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学者姓名：王凯
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Abstract ：
Sugarcane (Saccharum spp.), a leading sugar and energy crop, is seriously impacted by drought stress. However, the molecular mechanisms underlying sugarcane drought resistance, especially the functions of epigenetic regulators, remain elusive. Here, we show that a S. spontaneum KDM4/JHDM3 group JmjC protein, SsJMJ4, negatively regulates drought-stress responses through its H3K27me3 demethylase activity. Ectopic overexpression of SsJMJ4 in Arabidopsis reduced drought resistance possibly by promoting expression of AtWRKY54 and AtWRKY70, encoding two negative regulators of drought stress. SsJMJ4 directly bound to AtWRKY54 and AtWRKY70, and reduced H3K27me3 levels at these loci to ensure their proper transcription under normal conditions. Drought stress down-regulated both transcription and protein abundance of SsJMJ4, which was correlated with the reduced occupancy of SsJMJ4 at AtWRKY54 and AtWRKY70 chromatin, increased H3K27me3 levels at these loci, as well as reduced transcription levels of these genes. In S. spontaneum, drought stress-repressed transcription of SsWRKY122, an ortholog of AtWRKY54 and AtWRKY70, was associated with increased H3K27me3 levels at these loci. Transient overexpression of SsJMJ4 in S. spontaneum protoplasts raised transcription of SsWRKY122, paralleled with reduced H3K27me3 levels at its loci. These results suggest that the SsJMJ4-mediated dynamic deposition of H3K27me3 is required for an appropriate response to drought stress. SsJMJ4, a novel sugarcane H3K27me3 demethylase, plays an important role in dynamic trade-off between growth and drought-stress responses by anti-silencing negative regulators of drought stress.
Keyword ：
Drought stress Drought stress histone demethylase histone demethylase JmjC protein JmjC protein Saccharum spontaneum Saccharum spontaneum SsJMJ4 SsJMJ4
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| GB/T 7714 | Yu, Guangrun , Chen, Daoqian , Ye, Meiling et al. H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane [J]. | JOURNAL OF EXPERIMENTAL BOTANY , 2024 , 75 (10) : 3040-3053 . |
| MLA | Yu, Guangrun et al. "H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane" . | JOURNAL OF EXPERIMENTAL BOTANY 75 . 10 (2024) : 3040-3053 . |
| APA | Yu, Guangrun , Chen, Daoqian , Ye, Meiling , Wu, Xiaoge , Zhu, Zhiying , Shen, Yan et al. H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane . | JOURNAL OF EXPERIMENTAL BOTANY , 2024 , 75 (10) , 3040-3053 . |
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干旱严重影响甘蔗的产量和品质，是制约甘蔗产业发展的主要环境胁迫之一。中蔗系列品种具备较好的综合农艺性状和育种应用潜力，但其抗旱性及具体生理响应尚缺乏系统分析。研究以中蔗系列品种（系）中蔗1号（ZZ1）、中蔗2号（ZZ2）、中蔗5号（ZZ5）、中蔗6号（ZZ6）、中蔗9号（ZZ9）、中蔗13号（ZZ13）为对象，以新台糖22(ROC22)为参照材料，对幼苗进行土壤自然干旱处理后，系统分析了生长、根系活力、叶片相对含水量、抗氧化酶活性和氧化产物、渗透调节物质、光合参数和叶绿素荧光参数等24项指标的抗旱系数；采用主成分分析法、加权隶属函数分析和聚类分析法联合分析，结果显示：ZZ9、ZZ5抗旱能力最强，ZZ6与ZZ13次之，ZZ2、ZZ1与ROC22抗旱能力相似。关联分析表明，根系活力、生长情况、叶片相对含水量、光合参数和叶绿素荧光参数等指标与甘蔗苗期抗旱性密切相关，可以作为甘蔗苗期抗旱评价的优选指标。
Keyword ：
抗旱性 抗旱性 甘蔗 甘蔗 生理响应 生理响应 综合评价 综合评价
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| GB/T 7714 | 方自豪 , 王衍坤 , 韩金磊 et al. 中蔗系列品种（系）苗期抗旱性综合评价及抗旱指标筛选 [J]. | 南通大学学报(自然科学版) , 2023 , 22 (01) : 54-66 . |
| MLA | 方自豪 et al. "中蔗系列品种（系）苗期抗旱性综合评价及抗旱指标筛选" . | 南通大学学报(自然科学版) 22 . 01 (2023) : 54-66 . |
| APA | 方自豪 , 王衍坤 , 韩金磊 , 张鑫 , 张木清 , 王琼丽 et al. 中蔗系列品种（系）苗期抗旱性综合评价及抗旱指标筛选 . | 南通大学学报(自然科学版) , 2023 , 22 (01) , 54-66 . |
