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Inter-and Intra-specific Genetic Diversity in Diospyros Using SCoT and IRAP Markers

Horticultural Plant Journal 2020年第2期6卷 71-80页

作者： Changfei Guan Sadaruddin Chachar pingxian zhang Chaoqiong Hu RenziWang Yong Yang State Key Laboratory of Crop Stress Biology for Arid Areas College of HorticultureNorthwest A&F UniversityYanglingShaanxi 712100China Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China

The genus Diospyros contains more than 500 species, among them persimmon(Diospyros kaki Thunb.) is the most economically important species. However, the inter-and intra-specific genetic diversity remains unknown due to historic cultivation, domestication and introduction in different regions of China. In this study, we investigated the genetic diversity and relationship among 268 Diospyros accessions from different regions in China using start codon-targeted(SCo T) and inter-retrotransposon-amplified polymorphism(IRAP) markers. Among 268 samples,232 accessions were D. kaki varieties and 36 were closely related species, that is, D. lotus(21), D. glaucifolia(1), D. virginiana(5), D. kaki ***. silvestris(3), D. oleifera(5) and D. deyangnsis(1). In our study, a total of 90 and 97 polymorphic alleles were obtained from nine SCo T and nine IRAP markers, respectively, and these markers displayed rich polymorphisms for evaluation of the genetic diversity among 268 samples. A study on the relationship, genetic structure and analysis of molecular variance(AMOVA) showed that inter-and intra-specific gene exchanges were frequent among/within the samples from five regions. Moreover, the genetic distance between the Southwest China(SWC) and the other regions was relatively far;the samples from North China(NC), East China(EC), South and Central China(SCC), Northwest China(NWC) regions had a relatively close relationship. The unweighted pair group method with arithmetic means(UPGMA) and population structure analysis indicated that persimmons within geographic regions were clustered together, which revealed that the samples from various regions exhibited gene exchange, and the geographical proximity of persimmons resulted in a more frequent exchange. In addition, the persimmon had a close relationship with D. kaki var. silvestris, D. deyangnsis and D. oleifera species, and exhibited a far distance with respect to D. virginiana. These SCo T and IRAP markers will be helpful for

关键词： persimmon diospyros genetic diversity population structure different regions SCoT IRAP

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Plant synthetic epigenomic engineering for crop improvement

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Science China(Life Sciences) 2022年第11期65卷 2191-2204页

作者： Liwen Yang pingxian zhang Yifan Wang Guihua Hu Weijun Guo Xiaofeng Gu Li Pu Biotechnology Research Institute Chinese Academy of Agricultural SciencesBejing 10081China College of Life Science and Technology Huazhong Agriculural UniversityWuhan 430070China

Efforts have been directed to redesign crops with increased yield,stress adaptability,and nutritional value through synthetic biology—the application of engineering principles to biology.A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops,thus heralding the promise of“synthetic epigenetics.”In this review,we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques,epigenetic editing,and deep learning-driven predictive tools can rapidly extend these *** also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.

关键词： epigenetics synthetic biology synthetic epigenetics crop improvement

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PRMT6 physically associates with nuclear factor Y to regulate photoperiodic flowering in Arabidopsis

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aBIOTECH 2021年第4期2卷 403-414页

作者： pingxian zhang Xiulan Li Yifan Wang Weijun Guo Sadaruddin Chachar Adeel Riaz Yuke Geng Xiaofeng Gu Liwen Yang Biotechnology Research Institute Chinese Academy of Agricultural ScienceBeijing 100081China College of Life Science and Technology Huazhong Agricultural UniversityWuhan 430070HubeiChina College of Life and Environmental Sciences Minzu University of ChinaBeijing 100081China

The timing of floral transition is critical for reproductive success in flowering *** long-day(LD)plant Arabidopsis,the floral regulator gene FLOWERING LOCUS T(FT)is a major component of the mobile *** expression is rhythmically activated by CONSTANS(CO),and specifically accumu-lated at dusk of ***;the underlying mechanism of adequate regulation of FT transcription in response to day-length cues to warrant flowering time still remains to be ***,we identify a homolog of human protein arginine methyltransferases 6(HsPRMT6)in Arabidopsis,and confirm AtPRMT6 physically interacts with three positive regulators of flowering Nuclear Factors YC3(NF-YC3),NF-YC9,and *** investigations find that AtPRMT6 and its encoding protein accumulate at dusk of ***6-mediated H3 R2me2a modification enhances the promotion of NF-YCs on FT transcription in response to inductive LD ***,AtPRMT6 and its homologues proteins AtPRMT4a and AtPRMT4b coordinately inhibit the expression of FLOWERING LOCUS C,a suppressor of *** together,our study reveals the role of arginine methylation in photoperiodic pathway and how the PRMT6-mediating H3R2me2a system interacts with NF-CO module to dynamically control FT expression and facilitate flowering time.

