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Constructing the metabolic network of wheat kernels based on structure-guided chemical modification and multi-omics data

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Journal of genetics and Genomics 2024年第7期51卷 714-722页

作者： Zhitao Tian Jingqi Jia Bo Yin Wei Chen national Key Laboratory of Crop genetic Improvement and national center of plant gene research(Wuhan) Huazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan Laboratory WuhanHubei 430070China

Metabolic network construction plays a pivotal role in unraveling the regulatory mechanism of biological activities,although it often proves to be challenging and labor-intensive,particularly with non-model *** this study,we develop a computational approach that employs reaction models based on the structure-guided chemical modification and related compounds to construct a metabolic network in *** construction results in a comprehensive structure-guided network,including 625 identified metabolites and additional 333 putative reactions compared with the Kyoto Encyclopedia of genes and Genomes *** a combination of gene annotation,reaction classification,structure similarity,and correlations from transcriptome and metabolome analysis,a total of 229 potential genes related to these reactions are identified within this *** validate the network,the functionality of a hydroxycinnamoyltransferase(TraesCS3D01G314900)for the synthesis of polyphenols and a rhamnosyltransferase(TraesCS2D01G078700)for the modification of flavonoids are verified through in vitro enzymatic studies and wheat mutant tests,*** research thus supports the utility of structure-guided chemical modification as an effective tool in identifying causal candidate genes for constructing metabolic networks and further in metabolomic genetic studies.

关键词： Metabolic network Chemical modification genetic study Wheat kernel Multi-omics

The genetic basis and process of inbreeding depression in an elite hybrid rice

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Science China(Life Sciences) 2024年第8期67卷 1727-1738页

作者： Xiaodong Xu Yawen Xu Jian Che Xu Han Zhengji Wang Xianmeng Wang Qinghua Zhang Xu Li Qinglu Zhang Jinghua Xiao Xianghua Li Qifa Zhang Yidan Ouyang national Key Laboratory of Crop genetic Improvement and national Centre of plant gene research(Wuhan) Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Inbreeding depression refers to the reduced performance arising from increased homozygosity,a phenomenon that is the reverse of heterosis and exists among plants and *** a natural self-pollinated crop with strong heterosis,the mechanism of inbreeding depression in rice is largely *** understand the genetic basis of inbreeding depression,we constructed a successive inbreeding population from the F_(2)to F_(4)generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each *** expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle,11 for primary branches,and 12 for secondary branches,and these loci constitute the main correlation between heterosis and inbreeding ***,the genetic basis of inbreeding depression is also distinct from that of heterosis,such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected ***,two-locus interactions may change the extent and direction of the depression effects of the target loci,and overall interactions would promote inbreeding depression among *** an F_(2:3)variation population,the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after *** found inconsistent or various degrees of background depression from the F_(2)to F_(3)generation assuming different genotypes of the target locus,which may affect the actual depression effect of the locus due to *** results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms,which expand our understanding of the whole-genome architecture of inbreeding depression.

关键词： rice inbreeding depression spikelet development dominance segregation distortion epistasis

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The OsCLV2s-OsCRN1 co-receptor regulates grain shape in rice

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Journal of genetics and Genomics 2024年第7期51卷 691-702页

作者： Xingxing Li Meng-en Wu Juncheng Zhang Jingyue Xu Yuanfei Diao Yibo Li national Key Laboratory of Crop genetic Improvement and national Centre of plant gene research(Wuhan) Huazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan Laboratory WuhanHubei 430070China

The highly conserved CLV–WUS negative feedback pathway plays a decisive role in regulating stem cell maintenance in shoot and floral meristems in higher plants,including Arabidopsis,rice,maize,and ***,we find significant natural variations in the OsCLV2c,OsCLV2d,and OsCRN1 loci in a genome-wide association study of grain shape in ***2a,OsCLV2c,OsCLV2d,and OsCRN1 negatively regulate grain length–width ratio and show distinctive geographical distribution,indica–japonica differentiation,and artificial selection ***,OsCLV2a and OsCRN1 interact biochemically and genetically,suggesting that the two components function in a complex to regulate grain shape of ***,the genetic contributions of the haplotypes combining OsCLV2a,OsCLV2c,and OsCRN1 are significantly higher than those of each single gene alone in controlling key yield *** findings identify two groups of receptor-like kinases that may function as distinct co-receptors to control grain size in rice,thereby revealing a previously unrecognized role of the CLV class genes in regulating seed development and proposing a framework to understand the molecular mechanisms of the CLV–WUS pathway in rice and other crops.

