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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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Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)

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Progress in Natural Science:Materials International 2007年第10期17卷 1177-1184页

作者： Li Zhenxing, Ni Zhongfu, Peng Huiru, Liu Zhiyong, Nie Xiuling, Xu Shengbao, Liu Gang and Sun Qixin(key laboratory of Crop Heterosis and Utilization and State key laboratory for Agrobiotechnology, key laboratory of Crop Genomics and Genetic Improvement, Beijing key laboratory of Crop Genetic Improvement, Department of plant genetics & breeding, china agricultural University, Beijing 100094, china) key laboratory of Crop Heterosis and Utilization Department of Plant Genetics and Breeding China Agricultural University Beijing 100094 China key laboratory of Crop Genomics and Genetic Improvement Department of Plant Genetics and Breeding China Agricultural University Beijing 100094 China Beijing key laboratory of Crop Genetic Improvement Department of Plant Genetics and Breeding China Agricultural University Beijing 100094 China

Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together.

关键词： QTLs roots wheat seedling RIL P-deficiency.

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Identification of an S5^n allele in Oryza rufipogon Griff. and its effect on embryo sac fertility

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Chinese Science Bulletin 2010年第13期55卷 1255-1262页

作者： SHAHID Muhammad Qasim Provincial key laboratory of plant Molecular breeding South China Agricultural University

Oryza rufipogon exhibits abundant genetic diversity and contains many elite genes. In this work, a total of 441 accessions of O. rufipogon were genetically examined using the functional marker S5n, revealing that 18 accessions carried the S5n allele with a heterozygous genotype (S5nS5i/j). Of these accessions, 14 were from Guangdong Province, 2 from Guangxi Zhuang Autonomous Region, 1 from Hainan Province and 1 from Jiangxi Province. Further sequence analysis spanning both sides of the deletion in S5n allele of O. rufipogon confirmed that this allele is identical with that of 02428, a wide-compatibility variety of domesticated rice. The segregation ratio of the 3 genotypes (S5iS5i/S5jS5j:S5nS5i/j:S5nS5n) among 15 self-bred progenies of O. rufipogon significantly deviated from the Mendelian expectation (1:2:1) in that the proportion of plants exhibiting S5n heterozygous and homozygous genotypes was much lower in the progeny. Sequence analysis of full-length S5n alleles indicated that a few base pairs were different between O. rufipogon and O. sativa, and it was presumed that S5n may be an ancient allele. The fertility of the embryo sac in plants with an S5n heterozygous genotype was low, suggesting the existence of other genes controlling embryo sac fertility in the wild rice.

关键词：普通野生稻等位基因胚囊广西壮族自治区鉴定序列分析遗传多样性广亲和品种

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Abnormalities Occurring during Female Gametophyte Development Result in the Diversity of Abnormal Embryo Sacs and Leads to Abnormal Fertilization in indica/japonica Hybrids in Rice

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Journal of Integrative plant Biology 2009年第1期51卷 3-12页

作者： Yu-Xiang Zeng Chao-Yue Hu Yong-Gen Lu Jin-Quan Li Xiang-Dong Liu ( Guangdong Provincial key laboratory of plant Molecular breeding South China Agricultural University Guangzhou 510642 China)

Embryo sac abortion is one of the major reasons for sterility in indicaljaponica hybrids in rice. To clarify the causal mechanism of embryo sac abortion, we studied the female gametophyte development in two indicaljaponica hybrids via an eosin B staining procedure for embryo sac scanning using confocal laser scanning microscope. Different types of abnormalities occurred during megasporogenesis and megagametogenesis were demonstrated. The earliest abnormality was observed in the megasporocyte. A lot of the chalazal-most megaspores were degenerated before the mono-nucleate embryo sac stage. Disordered positioning of nucleus and abnormal nucellus tissue were characteristics of the abnormal female gametes from the mono-nucleate to four-nucleate embryo sac stages. The abnormalities that occurred from the early stage of the eight-nucleate embryo sac development to the mature embryo sac stage were characterized by smaller sizes and wrinkled antipodals. Asynchronous nuclear migration, abnormal positioning of nucleus, and degeneration of egg apparatus were also found at the eight-nucleate embryo sac stage. The abnormalities that occurred during female gametophyte development resulted in five major types of abnormal embryo sacs. These abnormal embryo sacs led to abnormal fertilization. Hand pollination using normal pollens on the spikelets during anthesis showed that normal pollens could not exclude the effect of abnormal embryo sac on seed setting.

关键词： indicaljaponica hybrid megagametogenesis megasporogenesis Oryza sativa whole-mount eosin B-staining confocal laser scanning microscopy.

