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Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)

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Zoological Research 2024年第2期45卷 329-340页

作者： Shao-Xuan Wu Qi-Fan Zeng Wen-Tao Han Meng-Ya Wang Hui Ding Ming-Xuan Teng Ming-Yi Wang Pei-Yu Li Xin Gao Zhen-Min Bao Bo Wang Jing-Jie Hu MOE Key laboratory of marine Genetics and breeding College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan ProvinceSanya Oceanographic InstitutionOcean University of ChinaQingdaoShandong/SanyaHainan 266100/572025China Hainan Seed Industry laboratory SanyaHainan 572025China Southern marine Science and Engineer Guangdong laboratory GuangzhouGuangdong 511458China

The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.

关键词： Plectropomus leopardus Whole-genome resequencing Growth Haplotype reference panel Single nucleotide polymorphisms

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Comparative Transcriptome Analysis of Shell-Matrix-Protein Genes and Observation of the Shell Microstructure in the Deep-Sea Clam Calyptogena marissinica

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Journal of Ocean University of China 2024年第3期23卷 797-810页

作者： SHI Yu LIU Dongting YAO Gaoyou HE Maoxian CAS Key laboratory of tropical marine Bio-resources and Ecology Guangdong Provincial Key Laboratory of Applied Marine BiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Southern marine Science and engineering Guangdong laboratory(Guangzhou) Guangzhou 511458China University of Chinese Academy of Sciences Beijing 100049China

The deep-sea clam Calyptogena marissinica is widely distributed in the Haima cold seep ecosystem on the northwes-tern slope of the South China Sea with low pH values,low temperature and high pressure.Limited information is available on the biomineralization of this species.In this research,we generated a comprehensive transcript dataset of C.marissinica’s mantle tissue,and a total of 19821 unigenes were assembled.Fourteen shell matrix proteins(SMP)-related genes were identified.The qPCR results showed that four out of six prismatic matrix genes(MSP2,MSP5,prisilkin-39,and shematrin),four out of the six nacreous matrix genes(perlucin,pif,pif97,and papilin),and two extrapallial fluid proteins(SPARC and calmodulin)were significantly expressed in the mantle.Both the nacreous and the prismatic layers are chrysanthemum-shaped,which are stacked on the top of each other to form a laminated nacreous structure.The alignment and phylogenetic analysis of MSP-5,Prisilkin-39,Perlucin,and Pif homologues showed that some amino acids of C.marissinica that differed from those detected in other molluscs may cause the different shape of the nacreous and prismatic layers,but do not lead to a change in the species’evolutionary status.These results indicated the conservation of the functions of SMP-related genes in C.marissinica,and the specific shape of the prismatic and nacreous layers of this deep-sea mollusc,which will contribute to the research on the molecular regulation mechanisms of biomineralization in C.marissinica and provide a new perspective to investigate biomineralization in deep-sea clams in general.

关键词： transcriptome biomineralization mantle tissue shell Calyptogena marissinica

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The gene encoding flavonol synthase contributes to lesion mimic in wheat

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The Crop Journal 2024年第3期12卷 814-825页