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Cassava is a tropical root crop that is sensitive to low temperature. While the transcriptome for cold-responsive genes has been extensively studied, information on their regulation is largely unavailable. Here, we conducted assays of plant morphology, the transcriptome, and open chromatin in cassava under moderate cold stress (10 celcius). We observed reversible morphological changes in cassava plants under continuous cold stress, in which plants showed wilting of the apical leaf blade and petiole at 5 h and recovery at 48 h. Consistently, distinct expressional dynamics for genes in response to cold were detected at 5 h and 48 h in both tissues. We examined the genome-wide DNase I-hypersensitive sites (DHSs) and their dynamics using cold-treated leaf blades and petioles. We revealed that cold-induced DHSs (coiDHSs) substantially differed among tissues and treatments. However, the putative coiDHS-derived transcription factors (TFs) largely co-occurred across tissues and treatments, and 61 TFs commonly shared by all samples were isolated. A putative functional network with 30 interconnected TFs was created. The frequent empirical interactions among these TFs indicate their roles in the cold response. Notably, we found that the two pairs of known cold-responsive TFs AGL20-RGA and ERF5-ERF105 showed highly frequent co-occurrence in coiDHSs. Moreover, the binding-site distances differed among TF pairs or samples, indicating that there are preferred distances between cooperative TFs and that such distances may depend on biological conditions. The identification of conserved TFs and their cooperativity provides valuable information for elucidating the transcriptional networks underlying cold gene expression in cassava.
Keyword ：
Cassava Cassava Cold response Cold response DNase I-hypersensitive site DNase I-hypersensitive site Regulatory network Regulatory network Transcription factor cooperativity Transcription factor cooperativity
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| GB/T 7714 | Yu, Guangrun , Ye, Feng , Zhang, Xin et al. Characterization of open chromatin in response to cold reveals transcription factor association with preferred binding distances in cassava [J]. | INDUSTRIAL CROPS AND PRODUCTS , 2023 , 202 . |
| MLA | Yu, Guangrun et al. "Characterization of open chromatin in response to cold reveals transcription factor association with preferred binding distances in cassava" . | INDUSTRIAL CROPS AND PRODUCTS 202 (2023) . |
| APA | Yu, Guangrun , Ye, Feng , Zhang, Xin , Cai, Jie , Zhu, Wenli , Zhang, Hui et al. Characterization of open chromatin in response to cold reveals transcription factor association with preferred binding distances in cassava . | INDUSTRIAL CROPS AND PRODUCTS , 2023 , 202 . |
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Autopolyploidy and allopolyploidy may represent an evolutionary advantage and are more common in plants than assumed. However, less attention has been paid to autopolyploidy than to allopolyploidy, and its evolutionary consequences are largely unclear, especially for plants with high ploidy levels. In this study, we developed oligonucleotide (oligo)-based chromosome painting probes to identify individual chromosomes in S. spontaneum. Using fluorescence in situ hybridization (FISH), we investigated chromosome behavior during pachytene, metaphase, anaphase, and telophase of meiosis I (MI) in autotetraploid, autooctoploid, and autodecaploid S. spontaneum clones. All autopolyploid clones showed stable diploi-dized chromosome behavior; so that homologous chromosomes formed almost exclusively bivalents dur-ing MI. Two copies of homologous chromosome 8 with