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A centromere map based on super pan-genome highlights the structure and function of rice centromeres

Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge Qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang Qiang Xu Yan Cui Qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou Qian Qian Longbiao Guo Lianguang Shang State Key laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Yazhouwan National laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National Key Facility for Crop Gene Resources and genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary factors.Rice centromeres are crucial for chromosome segregation,and contain some unreported genes.Due to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is needed.We constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.We showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary patterns.We also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution.Furthermore,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging.We investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 methods.By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement.

关键词： centromere super pan-genome CentoO satellite repeat rice

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Tissue distribution of cadmium and its effect on reproduction in Spodoptera exigua

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Journal of Integrative Agriculture 2024年第1期23卷 195-204页

作者： Honghua Su Menglu Wu Yong Yang Yan Deng Yizhong Yang Qingming Sun College of Plant Protection Yangzhou UniversityYangzhou 225009China Institute of Fruit Tree Research Guangdong Academy of Agricultural Sciences/Key Laboratory of South Subtropical Fruit Biology and Genetic Resource UtilizationMinistry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree ResearchGuangzhou 510640China

Vegetable fields are often contaminated by heavy metals,and Spodoptera exigua is a major vegetable pest which is stressed by heavy metals mainly by feeding.In this study,cadmium accumulation in the tissues of S.exigua exposed to cadmium and its effects on the growth and development of the parents and the offspring were investigated.Under the stress of different concentrations of cadmium(0.2,3.2,and 51.2 mg kg^(-1)),the cadmium content in each tissue of S.exigua increased in a dose-dependent manner.At the larval stage,the highest cadmium accumulation was found in midgut in all three cadmium treatments,but at the adult stage,the highest cadmium content was found in fat body.In addition,the cadmium content in ovaries was much higher than in testes.When F1S.exigua was stressed by cadmium and the F_(2)generation was not fed a cadmium-containing diet,the larval survival,pupation rate,emergence rate and fecundity of the F_(2)generation were significantly reduced in the 51.2 mg kg^(-1)treatment compared to the corresponding F1generation.Even in the F_(2)generation of the 3.2 mg kg^(-1)treatment,the fecundity was significantly lower than in the parental generation.The fecundity of the only-female stressed treatment was significantly lower than that of the only-male stressed treatment at the 3.2 and 51.2 mg kg^(-1)cadmium exposure levels.When only mothers were stressed at the larval stage,the fecundity of the F_(2)generation was significantly lower than that of the F1generation in the 51.2 mg kg^(-1)treatment,and it was also significantly lower than in the 3.2 and 0.2 mg kg^(-1)treatments.The results of our study can provide useful information for forecasting the population increase trends under different heavy metal stress conditions and for the reliable environmental risk assessment of heavy metal pollution.

关键词： heavy metal pollution cadmium Spodoptera exigua tissue distribution reproduction

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Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway

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The Crop Journal 2024年第1期12卷 164-176页

作者： Dongjiao Wang Wei Wang Shoujian Zang Liqian Qin Yanlan Liang Peixia Lin Yachun Su Youxiong Que Key laboratory of Sugarcane Biology and genetic Breeding Ministry of Agriculture and Rural AffairsKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina National Key laboratory for Tropical Crop Breeding Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesSanya 572024HainanChina

WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen infection.However,the resistance mechanisms of WRKY genes in sugarcane remain unclear.In the present study,gene ontology(GO)enrichment analysis revealed that WRKY gene family in sugarcane was extensively involved in the response to biotic stress and in defense response.We identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar ROC22.This gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)stress.Interestingly,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium scitamineum.Moreover,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani var.coeruleum and caused down-regulated expression of immune marker-related genes.Transcriptome analysis indicated suppressed expression of most JAZ genes in the signal transduction pathway.ScWRKY4 interacted with ScJAZ13 to repress its expression.We thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling pathway.The present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation.