作者： Tingting Dong Hongchun Xiong Huijun Guo Yongdun Xie Linshu Zhao Jiayu Gu Huiyuan Li Shirong Zhao Yuping Ding Xiyun Song Luxiang Liu College of Life Sciences Key Laboratory of Major Crop Germplasm Innovation and Application in QingdaoQingdao Agricultural UniversityQingdao 266109ShandongChina State Key laboratory of Crop Gene resources and breeding/National engineering laboratory of Crop Molecular breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Lesion mimic often exhibits leaf disease-like symptoms even in the absence of pathogen infection,and is characterized by a hypersensitive-response(HR)that closely linked to plant disease resistance.Despite this,only a few lesion mimic genes have been identified in wheat.In this investigation,a lesion mimic wheat mutant named je0297 was discovered,showing no alteration in yield components when compared to the wild type(WT).Segregation ratio analysis of the F_(2)individuals resulting from the cross between the WT and the mutant revealed that the lesion mimic was governed by a single recessive gene in je0297.Using Bulked segregant analysis(BSA)and exome capture sequencing,we mapped the lesion mimic gene designated as lm6 to chromosome 6BL.Further gene fine mapping using 3315 F_(2)individuals delimited the lm6 within a 1.18 Mb region.Within this region,we identified 16 high-confidence genes,with only two displaying mutations in je0297.Notably,one of the two genes,responsible for encoding flavonol synthase,exhibited altered expression levels.Subsequent phenotype analysis of TILLING mutants confirmed that the gene encoding flavonol synthase was indeed the causal gene for lm6.Transcriptome sequencing analysis revealed that the DEGs between the WT and mutant were significantly enriched in KEGG pathways related to flavonoid biosynthesis,including flavone and flavonol biosynthesis,isoflavonoid biosynthesis,and flavonoid biosynthesis pathways.Furthermore,more than 30 pathogen infection-related(PR)genes exhibited upregulation in the mutant.Corresponding to this expression pattern,the flavonoid content in je0297 showed a significant decrease in the 4^(th)leaf,accompanied by a notable accumulation of reactive oxygen,which likely contributed to the development of lesion mimic in the mutant.This investigation enhances our comprehension of cell death signaling pathways and provides a valuable gene resource for the breeding of disease-resistant wheat.

关键词： Lesion mimic mutant Wheat Gene mapping Flavonol synthase gene Flavonoid

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Linking coral fluorescence phenotypes to thermal bleaching in the reef-building Galaxea fascicularis from the northern South China Sea

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marine Life Science & Technology 2024年第1期6卷 155-167页

作者： Sanqiang Gong Jiayuan Liang Gang Li Lijia Xu Yehui Tan Xinqing Zheng Xuejie Jin Kefu Yu Xiaomin Xia Key laboratory of tropical marine Bio-resources and Ecology&Guangdong Provincial Key laboratory of Applied marine Biology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Southern marine Science and engineering Guangdong laboratory(Guangzhou) Guangzhou 510301China Coral Reef Research Center of China Guangxi UniversityNanning 53004China South China Institute of Environmental Sciences The Ministry of Ecology and Environment of PRCGuangzhou 510530China Third Institute of Oceanography Ministry of Natural ResourcesXiamen 361005China

Coral fluorescence phenotypes have been suggested as an adaptation to a broad range of environmental conditions,yet the mechanisms linking thermal bleaching tolerance in reef-building coral populations,associated with fluorescence phenotypes due to GFP-like proteins,remains unclear.In this study,the relationship between the thermal sensitivity and phenotypic plasticity of corals was investigated using two phenotypes of Galaxea fascicularis,green and brown.The results reveal that brown G.fascicularis was more susceptible to bleaching than green G.fascicularis when exposed to a higher growth temperature of 32℃.Both phenotypes of G.fascicularis were associated with the thermotolerant Symbiodiniaceae symbiont,Durusdinium trenchii.However,the brown G.fascicularis showed a significant decrease in Symbiodiniaceae cell density and a significant increase in pathogenic bacteria abundance when the growth temperature was raised from 29 to 32℃.The physiological traits and transcriptomic profiles of Symbiodiniaceae were not notably affected,but there were differences in the transcriptional levels of certain genes between the two phenotype hosts of G.fascicularis.Under heat stress of 32℃,the gene encoding green fluorescent protein(GFP)-like and chromosome-associated proteins,as well as genes related to oxidative phosphorylation,cell growth and death showed lower transcriptional levels in the brown G.fascicularis compared to the green G.fascicularis.Overall,the results demonstrate that the green form of G.fascicularis is better able to tolerate ocean warming and defend against pathogenic bacteria,likely due to higher gene transcription levels and defense ability.