similar sizes in the autotetraploid clone showed preferential pairing with each other with respect to the other copies. However, sequence variation analysis showed no apparent differences among homologs of chromosome 8 and all other chromosomes. We suggest that either the stable diploidized pairing or the preferential pairing between homologous copies of chromosome 8 in the studied autopolyploid sugarcane are accounted for by unknown mechanisms other than DNA sequence similarity. Our results reveal evolutionary consequences of stable meiotic behavior in autopolyploid plants.(c) 2023 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keyword ：
Autopolyploidy Autopolyploidy Chromosome behavior Chromosome behavior Chromosome pairing Chromosome pairing Meiosis I Meiosis I Saccharum spontaneum Saccharum spontaneum
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| GB/T 7714 | Zhang, Xin , Meng, Zhuang , Han, Jinlei et al. Characterization of meiotic chromosome behavior in the autopolyploid Saccharum spontaneum reveals preferential chromosome pairing without distinct DNA sequence variation [J]. | CROP JOURNAL , 2023 , 11 (5) : 1550-1558 . |
| MLA | Zhang, Xin et al. "Characterization of meiotic chromosome behavior in the autopolyploid Saccharum spontaneum reveals preferential chromosome pairing without distinct DNA sequence variation" . | CROP JOURNAL 11 . 5 (2023) : 1550-1558 . |
| APA | Zhang, Xin , Meng, Zhuang , Han, Jinlei , Khurshid, Haris , Esh, Ayman , Hasterok, Robert et al. Characterization of meiotic chromosome behavior in the autopolyploid Saccharum spontaneum reveals preferential chromosome pairing without distinct DNA sequence variation . | CROP JOURNAL , 2023 , 11 (5) , 1550-1558 . |
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Modern sugarcane cultivars are derived from the hybridization of Saccharum officinarum (2n = 80) and S. spontaneum (2n = 40-128), leading to a variety of complex genomes with highly polyploid and varied chromosome structures. These complex genomes have hindered deciphering the genome structure and marker-assisted selection in sugarcane breeding. Ten cultivars were analyzed by fluorescence in situ hybridization adopting chromosome painting and S. spontaneum-specific probes. The results showed six types of chromosomes in the studied cultivars, including S. spontaneum or S. officinarum chromosomes, interspecific recombinations from homoeologous or nonhomoeologous chromosomes, and translocations of S. spontaneum or S. officinarum chromosomes. The results showed unexpectedly high proportions of interspecific recombinations in these cultivars (11.9-40.9%), which renew our knowledge that less than 13% of chromosomes result from interspecific exchanges. Also, the results showed a high frequency of translocations (an average of 2.15 translocations per chromosome) between S. officinarum chromosomes. The diverse types of chromosomes in cultivars imply that hybrid gametes of S. spontaneum and S. officinarum may form unusual chromosome pairs, including homoeologous or nonhomoeologous chromosomes either between or within S. spontaneum and S. officinarum. Moreover, we consistently observed 11 or 12 copies for the four studied chromosomes, i.e., chromosomes 1, 2, 7, and 8, suggesting steady transmission during the breeding program. By comparison, we found a relatively fewer copies of S. spontaneum chromosome 1 than those of S. spontaneum chromosomes 2, 7, and 8. These results provide deep insights into the structure of cultivars and may facilitate chromosome-assisted selection in sugarcane breeding.