关键词： Rice Grain shape OsCLV2s OsCRN1 Natural variations Indica-japonica differentiation

Gibberellin promotes cambium reestablishment during secondary vascular tissue regeneration after girdling in an auxin-dependent manner in Populus

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Journal of Integrative plant Biology 2024年第1期66卷 86-102页

作者： Yufei Zhang Lingyan Wang Yuexin Wu Donghui Wang Xin‐Qiang He State Key Laboratory of Protein and plant gene research School of Life SciencesPeking UniversityBeijing 100871China

Secondary vascular tissue(SVT)development and regeneration are regulated by *** this study,we used an in vitro SVT regeneration system to demonstrate that gibberellin(GA)treatment significantly promotes auxin-induced cambium *** GA content by overexpressing or knocking down ent-kaurene synthase(KS)affected secondary growth and SVT regeneration in *** poplar DELLA gene GIBBERELLIC ACID INSENSITIVE(PtoGAI)is expressed in a specific pattern during secondary growth and cambium regeneration after *** of PtoGAI disrupted poplar growth and inhibited cambium regeneration,and the inhibition of cambium regeneration could be partially restored by GA *** analysis of the PtaDR5:GUS transgenic plants,the localization of PIN-FORMED 1(PIN1)and the expression of auxin-related genes found that an additional GA treatment could enhance the auxin response as well as the expression of PIN1,which mediates auxin transport during SVT *** together,these findings suggest that GA promotes cambium regeneration by stimulating auxin signal transduction.

关键词： auxin cambium gibberellin Populus secondary vascular tissue regeneration

Guardian of the rice:Unveiling OsSSP1 for broad-spectrum disease resistance

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Molecular plant 2024年第7期17卷 996-998页

作者： You-Jin Lim Yong-Hwan Lee research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Department of Agricultural Biotechnology Seoul National UniversitySeoul 08826Republic of Korea interdisciplinary Program in Agricultural Genomics Center for Fungal Genetic ResourcesPlant Immunity Research Centerand Center for Plant Microbiome ResearchSeoul National UniversitySeoul 08826Republic of Korea

plants are continuously exposed to numerous biotic stresses throughout their *** arms race-driven coevolution with pathogens,plants have developed sophisticated immune systems,including pathogen-associated molecular pattern(PAMP)-triggered immunity(PTI)and effector-triggered immunity(ETI).PTI is initiated by the binding of danger signals to extracellular membrane-localized receptors calledpattern recognition receptors(PRRs).PTI triggers responses,including reactive oxygen species(ROS)bursts and the expression of defenseassociated ***,pathogens adapted to PTl secrete virulence proteins,effectors,to aid colonization,and ETl is then triggered by the recognition of these effectors by resistance proteins with a nucleotide-binding domain leucinerich repeat receptor(NLR).To circumvent this immune response,pathogens secrete various effectors into the host intracellular region and induce effector-triggered susceptibility(Zhou and Zhang.,2020).Currently,research on plant immunity has been primarily focused on plasma membrane and cytoplasmlocalized proteins,including oligomeric NLRs,resistosomes,and the secretion mechanisms of cytoplasmic effectors.

关键词： immunity resistance Guard

genetic analysis and fine mapping of a grain size QTL in the smallgrain sterile rice line Zhuo201S

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Journal of Integrative Agriculture 2024年第7期23卷 2155-2163页

作者： Bin Lei Jiale Shao Feng Zhang Jian Wang Yunhua Xiao Zhijun Cheng Wenbang Tang Jianmin Wan College of Agronomy Hunan Agricultural UniversityChangsha 410128China national Key Facility for Crop gene Resources and genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory for Crop genetics and Germplasm Enhancement/Jiangsu plant gene Engineering research center Nanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China

The development and application of the small-grain rice sterile line Zhuo201S(Z201S)has demonstrated its potential for mechanized hybrid rice seed production,leading to significant cost ***,the molecular mechanism responsible for the small-grain size characteristic of Z201S remains *** this study,we conducted a genetic analysis using near-isogenic lines constructed from Z210S,a small-grain rice sterile line,and R2115,a normal-grain *** results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain *** mapping,we localized the causal gene to the short arm of chromosome 2,within a 113 kb physical region delimited by the molecular markers S2-4-1 and *** analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene,suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.