关键词： Arginine methylation Protein arginine methyltransferases 6 Nuclear factors Y Flowering time

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SMOC:a smart model for open chromatin region prediction in rice genomes

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Journal of Genetics and Genomics 2022年第5期49卷 514-517页

作者： Weijun Guo Hanqing Liu Yifan Wang pingxian zhang Dongwei Li Tuoyu Liu Qian zhang Liwen Yang Li Pu Jian Tian Xiaofeng Gu Biotechnology Research Institute Chinese Academy of Agriculture SciencesBeijing 100081China College of Life Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China

In eukaryotic genomes, the fundamental unit of chromatin is the nucleosome, which is composed of a histone octamer that contains two copies of each histone, H3, H2A, H2B, and H4 (Bell et al., 2011).Chromatin is wrappe... 详细信息

关键词： smart prediction helical

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Transcriptional landscape of rice roots at the single-cell resolution

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Molecular Plant 2021年第3期14卷 384-394页

作者： Qing Liu Zhe Liang Dan Feng Sanjie Jiang Yifan Wang Zhuoying Du Ruoxi Li Guihua Hu pingxian zhang Yanfei Ma Jan ULohmann Xiaofeng Gu Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China Centre for Organismal Studies Heidelberg UniversityHeidelberg 69120Germany BGI Genomics Shenzhen 518083China Fu Foundation School of Engineering and Applied Science Columbia UniversityNew YorkNY 10027USA These authors contributed equally.

There are two main types of root systems in flowering plants,namely taproot systems of dicots and fibrous root systems found in *** this fundamental split,our current knowledge of cellular and molecular mechanism driving root development is mainly based on studies of the dicot model ***,the world major crops are monocots and little is known about the transcriptional programs underlying cell-type specification in this ***,we report the transcriptomes of more than 20000 single cells derived from root tips of two agronomically important rice *** combined computational and experimental analyses we were able to robustly identify most of the major cell types and define novel cell-type-specific marker genes for both ***,we found divergent cell types associated with specific regulatory programs,including phytohormone biosynthesis,signaling,and response,which were well conserved between the two rice *** addition,we detected substantial differences between the cell-type transcript profiles of Arabidopsis and *** species-specific features emphasize the importance of analyzing tissues across diverse model species,including *** together,our study provides insight into the transcriptomic landscape of major cell types of rice root tip at single-cell resolution and opens new avenues to study cell-type specification,function,and evolution in plants.

关键词： single-cell RNA-seq transcriptional landscape rice root plants

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N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression,Plant Development, and Stress Responses

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Molecular Plant 2018年第12期11卷 1492-1508页

作者： Qian zhang Zhe Liang Xuean Cui Changmian Ji Yun Li pingxian zhang Jingrong Liu Adeel Riaz Pu Yao Min Liu Yunpeng Wang Tiegang Lu Hao Yu Donglei Yang Hongkun Zheng Xiaofeng Gu Biotechnology Research Institute Chinese Academy of Agricultural Sciences Beijing 100081 China Department of Biological Sciences and Temasek Life Sciences Laboratory National University of Singapore Singapore 117543 Singapore Biomarker Technologies Beijing 101300 China State Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural University Nanjing 210095 China institute of Clinical Medicine University of Oslo Oslo 0450 Norway These authors contributed equally to this article.

N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis ***,the conservation and divergence of 6mA distribution patterns and functions in plants remain *** we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and *** found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.

关键词： N6-methyladenine 6mA DNA rnethylation Methylome Oryza sativa Stress

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Genome-edited ATP BINDING CASSETTE B1 transporter SD8 knockouts show optimized rice architecture without yield penalty

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Plant Communications 2022年第5期3卷 1-4页

作者： Ruihong Qu pingxian zhang Qing Liu Yifan Wang Weijun Guo Zhuoying Du Xiulan Li Liwen Yang Shuangyong Yan Xiaofeng Gu Biotechnology Research Institute Chinese Academy of Agricultural ScienceBeijing 100081China College of Life Science and Technology Huazhong Agricultural UniversityWuhan430070 HubeiChina Tianjin Key Laboratory of Crop Genetics and Breeding Tianjin Crop Research InstituteTianjin Academy of Agricultural SciencesTianjin 300384China College of Life Sciences Hebei Agricultural UniversityBaoding071001 HebeiChina

Dear editor,In the 1960s,the use of semi-dwarf rice and wheat varieties ushered in the‘‘Green Revolution,’’leading to reduced lodging and increased harvest *** rice,essentially all modern semidwarf varieties carry a specific null mutation or weak alleles of Semi-Dwarf1(SD1),which encodes a GA20-2 oxidase in the gibberellin biosynthetic pathway(Monna et al.,2002;Sasaki et al.,2002;Spielmeyer et al.,2002).In addition to gibberellins,other plant hormones such as brassinosteroids,strigolactones,and auxin also function in reducing rice height(Ferrero-Serrano et al.,2019).However,many dwarf or semi-dwarf mutants have not been widely used in rice-breeding programs because they adversely impact grain yield(Ferrero-Serrano et al.,2019).