关键词： Disease resistance Expression profile Transcriptome analysis WRKY transcription factors

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The auxin transporter OsAUX1 regulates tillering in rice(Oryza sativa)

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Journal of Integrative Agriculture 2024年第5期23卷 1454-1467页

作者： Luqi Jia Yongdong Dai Ziwei Peng Zhibo Cui Xuefei Zhang Yangyang Li Weijiang Tian Guanghua He Yun Li Xianchun Sang Chongqing Key laboratory of Crop Molecular Improvement/Rice Research Institute Academy of Agricultural SciencesSouthwest UniversityChongqing400715China Rice and Sorghum Research Institute Sichuan Academy of Agricultural Sciences/Key Laboratory of Southwest Rice Biology and Genetic BreedingMinistry of Agriculture and Rural AffairsDeyang 618000China

Tillering is an important agronomic trait of rice(Oryza sativa)that affects the number of effective panicles,thereby affecting yields.The phytohormone auxin plays a key role in tillering.Here we identified the high tillering and semi-dwarf 1(htsd1)mutant with auxin-deficiency root characteristics,such as shortened lateral roots,reduced lateral root density,and enlarged root angles.htsd1 showed reduced sensitivity to auxin,but the external application of indole-3-acetic acid(IAA)inhibited its tillering.We identified the mutated gene in htsd1 as AUXIN1(OsAUX1,LOC_Os01g63770),which encodes an auxin influx transporter.The promoter sequence of OsAUX1 contains many SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL)binding sites,and we demonstrated that SPL7 binds to the OsAUX1 promoter.TEOSINTE BRANCHED1(OsTB1),a key gene that negatively regulates tillering,was significantly downregulated in htsd1.Tillering was enhanced in the OsTB1 knockout mutant,and the external application of IAA inhibited tiller elongation in this mutant.Overexpressing OsTB1 restored the multi-tiller phenotype of htsd1.These results suggest that SPL7 directly binds to the OsAUX1 promoter and regulates tillering in rice by altering OsTB1 expression to modulate auxin signaling.

关键词： rice(Oryza sativa L.) tillering indole-3-acetic acid(IAA) OsAUX1 OsTB1

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Characteristics of genetic basis copy number variation in production and adaptation traits of Chinese indigenous sheep

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Journal of genetics and Genomics 2024年第5期51卷 566-569页

作者： Meilin Jin Gang Liu Jian Lu Zhiqiang Chen Huihua Wang Taotao Li Caihong Wei State Key laboratory of Animal Biotech Breeding Institute of Animal SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100193China College of Animal Science and Technology China Agricultural UniversityBeijing100193China National Animal Husbandry Service National Center of Preservation&Utilization of Animal Genetic ResourcesBeijing 100125China Glbizzia Biosciences Beijing 102629China

Copy number variations(CNVs)range in size from 50 base pairs(bp)to several megabases(Mb)and encompass various types of structural variations,such as insertions,deletions,duplications,and complex multiallelic events(MacDonald et al.,2014).These genomic alterations modulate phenotype by altering gene dosage and transcriptional regulation,and are key drivers of biological evolution and determinants of genetic diversity and phenotypic variation.In recent years,CNVs have been detected in the genomes of various livestock species(Yuan et al.,2021;Chen et al.,2022).Upadhyay et al.(2017)conducted a comprehensive analysis of CNV distribution in the European cattle genome and determined that the Kit gene is associated with color-sidedness in English longhorn cattle.Another study presented extensive genome-wide information on CNVs in wild,commercial,and local chicken breeds to gain an integrated understanding of the domestication process and exclusively identified the genes involved(Chen et al.,2022).

关键词： sided number dosage

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Amino acids TORC(talk) to anabolism through uncharged tRNA

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Science China Life Sciences 2024年第8期 1775-1776页

作者： Zhen-Zhen Ma Shi-Min Zhao The Obstetrics & Gynecology Hospital of Fudan University State Key Laboratory of Genetic EngineeringShanghai Key Laboratory of Metabolic Remodelling and HealthFudan University

Anabolism is essential for proliferation as well as to replenish dysfunctional macromolecules in cells.Due to that both substantial building blocks and energy are required for anabolism,cells must double check whether these prerequisites are met before deciding to start anabolism.Amino acids are building blocks of protein synthesis,their sufficiency in cells is closely monitored by several mechanisms,which all are linked to protein synthesis.