关键词： rice grain size map-based cloning

The Os14-3-3 family genes regulate grain size in rice

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Journal of genetics and Genomics 2024年第4期51卷 454-457页

作者： Yingying Song Huaizhou Yang Wenran Zhu Huili Wang Juncheng Zhang Yibo Li national Key Laboratory of Crop genetic Improvement and national Centre of plant gene research(Wuhan) Huazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan Laboratory WuhanHubei 430070China

Rice is one of the most important cereal crops in the world,providing food for more than half of the global population;therefore,increasing grain yield is a major goal of rice *** grain yield is largely dependent on grain size,which is specified by its three dimensions(grain length,width,and thickness)and by the degree of grain filling(Xing and Zhang,2010;Fan and Li,2019).Grain size is an important agronomic trait for stable yield,appearance,milling quality,and domestication in rice that is controlled by multiple ***,discovering more genes regulating grain size for understanding the regulatory mechanisms underlying natural variations is important in crop molecular breeding(Zuo and Li,2014).

关键词： breeding crops grain

Rice gene OsUGT75A regulates seedling emergence under deep-sowing conditions

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The Crop Journal 2024年第1期12卷 133-141页

作者： Jia Zhao Siyu Liu Xiaoqian Zhao Zhibo Huang Shan Sun Zixuan Zeng Yongqi He Zhoufei Wang The Laboratory of Seed Science and Technology Guangdong Key Laboratory of Plant Molecular BreedingNational Engineering Research Center of Plant Space BreedingSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field *** we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot *** of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing *** of free abscisic acid(ABA)and jasmonates(JA)were higher in shoots of OsUGT75A mutants than in those of wild-type plants,and OsUGT75A mutants were more sensitive to ABA and JA *** shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in *** extension by OsUGT75A is achieved mainly by promotion of cell *** elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice ***75A acts to increase seedling emergence under deep-sowing conditions.

关键词： Abscisic acid Deep-sowing Jasmonic acid Rice Shoot length

Haploids can be induced in knockout mutants of OsPLA1,but not OsDMP3 or OsDMP6,in rice

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The Crop Journal 2024年第1期12卷 213-221页

作者： Zongkai Liu Yu Zhong Xiaolong Qi Tai An Shuwei Guo Dong Wang Yuwen Wang Bin Feng Zuofeng Zhu Shaojiang Chen Chenxu Liu national Maize Improvement center Engineering Research Center of Ministry of EducationChina Agricultural UniversityBeijing 100193China national center for Evaluation of Agricultural Wild plants(Rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Doubled haploid(DH)technology is an important tool in crop breeding because it can significantly accelerate the breeding ***1/MATL/NLD and ZmDMP are two key genes controlling haploid induction(HI)in maize,exhibiting a synergistic ***,it is unknown whether knock out of ZmDMP orthologs can stimulate HI in *** this study,a ZmPLA1 ortholog(OsPLA1)and two ZmDMP orthologs(OsDMP3 and OsDMP6)were identified in *** three genes encode plasma membrane-localized proteins and were highly expressed in mature *** of OsPLA1 in both Minghui 63 and Nipponbare resulted in reduced seed setting rate(SSR)and caused *** osdmp3,osdmp6 and the double mutant failed to trigger HI independently,nor increased the haploid induction rate(HIR)when combined with *** pollinations operations of QX654A with the ospla1 mutant significantly improve SSR,while reducing ***-seq profiling of mature ospla1 mutant anthers indicated that a large number of differentially expressed genes(DEGs)were enriched in redox homeostasis and lipid metabolic GO terms,plant hormone signal transduction,and MAPK signaling *** findings provide important insights towards construction of an efficient DH breeding technology and study of the molecular mechanism of HI in rice.

关键词： Doubled haploid breeding Haploid induction Mutation anlaysis Rice