关键词： Fluorescence phenotype Thermal bleaching Microbiome Galaxea fascicularis Ocean warming

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Revealing the role of CCoAOMT1: fine-tuning bHLH transcription factors for optimal anther development

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Science China(Life Sciences) 2024年第3期67卷 565-578页

作者： Zesen Lai Jianzheng Wang Ying Fu Menghan Wang Hong Ma Shiqing Peng Fang Chang State Key laboratory of Genetic engineering Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity SciencesInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China School of tropical Agriculture and Forestry Agriculture-Rural Affairs and Rural RevitalizationHainan UniversityHaikou 570228China Key laboratory of Biology and Genetic resources of tropical Crops Ministry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou 571101China Department of Biology Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPA 16802USA

The tapetum,a crucial innermost layer encompassing male reproductive cells within the anther wall,plays a pivotal role in normal pollen development.The transcription factors (TFs) bHLH010/089/091 redundantly facilitate the rapid nuclear accumulation of DYSFUNCTIONAL TAPETUM 1,a gatekeeper TF in the tapetum.Nevertheless,the regulatory mechanisms governing the activity of bHLH010/089/091 remain unknown.In this study,we reveal that caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1) is a negative regulator affecting the nuclear localization and function of bHLH010 and bHLH089,probably through their K259 site.Our findings underscore that CCoAOMT1 promotes the nuclear export and degradation of bHLH010 and bHLH089.Intriguingly,elevated CCoAOMT1 expression resulted in defective pollen development,mirroring the phenotype observed in bhlh010 bhlh089 mutants.Moreover,our investigation revealed that the K259A mutation in the bHLH089 protein disrupted its translocation from the nucleus to the cytosol and impeded its degradation induced by CCoAOMT1.Importantly,transgenic plants with the probHLH089::bHLH089^(K259A)construct failed to rescue proper pollen development or gene expression in bhlh010 bhlh089 mutants.Collectively,these findings emphasize the need to maintain balanced TF homeostasis for male fertility.They firmly establish CCoAOMT1 as a pivotal regulator that is instrumental in achieving equilibrium between the induction of the tapetum transcriptional network and ensuring appropriate anther development.

关键词： anther development nuclear localization bHLH O-methyltransferase transcription factor homeostasis

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Differences in spring precipitation over southern China associated with multiyear La Ni?a events

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Acta Oceanologica Sinica 2024年第2期43卷 1-10页

作者： Guangliang Li Licheng Feng Wei Zhuang Fei Liu Ronghua Zhang Cuijuan Sui National marine Environmental Forecasting Center Ministry of Natural ResourcesBeijing 100081China State Key laboratory of marine Environmental Science College of Ocean and Earth SciencesXiamen UniversityXiamen 361102China Southern marine Science and engineering Guangdong laboratory(Zhuhai) Zhuhai 519082China Key laboratory of tropical Atmosphere-Ocean System of Ministry of Education/School of Atmospheric Sciences Sun Yat-Sen UniversityZhuhai 519082China School of marine Sciences Nanjing University of Information Science and TechnologyNanjing 210044China

Composite analyses were performed in this study to reveal the difference in spring precipitation over southern China during multiyear La Ni?a events during 1901 to 2015. It was found that there is significantly below-normal precipitation during the first boreal spring, but above-normal precipitation during the second year. The difference in spring precipitation over southern China is correlative to the variation in western North Pacific anomalous cyclone(WNPC), which can in turn be attributed to the different sea surface temperature anomaly(SSTA) over the tropical Pacific. The remote forcing of negative SSTA in the equatorial central and eastern Pacific and the local air-sea interaction in the western North Pacific are the usual causes of WNPC formation and maintenance.SSTA in the first spring is stronger than those in the second spring. As a result, the intensity of WNPC in the first year is stronger, which is more likely to reduce the moisture in southern China by changing the moisture transport, leading to prolonged precipitation deficits over southern China. However, the tropical SSTA signals in the second year are too weak to induce the formation and maintenance of WNPC and the below-normal precipitation over southern China. Thus, the variation in tropical SSTA signals between two consecutive springs during multiyear La Ni?a events leads to obvious differences in the spatial pattern of precipitation anomaly in southern China by causing the different WNPC response.