Keyword ：
Chromosome painting Chromosome painting FISH FISH Genome structure Genome structure Interspecific recombination Interspecific recombination Sugarcane cultivar Sugarcane cultivar
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| GB/T 7714 | Wang, Kai , Cheng, Hon , Han, Jinlei et al. A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars [J]. | CHROMOSOME RESEARCH , 2022 , 30 (1) : 29-41 . |
| MLA | Wang, Kai et al. "A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars" . | CHROMOSOME RESEARCH 30 . 1 (2022) : 29-41 . |
| APA | Wang, Kai , Cheng, Hon , Han, Jinlei , Esh, Ayman , Liu, Jiayong , Zhang, Yuebin et al. A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars . | CHROMOSOME RESEARCH , 2022 , 30 (1) , 29-41 . |
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| GB/T 7714 | Wang, Kai , Cheng, Hon , Han, Jinlei et al. A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars (vol 30, pg 29, 2022) [J]. | CHROMOSOME RESEARCH , 2022 , 30 (4) : 493-494 . |
| MLA | Wang, Kai et al. "A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars (vol 30, pg 29, 2022)" . | CHROMOSOME RESEARCH 30 . 4 (2022) : 493-494 . |
| APA | Wang, Kai , Cheng, Hon , Han, Jinlei , Esh, Ayman , Liu, Jiayong , Zhang, Yuebin et al. A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars (vol 30, pg 29, 2022) . | CHROMOSOME RESEARCH , 2022 , 30 (4) , 493-494 . |
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Crop wild relatives are an important reservoir of natural biodiversity. However, incorporating wild genetic diversity into breeding programs is often hampered by reproductive barriers and a lack of accurate genomic information. We assembled a high-quality, accurately centromere-anchored genome of Gossypium anomalum, a stress-tolerant wild cotton species. We provided a strategy to discover and transfer agronomically valuable genes from wild diploid species to tetraploid cotton cultivars. With a (Gossypium hirsutum 3 G. anomalum)2 hexaploid as a bridge parent, we developed a set of 74 diploid chromosome segment substitution lines (CSSLs) of the wild cotton species G. anomalum in the G. hirsutum background. This set of CSSLs included 70 homozygous substitutions and four heterozygous substitutions, and it collectively contained about 72.22% of the G. anomalum genome. Twenty-four quantitative trait loci associated with plant height, yield, and fiber qualities were detected on 15 substitution segments. Integrating the reference genome with agronomic trait evaluation of the CSSLs enabled location and cloning of two G. anomalum genes that encode peroxiredoxin and putative callose synthase 8, respectively, conferring drought tolerance and improving fiber strength. We have demonstrated the power of a high-quality wild-species reference genome for identifying agronomically valuable alleles to facilitate interspecific introgression breeding in crops.
Keyword ：
chromosome segment substitution lines chromosome segment substitution lines drought tolerance drought tolerance fiber strength fiber strength genome genome Gossypium anomalum Gossypium anomalum wild diploid species wild diploid species
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| GB/T 7714 | Xu, Zhenzhen , Chen, Jiedan , Meng, Shan et al. Genome sequence of Gossypium anomalum facilitates interspecific introgression breeding [J]. | PLANT COMMUNICATIONS , 2022 , 3 (5) . |
| MLA | Xu, Zhenzhen et al. "Genome sequence of Gossypium anomalum facilitates interspecific introgression breeding" . | PLANT COMMUNICATIONS 3 . 5 (2022) . |
| APA | Xu, Zhenzhen , Chen, Jiedan , Meng, Shan , Xu, Peng , Zhai, Caijiao , Huang, Fang et al. Genome sequence of Gossypium anomalum facilitates interspecific introgression breeding . | PLANT COMMUNICATIONS , 2022 , 3 (5) . |
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植物组织培养是一个复杂的发育过程,可分为愈伤组织诱导、不定芽分化和不定根诱导3个主要阶段,将外植体成功诱导出愈伤组织在生物科学的研究中具有重要意义。植物愈伤组织诱导是指将已分化的细胞逆转为多能性干细胞,是分化细胞内部的基因在复杂的外界因素刺激下相互作用的结果,不但受到众多外源信号的调控,还受到内部多样的表观遗传修饰的影响。生物体内表观遗传信息的改变比基因组DNA序列的改变影响更为深远,可影响到植物组织培养的每个环节。前期研究表明,表观遗传修饰在植物愈伤组织的诱导过程中起到了重要作用。综述了DNA甲基化、组蛋白修饰、小RNA、转座子及染色质重塑等常见的表观遗传修饰对植物愈伤组织诱导的影响,分析了其中的调控机制,总结了表观遗传修饰在该领域存在的主要问题,并展望了未来的研究方向,以推动表观遗传学在该领域的深入研究,不但有助于深化对愈伤组织诱导过程的理解,更有助于顽拗植物愈伤组织的诱导工作,甚至对推动转基因植物的开发都有一定的帮助作用。
Keyword ：
DNA甲基化 DNA甲基化 小RNA 小RNA 愈伤组织诱导 愈伤组织诱导 染色质重塑 染色质重塑 组蛋白修饰 组蛋白修饰
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| GB/T 7714 | 王建勇 , 邹永梅 , 葛言彬 et al. 植物愈伤组织诱导过程中的表观遗传修饰研究进展 [J]. | 生物技术通报 , 2021 , 37 (08) : 253-262 . |
| MLA | 王建勇 et al. "植物愈伤组织诱导过程中的表观遗传修饰研究进展" . | 生物技术通报 37 . 08 (2021) : 253-262 . |
| APA | 王建勇 , 邹永梅 , 葛言彬 , 王凯 , 席梦利 . 植物愈伤组织诱导过程中的表观遗传修饰研究进展 . | 生物技术通报 , 2021 , 37 (08) , 253-262 . |
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The assembly of centromeric regions has become one of the most intractable tasks in whole-genome sequencing due to the enrichment of highly repetitive DNA sequences in most eukaryotic centromeres. Here, we describe a method used to identify centromeric DNAs through chromatin immunoprecipitation and sequencing (ChIP-seq). By mapping ChIP-seq reads, centromeric regions can be indicated in genome assemblies. We demonstrated that the assembly quality of centromeres obtained using ChIP-seq mapping can reflect and indicate the quality of a whole-genome assembly. We discuss an expected 'high-quality' centromere assembly obtained via centromere ChIP-seq mapping.