关键词： dwarf breeding editor

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Correction to:PRMT6 physically associates with nuclear factor Y to regulate photoperiodic flowering in Arabidopsis

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aBIOTECH 2022年第1期3卷 85-88页

In this artice Figs.2 and 3 were wrongly numbered;Fig.2 should have been Fig.3 and vice versa as shown ***,the Fig.3 indications have been revised as shown:the sentence"Next,two transfer DNA(T-DNA)insertion single-mutant prmt6-1(Sail 385_A06)and prmt6-2(Salk 151679C)(Figs.2A;S3)..'has been revised as“Next,two transfer DNA(T-DNA)inser-tion single-mutant prmt6-1(Sail 385_A06)and prmt6-2(Salk 151679C)(Figs.3A;S3..".

关键词： photoperiod revised Arabidopsis

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Rice Homolog of Sin3-Associated Polypeptide 30, OsSFL1, Mediates Histone Deacetylation to Regulate Flowering Time during Short Days

Rice Homolog of Sin3-Associated Polypeptide 30, OsSFL1, Medi...

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中国生物工程学会第十三届学术年会暨2019年全国生物技...

作者： Yuke Geng pingxian zhang Qing Liu Ziwei Wei Adeel Riaz Sadaruddin Chachar Xiaofeng Gu Biotechnology Research Institute Chinese Academy of Agricultural Science

Flowering time is critical for plants;the regulation of flowering time allows plants to grow during different seasons as well as at different latitudes and altitudes. In rice(Oryza sativa), flowering time is usually associated with yield production. Histone deacetylases(HDACs) function to remove the acetyl groups from histones, leading to a condensed chromatin structure and repressing gene expression. However, in rice, the primary biological role of HDACs in modulating flowering time remains unclear. Here, we report the characterization of the core HDAC component, an ortholog of yeast SAP30, named SAP30 FUNCTION-LIKE 1(OsSFL1), which delays the flowering time of rice under short-day conditions(SDs). The loss of Os SFL1 function altered the photoperiodic rhythm of Heading date 1(Hd1) and then repressed Heading date 3 a(Hd3 a) expression at the end of short days. Os SFL1 can specifically accumulate on the Hd1 locus at dusk under SDs. Moreover, the knock-down of Os SFL1 leads to an increase in histone acetylation at the same locus as Hd1 under SDs. In rice, OsSFL1 can also directly interact with other HDACs, OsSAP18 and OsHDAC2, to form HDAC complexes. These studies reveal that a core HDAC component, OsSFL1, controls flowering time in rice.

关键词： Histone deacetylation Heading date Photoperiodic flowering HDAC OsSFL1 rice

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基于SRAP的部分柿砧木遗传多样性分析

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中国南方果树 2016年第4期45卷 23-27页

作者：汤红张平贤王燕李慧郭大勇华中农业大学园艺植物生物学教育部重点实验室武汉430070

柿Diospyros kaki Thunb.常见的砧木有君迁子*** L.、浙江柿*** Met.、油柿*** Cheng及本砧,其遗传关系尚不完全清楚。以21份柿属砧木资源和5份栽培柿品种为试材,利用SRAP分子标记技术分析供试材料之间的亲缘关系。SRAP扩增结果表明,(1... 详细信息

柿Diospyros kaki Thunb.常见的砧木有君迁子*** L.、浙江柿*** Met.、油柿*** Cheng及本砧,其遗传关系尚不完全清楚。以21份柿属砧木资源和5份栽培柿品种为试材,利用SRAP分子标记技术分析供试材料之间的亲缘关系。SRAP扩增结果表明,(1)筛选出9对多态性较好的引物,共扩增出113条清晰、可重复谱带,其中多态性带111条,多态性比例分别为98.23%;(2)UPGMA聚类分析结果显示两份本砧种质"小果甜柿"和"牛眼柿"与5份柿栽培品种聚类较近,台湾乌柿与浙江柿、油柿及浙江光叶柿聚类成组,而与其他君迁子类型的遗传关系相对较远。以上结果表明,柿砧木遗传多样性丰富,有望进一步从中挖掘新的种质类型。

关键词：柿砧木 SRAP 遗传多样性君迁子

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