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genetic diversity of RNA viruses infecting invertebrate pests of rice

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Science China(Life Sciences) 2024年第1期67卷 175-187页

作者： Haoran Wang Shufen Chao Qing Yan Shu Zhang Guoqing Chen Chonghui Mao Yang Hu Fengquan Yu Shuo Wang Liang Lv Baojun Yang Jiachun He Songbai Zhang Liangsheng Zhang Peter Simmonds Guozhong Feng State Key laboratory of Rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311400China State Key laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Institute of Plant Protection&Soil Fertilizer Hubei Academy of Agricultural SciencesWuhan 430064China Institute of Plant Protection Guizhou Academy of Agricultural SciencesGuiyang 550000China Institute of Plant Protection Liaoning Academy of Agricultural SciencesShenyang 110161China Sanya Agricultural Technology Extension and Service Centre Sanya 572000China College of Agriculture Yangtze UniversityJingzhou 434000China Fujian Provincial Key laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry UniversityFuzhou 350002China Genomics and genetic Engineering laboratory of Ornamental Plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310012China Nuffield Department of Medicine Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxford OX13SYUnited Kingdom

Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop fields.However,information on viruses infecting invertebrate pests of crops is limited.In this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields.We identified 296 new RNA viruses and 13 known RNA viruses.These viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and genera.Of the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of mycoviruses.We detected known rice viruses in novel invertebrate hosts at high abundances.Furthermore,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species.Fortyfive potential insect pathogenic RNA viruses were detected in invertebrate species.Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity.Cross-species transmission of RNA viruses was detected between invertebrate hosts.Newly identified viral genomes showed extensive variation for invertebrate viral families or genera.Together,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

关键词： invertebrate species metatranscriptome viral diversity viral transmission viral genomes

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Identification of P-type plasma membrane H^(+)-ATPases in common wheat and characterization of TaHA7 associated with seed dormancy and germination

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Journal of Integrative Agriculture 2024年第7期23卷 2164-2177页

作者： Bingli Jiang Wei Gao Yating Jiang Shengnan Yan Jiajia Cao Litian Zhang Yue Zhang Jie Lu Chuanxi Ma Cheng Chang Haiping Zhang Key laboratory of Wheat Biology and genetic Improvement on Southern Yellow&Huai River Valley Ministry of Agriculture and Rural Affairs/College of AgronomyAnhui Agricultural UniversityHefei 230036China

The P-type plasma membrane(PM)H^(+)-ATPases(HAs)are crucial for plant development,growth,and defense.The HAs have been thoroughly characterized in many different plants.However,despite their importance,the functions of HAs in germination and seed dormancy(SD)have not been validated in wheat.Here,we identified 28 TaHA genes(TaHA1-28)in common wheat,which were divided into five subfamilies.An examination of gene expression in strong-and weak-SD wheat varieties led to the discovery of six candidate genes(TaHA7/-12/-14/-16/-18/-20).Based on a single nucleotide polymorphism(SNP)mutation(C/T)in the TaHA7 coding region,a CAPS marker(HA7)was developed and validated in 168 wheat varieties and 171 Chinese mini-core collections that exhibit diverse germination and SD phenotypes.We further verified the roles of the two allelic variations of TaHA7 in germination and SD using wheat mutants mutagenized with ethyl methane sulphonate(EMS)in‘Jimai 22’and‘Jing 411’backgrounds,and in transgenic Arabidopsis lines.TaHA7 appears to regulate germination and SD by mediating gibberellic acid(GA)and abscisic acid(ABA)signaling,metabolism,and biosynthesis.The results presented here will enable future research regarding the TaHAs in wheat.