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Crossability Barriers in the Interspecific Hybridization between Oryza sativa and ***

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Journal of Integrative plant Biology 2009年第1期51卷 21-28页

作者： Xue-Lin Fu Yong-Gen Lu Xiang-Dong Liu Jin-Quan Li Guangdong Provincial key laboratory of plant Molecular breeding South China Agricultural University Guangzhou 510642 China

Oryza meyeriana Baill （GG genome） is a precious germplasm in the tertiary gene pool of cultivated rice （AA genome）, and possesses important traits such as resistance and tolerance to biotic and abiotic stress. However, interspeciflc crossability barrier, a critical bottleneck restricting genes transfer from O. meyeriana to cultivars has led to no hybrids through conventional reproduction. Therefore, the reasons underlying incrossability were investigated in the present report. The results showed that：（i） at 3-7 d after pollination （DAP）, many hybrid embryos degenerated at the earlier globular-shaped stage, and could not develop into the later pear-shaped stage. Meanwhile, free endosperm nuclei started to degenerate at 1 DAP, and cellular endosperm could not form at 3 DAP, leading to nutrition starvation for young embryo development; （ii） at 11-13 DAP, almost all hybrid ovaries aborted. Even though 72.22% of hybrid young embryos were produced in the interspecific hybridization between O. sativa and O. meyeriana, young embryos were not able to further develop into hybrid plantlets via culturing in vitro. The main reason for the incrossability was hybrid embryo inviability, presenting as embryo development stagnation and degeneration since 3 DAP. Some possible approaches to overcome the crossability barriers in the interspecific hybridization between O. sativa and O. meyeriana are discussed.

关键词： crossability embryo development interspecific hybridization Oryza sativa O. meyeriana.

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Genetic dissection of maize seedling root system architecture traits using an ultra-high density bin-map and a recombinant inbred line population

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Journal of Integrative plant Biology 2016年第3期58卷 266-279页

作者： Weibin Song Baobao Wang Andrew L Hauck Xiaomei Dong Jieping Li Jinsheng Lai State key laboratory of Agrobiotechnology and National Maize Improvement Center of china Department of Plant Genetics and BreedingChina Agricultural University

Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the widely adapted Chinese hybrid ZD958（Zheng58 Chang7-2）,genotyped by sequencing（GBS） and evaluated as seedlings for 24 RSA related traits divided into primary,seminal and total root classes. Signi ficant differences between the means of the parental phenotypes were detected for 18 traits,and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci（QTL） were identi fied that individually explained from1.6% to 11.6%（total root dry weight/total seedling shoot dry weight） of the phenotypic variation. Eighteen,24 and 20 QTL were identi fied for primary,seminal and total root classes of traits,respectively. We found hotspots of 5,3,4 and 12 QTL in maize chromosome bins 2.06,3.02-03,9.02-04,and 9.05-06,respectively,implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.

关键词： Maize root system architecture QTL bin map genotyping by sequencing(GBS)

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Identification and Physical Mapping of New PCR-Based Markers Specific for the Long Arm of Rye(Secale cereale L.) Chromosome 6

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Journal of genetics and Genomics 2016年第4期43卷 199-206页

作者： Meng Li Zongxiang Tang Ling Qiu Yangyang Wang Shuyao Tang Shulan Fu Province key laboratory of plant breeding and genetics Sichuan Agricultural University Agronomy College Sichuan Agricultural University

To effectively use elite genes on the long arm of rye chromosome 6（the 6RL arm） in wheat breeding programs,precise and fast identification of 6RL chromatin in wheat backgrounds is ***-based 6RL-specific markers can facilitate the detection of elite genes on 6RL in wheat ***,only a limited number of 6RL-specific markers have been *** the present study.300 new PCR-based 6RL-specific markers were identified using specific length amplified fragment sequencing（SLAF-seq） technology,and were further physically mapped to four regions on the 6RL arm using 6R and 6RL deletion ***,127 of the 300 markers were physically localized to a region from the site between 2.3 and 2.5 to the telomere,the same region where the powdery mildew resistance gene was *** addition,95 of the 300 markers exhibit polymorphisms,which can be used to investigate the diversity of rye 6RL *** markers developed in this study can be used to identify given segments of 6RL in wheat backgrounds and accelerate the utilization of elite genes on 6RL in wheat breeding.