关键词： multiyear La Nina precipitation anomaly anomalous western North Pacific cyclone southern China

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Two polyoxovanadoborates with over 100 nuclei assembled from a {V14Co12B72} cluster

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Science China Chemistry 2024年第8期67卷 2578-2585页

作者： Shuang-Xue Wu Yu-Jiao Dong Yang Yang Chao Qin Chun-Yi Sun Wei Guan Xin-Long Wang Zhong-Min Su Key laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education Northeast Normal University School of Chemistry and Environmental engineering Changchun University of Science and Technology Key laboratory of Advanced Materials of tropical Island resources Hainan University

Combining theoretical prediction and experimental exploration, the first sandwich-type polyoxovanadoborate（POVB） with an odd number of nuclei, [V11B26O73（OH）10]8-（1）, was discovered under hydrothermal conditions. Density-functional theory（DFT）gives a rationalization for the existence of this structure and the structural feature is consistent with the {VNB2N+X}（X = 2, 4, 6, 8）general formula. Excitingly, when Co and 1,10-phenanthroline（phen） are introduced into the synthesis of vanadoborates system,a 100-nuclei [Co6（phen）10（H2O）8][V14Co12B72O144（OH）20]·28H2O（2） and a 102-nuclei [Co6（phen）14（H2O）4][V14Co12B72O144（OH）20]·23H2O（3） with the same core structure of [V14Co12B72]12-are obtained. The vase-shaped [V14Co12B72] polyanion is a multilayered sandwich-type structure containing seven distinct structural layers and is the largest known POVB. Furthermore, 2demonstrates exceptional thermal and chemical stability and serves as an efficient and stable catalyst for the photoreduction of carbon dioxide.

关键词： boronate metallic materials CO2 reduction density functional theory photocatalysis polyoxovanadoborates

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Striking a growth–defense balance:Stress regulators that function in maize development

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Journal of Integrative Plant Biology 2024年第3期66卷 424-442页

作者： Shiyi Xie Hongbing Luo Wei Huang Weiwei Jin Zhaobin Dong Maize engineering and Technology Research Center of Hunan Province College of AgronomyHunan Agricultural UniversityChangsha 410128China State Key laboratory of Maize Bio-breeding National Maize Improvement CenterFrontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijing 100193China Tianjin Key laboratory of Intelligent breeding of Major Crops Fresh Corn Research Center of BTHCollege of Agronomy&Resources and EnvironmentTianjin Agricultural UniversityTianjin 300384China

Maize(Zea mays)cultivation is strongly affected by both abiotic and biotic stress,leading to reduced growth and productivity.It has recently become clear that regulators of plant stress responses,including the phytohormones abscisic acid(ABA),ethylene(ET),and jasmonic acid(JA),together with reactive oxygen species(ROS),shape plant growth and development.Beyond their well established functions in stress responses,these molecules play crucial roles in balancing growth and defense,which must be finely tuned to achieve high yields in crops while maintaining some level of defense.In this review,we provide an in-depth analysis of recent research on the developmental functions of stress regulators,focusing specifically on maize.By unraveling the contributions of these regulators to maize development,we present new avenues for enhancing maize cultivation and growth while highlighting the potential risks associated with manipulating stress regulators to enhance grain yields in the face of environmental challenges.

