. After digestion with restriction endonucleases, the amplified products were ligated into the prokaryotic expression vector pET30a（＋）. The prokaryotically expressed recombinant proteins and gliadin isolated from the Lankao 906 seed were analyzed on the same acid polyacrylamide gel electrophoresis. All four prokaryotically expressed secalin bands had corresponding seed-expressed gliadin bands. The four corresponding gliadin bands were confirmed to be the expression products of the four ω-secalin genes by liquid chromatography tandem mass spectrometry （LC-MS/MS）. This conclusion was further confirmed because the four ω-secalin bands could be detected in all 14 wheat 1BL/1 RS translocation cultivars used in the study, although there was some interference for the detection of one ω-secalin band from nearby wheat gliadin bands. The sequence information of ω-secalin genes with expression activity will be helpful for improving the processing quality of wheat with 1BL/1RS translocations by using RNA interference method to silence the expression of the ω-secalin genes.

关键词： Triticum aestivum processing quality storage proteins prokaryotic expression LC-MS/MS

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Effects of tourmaline on nitrogen removal performance and biofilm structures in the sequencing batch biofilm reactor

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Journal of Environmental Sciences 2018年第5期30卷 127-135页

作者： Chong Tan Haoran Xu Di Cui Jinlong Zuo Junsheng Li Yubin Ji Shan Qiu Lin Yao Ying Chen Yingjie Liu Research Center on Life Sciences and Environmental Sciences Harbin University of Commerce School of Municipal and Environmental engineering Harbin Institute of Technology Key laboratory of Molecular and Cytogenetics and genetic breeding of Heilongjiang province Harbin Normal University

The effects of tourmaline on nitrogen removal performance and biofilm structures were comparatively investigated in two identical laboratory-scale sequencing batch biofilm reactors（SBBRs）（denoted SBBR1 and SBBR2） at different nitrogen loading rates（NLRs） varying from（0.24 ± 0.01） to（1.26 ± 0.02） g N/（L·day）. SBBR1 was operated in parallel with SBBR2, but SBBR1 was filled with polyurethane foam loaded tourmaline（TPU） carriers and another（SBBR2） filled with polyurethane foam（PU） carriers. Results obtained from this study showed that the excellent and stable performance of SBBR1 was obtained. Ammonia nitrogen removal and total nitrogen removal were higher in SBBR1 than that in SBBR2 with increase of NLR. At an NLR of（0.24 ± 0.01） g N/（L·day）, the majority of the spherical and elliptical bacteria were surrounded by the extracellular polymeric substance（EPS） and bacillus or filamentous bacteria in two SBBRs biofilms. When NLR increased to（1.26 ± 0.02） g N/（L·day）, the clusters were more obvious in the SBBR1 biofilm than that in the SBBR2 biofilm. Bacteria in SBBR1 were inclined to synthesis more EPS, and the formed EPS could protect the bacteria from free ammonia（FA） under extreme condition NLR（1.26 ± 0.02） g N/（L·day）. The results of polymerase chain reaction-denaturing gradient gel electrophoresis analysis showed that the microbial community similarity in SBBR2 decreased more obviously than that in SBBR1 with the increase of NLR, which the microbial community in SBBR1 was relatively stable.

关键词： tourmaline Nitrogen removal performance Biofilm structures Population dynamics Sequencing batch biofilmreactor (SBBR)

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GGVD:A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions

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Journal of genetics and Genomics 2021年第3期48卷 248-256页

作者： Weiwei Fu Rui Wang Jiantao Yu Dexiang Hu Yudong Cai Junjie Shao Yu Jiang Key laboratory of Animal genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi 712100China College of Information engineering Northwest A&F UniversityYanglingShaanxi 712100China

Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic *** the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples,a user-friendly database making efficient reuse of these important resources is ***,we use the genomes of 208 modern domestic goats,24 bezoars,46 wild ibexes,and 82 ancient goats to present a comprehensive goat genome variation database(GGVD).GGVD hosts a total of~41.44 million SNPs,~5.14 million indels,6,193 selected loci,and 112 introgression *** can freely visualize the frequency of genomic variations in geographical maps,selective sweeps in interactive tables,Manhattan plots,or line charts,as well as the heatmap patterns of the SNP *** data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early,middle,and late *** facilitating access to sequence features,the UCSC Genome Browser,BLAT,BLAST,Lift Over,and pcadapt are also integrated into *** will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs,and it is publicly available at http://***/Goat Var.

关键词： Goat genetic structure Variation Selective signature Introgression Database

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A transient expression system in soybean mesophyll protoplasts reveals the formation of cytoplasmic GmCRY1 photobody-like structures

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Science China(Life Sciences) 2019年第8期62卷 1070-1077页

作者： Lu Xiong Cong Li Hongyu Li Xiangguang Lyu Tao Zhao Jun Liu Zecheng Zuo Bin Liu Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing100081China Jilin province engineering laboratory of plant genetic Improvement College of Plant ScienceJilin UniversityChangchun130062China

Soybean(Glycine max(L.) Merr.), grown for its plant oils and proteins, is one of the most important crops throughout the *** stable and heritable transgenic soybeans is relatively inefficient;therefore, there is an urgent need for a simple and high-efficient transient transformation method by which to enable the investigation of gene functions in soybeans, which will facilitate the elucidation and improvement of the molecular mechanisms regulating the associated agronomic traits. We established a system of transient expression in soybean mesophyll protoplasts and obtained a high level of protoplast transfection efficiency(up to 83.5%). The subcellular activity of the protoplasts was well preserved, as demonstrated by the dynamic formation of GmCRY nucleus photobodies(NPs) and/or cytoplasmic photobody-like structures(CPs) in response to blue *** addition, we showed that GmCRY1b CPs colocalized with GmCOP1b, a co-ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1(COP1), which provided new insight into the potential roles of GmCRY1s in the cytoplasm.

关键词： soybean protoplast transfection subcellular localization cryptochrome photobodies

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