关键词： Wheat Rye 6RL-specific marker Physical mapping SLAF-seq Powdery mildew

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Efficiency and Inheritance of Targeted Mutagenesis in Maize Using CRISPR-Cas9

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Journal of genetics and Genomics 2016年第1期43卷 25-36页

作者： Jinjie Zhu Ning Song Silong Sun Weilong Yang Haiming Zhao Weibin Song Jinsheng Lai State key laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University

CRISPR/Cas （clustered regularly interspaced short palindromic repeats/CR1SPR-associated proteins） is an adaptive immune system in bacteria and archaea to defend against invasion from foreign DNA fragments. Recently, it has been developed as a powerful targeted genome editing tool for a wide variety of species. However, its application in maize has only been tested with transiently expressed somatic cells or with a limited number of stable transgenic To plants. The exact efficiency and specificity of the CRISPR/Cas system in the highly complex maize genome has not been documented yet. Here we report an extensive study of the well-studied type II CRISPR-Cas9 system for targeted genome editing in maize, with the codon-optimized Cas9 protein and the short non-coding guide RNA generated through a functional maize U6 snRNA promoter. Targeted gene mutagenesis was detected for 90 loci by maize protoplast assay, with an average cleavage efficiency of 10.67 %. Stable knockout transformants for maize phytoene synthase gene （PSYI） were obtained. Mutations occurred in germ ceils can be stably inherited to the next generation. Moreover, no off-target effect was detected at the computationally predicted putative off-target loci. No significant difference between the transcriptomes of the Cas9 expressed and non-expressed lines was detected. Our results confirmed that the CRISPR-Cas9 could be successfully applied as a robust targeted genome editing system in maize.

关键词： CRISPR-Cas9 Targeted mutagenesis Heritability Maize

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Defective Kernel 39 encodes a PPR protein required for seed development in maize

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Journal of Integrative plant Biology 2018年第1期60卷 45-64页

作者： Xiaojie Li Wei Gu Silong Sun Zongliang Chen Jing Chen Weibin Song Haiming Zhao Jinsheng Lai State key laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University

RNA editing is a posttranscriptional process that is important in mitochondria and plastids of higher plants. All RNA editing-specific trans-factors reported so far belong to PLS-class of pentatricopeptide repeat(PPR)proteins. Here, we report the map-based cloning and molecular characterization of a defective kernel mutant dek39 in maize. Loss of Dek39 function leads to delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality. Dek39 encodes an E subclass PPR protein that targets to both mitochondria and chloroplasts, and is involved in RNA editing in mitochondrial NADH dehydrogenase3(nad3) at nad3-247 and nad3-275. C-to-U editing of nad3-275 is not conserved and even lost in Arabidopsis, consistent with the idea that no close DEK39 homologs are present in Arabidopsis. However, the amino acids generated by editing nad3-247 and nad3-275 are highly conserved in many other plant species, and the reductions of editing at these two sites decrease the activity of mitochondria NADH dehydrogenase complex I,indicating that the alteration of amino acid sequence is necessary for Nad3 function. Our results indicate that Dek39 encodes an E sub-class PPR protein that is involved in RNA editing of multiple sites and is necessary for seed development of maize.

关键词： PPR Defective Kernel 39 encodes a PPR protein required for seed development in maize

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Effect of HSPB9 on Apoptosis of DF-1 Cells

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Biomedical and Environmental Sciences 2019年第2期32卷 107-120页

作者： XU Yong Jie HU Mei Ling ZHOU Liang Hui WANG Qi ZHANG Xi Quan LUO Qing Bin Department of Animal genetics Breeding and Reproduction College of Animal Science/Key Laboratory of Chicken Genetics Breeding and Reproduction Ministry of Agriculture South China Agricultural University

Objective Our aim was to explore whether heat stress protein(HSP) 9 preferentially expresses under heat stress and affects the expression of other heat stress proteins as well as to explore the effect of HSPB9 overexpression and knockdown on apoptosis in DF-1. Methods We used gene cloning to construct an overexpression vector of the target gene, and synthesized the target gene interference fragment to transfect the chicken fibroblast cell line. Gene and protein expression, as well as apoptosis, were detected by RT-qPCR, Western blot, and flow cytometry. Results Chicken DF-1 cells showed an early state of apoptosis in the early stages of HSPB9 overexpression. In the later stages, as HSPB9 expression increased, the cells showed inhibition of apoptosis. When the cells were under heat stress, HSPB9 expression was much higher and earlier than the expression of HSPB1 and HSPA2. In addition, high expression of HSPB9 had a negative effect on HSPB1 and HSPA2 expression. This negative feedback decreased the percentage of early stages of apoptotic cells and promoted cell survival. Conclusion HSPB9 expression, although rapid, is detrimental to cell survival early during its overexpression. In heat stress, HSPB9 overexpression, while inhibiting the expression of HSPA2 and HSPB1, is beneficial to cell survival.

关键词： Heat stress HSPB9 HSPB1 HSPA2 Apoptosis

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