关键词： wheat P-type plasma membrane H^(+)-ATPase seed dormancy abscisic acid gibberellin

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DIA-based proteome profiling with PRM verification reveals the involvement of ER-associated protein processing in pollen abortion in Ogura CMS cabbage

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Horticultural Plant Journal 2024年第3期10卷 755-770页

作者： Peiwen Wang Lin Zhu Ziheng Li Mozhen Cheng Xiuling Chen Aoxue Wang Chao Wang Xiaoxuan Zhang Key laboratory of Biology and genetic Improvement of Horticultural Crops(Northeast Region) Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbinHeilongjiang 150030China College of Horticulture and Landscape Architecture Northeast Agricultural UniversityHarbinHeilongjiang 150030China

Ogura cytoplasmic male sterility(Ogura CMS)is extensively applied in hybrid seed production in cruciferous crops.However,the posttranscriptional molecular basis of Ogura CMS in cruciferous crops remains elusive.Here,a data-independent acquisition-based proteomic approach coupled with a parallel reaction monitoring-based targeted proteomic assay was used to analyze the proteome dynamics of Ogura CMS cabbage line RM and its maintainer line RF during floral bud development to obtain insights into the mechanism underlying Ogura CMS in cruciferous crops.A total of 9162 proteins corresponding to 61464 peptides were identified in RM and RF floral buds.The proteomic fluctuation of RM was weaker than that of RF.Differences in protein expression between RM and RF gradually enlarged with floral bud development.Fifteen continually up-regulated and eight continually down-regulated proteins were found in RM relative to RF throughout floral bud development.Differentially expressed proteins between RM and RF during floral bud development were implicated in the endoplasmic reticulum(ER)-associated protein processing pathway,in which most of them exhibited down-regulated expression in RM.These data suggest that ER-associated protein processing may be involved in pollen abortion in Ogura CMS cabbage by inhibiting the expression of critical factors.Our findings not only deepen the understanding of the molecular mechanisms of Ogura CMS in cruciferous crops but also provide better guidance for applying Ogura CMS in the hybrid breeding of cruciferous crops.

关键词： Ogura cytoplasmic male sterility(Ogura CMS) Cabbage Data-independent acquisition(DIA) Parallel reaction monitoring(PRM) Pollen development

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Engineering disease-resistant plants with alternative translation efficiency by switching u ORF types through CRISPR

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Science China Life Sciences 2024年第8期 1715-1726页

作者： Jingjing Tian Zhijuan Tang Ruixia Niu Yulu Zhou Dan Yang Dan Chen Ming Luo Rui Mou Meng Yuan Guoyong Xu National Key laboratory of Crop genetic Improvement National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural University State Key laboratory of Hybrid Rice Institute for Advanced Studies (IAS)Wuhan University Hubei Hongshan laboratory

Engineering disease-resistant plants can be a powerful solution to the issue of food security.However,it requires addressing two fundamental questions:what genes to express and how to control their expressions.To find a solution,we screen CRISPR-edited upstream open reading frame(u ORF) variants in rice,aiming to optimize translational control of disease-related genes.By switching u ORF types of the 5′-leader from Arabidopsis TBF1,we modulate the ribosome accessibility to the downstream firefly luciferase.We assume that by switching u ORF types using CRISPR,we could generate u ORF variants with alternative translation efficiency(CRISPR-a Tr E-u ORF).These variants,capable of boosting translation for resistance-associated genes and dampening it for susceptible ones,can help pinpoint previously unidentified genes with optimal expression levels.To test the assumption,we screened edited u ORF variants and found that enhanced translational suppression of the plastic glutamine synthetase 2 can provide broad-spectrum disease resistance in rice with minimal fitness costs.This strategy,which involves modifying u ORFs from none to some,or from some to none or different ones,demonstrates how translational agriculture can speed up the development of disease-resistant crops.This is vital for tackling the food security challenges we face due to growing populations and changing climates.

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