关键词： stress regulators maize development ABA ET JA ROS

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BoMyrosinase plays an essential role in sulforaphane accumulation in response to selenite treatment in broccoli

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Horticultural Plant Journal 2024年第2期10卷 488-502页

作者： Qiuyun Wu Qi Wu Yuxiao Tian Chunyan Zhou Shuxiang Mao Junwei Wang Ke Huang College of Horticulture Hunan Agricultural UniversityChangshaHunan 410128China engineering Research Center for Horticultural Crop germplasm Creation and New Variety breeding Ministry of EducationChangshaHunan 410128China Key laboratory for Vegetable Biology of Hunan Province ChangshaHunan 410128China Key laboratory for Evaluation and Utilization of Gene resources of Horticultural Crops Ministry of Agriculture and Rural Affairs of ChinaChangshaHunan 410128China

Sulforaphane, a naturally specialized metabolite, plays significant roles in human disease prevention and plant defense. Myrosinase(MY) is a key gene responsible for the catalysis of sulforaphane formation, but the molecular mechanisms through which MY regulates sulforaphane biosynthesis in plants remains largely unknown. Here, we discovered that the change of sulforaphane content in broccoli sprouts caused by exogenous selenite treatments is positively related to BoMY expression. BoMY overexpression in the Arabidopsis thaliana tgg1 mutants could dramatically increase myrosinase activity and sulforaphane content in the rosette leaves of 35S::BoMY/tgg1 and rescue its phenotypes.Moreover, an obvious increase of myrosinase activity and sulforaphane content was displayed in transgenic BoMY-overexpressed broccoli lines.In addition, a 2 033 bp promoter fragment of BoMY was isolated. Yeast one-hybrid(Y1H) library screening experiment uncovered that one bHLH transcription factor, BoFAMA, could directly bind to BoMY promoter to activate its expression, which was further evidenced by Y1H assay and dual-luciferase reporter assay. BoFAMA is a selenite-responsive transcription factor that is highly expressed in broccoli leaves;its protein is solely localized to nucleus. Additionally, genetic evidence suggested that the knockdown of FAMA gene in Arabidopsis thaliana could significantly decrease sulforaphane yield by inhibiting the expression of myrosinase genes. Interestingly, exogenous selenite supply could partially restore the low level of sulforaphane content in transgenic Arabidopsis FAMA-silencing plants. Our findings uncover a novel function of FAMAMY module in the regulation of selenite-mediated sulforaphane synthesis and provide a new insights into the molecular mechanism by which selenite regulates the accumulation of sulforaphane in plants.

关键词： Brassica oleracea var.italica Myrosinase BoMY Sulforaphane Selenite treatment

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The UDP-glycosyltransferase OsUGT706D2 positively regulates cold and submergence stress tolerance in rice

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The Crop Journal 2024年第3期12卷 732-742页

作者： Qing Liu Lanlan Zhang Shuwei Lyu Hang Yu Wenjie Huang Liqun Jiang Jing Zhang Bingrui Sun Xingxue Mao Pingli Chen Junlian Xing Wenfeng Chen Zhilan Fan Shijuan Yan Chen Li Guangdong Key laboratory of New Technology in Rice breeding/Guangdong Rice engineering laboratory/Key laboratory of Genetics and breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsRice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina Guangdong Key laboratory for Crop germplasm resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

In a genome-wide association study,we identified a rice UDP-glycosyltransferase gene,OsUGT706D2,whose transcription was activated in response to cold and submergence stress and to exogenous abscisic acid(ABA).OsUGT706D2 positively regulated the biosynthesis of tricin-4’-O-(syringyl alcohol)ether-7-O-glucoside at both the transcriptional and metabolic levels.OsUGT706D2 mediated cold and submergence tolerance by modulating the expression of stress-responsive genes as well as the abscisic acid(ABA)signaling pathway.Gain of function of OsUGT706D2 increased cold and submergence tolerance and loss of function of OsUGT706D2 reduced cold tolerance.ABA positively regulated OsUGT706D2-mediated cold tolerance but reduced submergence tolerance.These findings suggest the potential use of OsUGT706D2 for improving abiotic stress tolerance in rice.

关键词： UDP-glycosyltransferase Rice Cold tolerance Submergence tolerance ABA

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