Keyword ：
CENH3 CENH3 Centromere Centromere ChIP-seq ChIP-seq Genome assembly Genome assembly Monocentromere Monocentromere
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| GB/T 7714 | Han, Miaomiao , Yang, Yae , Zhang, Muqing et al. Considerations regarding centromere assembly in plant whole-genome sequencing [J]. | METHODS , 2021 , 187 : 54-56 . |
| MLA | Han, Miaomiao et al. "Considerations regarding centromere assembly in plant whole-genome sequencing" . | METHODS 187 (2021) : 54-56 . |
| APA | Han, Miaomiao , Yang, Yae , Zhang, Muqing , Wang, Kai . Considerations regarding centromere assembly in plant whole-genome sequencing . | METHODS , 2021 , 187 , 54-56 . |
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Centromeres in eukaryotes are composed of tandem DNAs and retrotransposons. However, centromeric repeats exhibit considerable diversity, even among closely related species, and their origin and evolution are largely unknown. We conducted a genome-wide characterization of the centromeric sequences in sugarcane (Saccharum officinarum). Four centromeric tandem repeat sequences, So1, So103, So137 and So119, were isolated. So1 has a monomeric length of 137 bp, typical of a centromeric satellite, and has evolved four variants. However, these So1 variants had distinct centromere distributions and some were unique to an individual centromere. The distributions of the So1 variants were unexpectedly consistent among the Saccharum species that had different basic chromosome numbers or ploidy levels, thus suggesting evolutionary stability for approximately 7 million years in sugarcane. So103, So137 and So119 had unusually longer monomeric lengths that ranged from 327 to 1371 bp and lacked translational phasing on the CENH3 nucleosomes. Moreover, So103, So137 and So119 seemed to be highly similar to retrotransposons, which suggests that they originated from these mobile elements. Notably, all three repeats were flanked by direct repeats, and formed extrachromosomal circular DNAs (eccDNAs). The presence of circular molecules for these retrotransposon-derived centromeric satellites suggests an eccDNA-mediated centromeric satellite formation pathway in sugarcane.
Keyword ：
centromere centromere extrachromosomal circular DNA extrachromosomal circular DNA rolling circle amplification rolling circle amplification satellite repeat satellite repeat sugarcane sugarcane
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| GB/T 7714 | Huang, Yongji , Ding, Wenjie , Zhang, Muqing et al. The formation and evolution of centromeric satellite repeats in Saccharum species [J]. | PLANT JOURNAL , 2021 , 106 (3) : 616-629 . |
| MLA | Huang, Yongji et al. "The formation and evolution of centromeric satellite repeats in Saccharum species" . | PLANT JOURNAL 106 . 3 (2021) : 616-629 . |
| APA | Huang, Yongji , Ding, Wenjie , Zhang, Muqing , Han, Jinlei , Jing, Yanfen , Yao, Wei et al. The formation and evolution of centromeric satellite repeats in Saccharum species . | PLANT JOURNAL , 2021 , 106 (3) , 616-629 . |
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