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Characterization of the pheromone receptors in Mythimna loreyi reveals the differentiation of sex pheromone recognition in Mythimna species

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Insect Science 2024年第1期31卷 173-185页

作者： Chan Wang Lei Liu Tian-Yu Huang Yu Zhang Yang Liu Gui-Rong Wang State Key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina Guangdong laboratory of Lingnan Modern Agriculture ShenzhenGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina School of Forestry Northeast Forestry UniversityHarbinChina Key laboratory of Biohazard Monitoring Green Prevention and Control for Artificial GrasslandMinistry of Agriculture and Rural AffairsInstitute of Grassland Research of Chinese Academy of Agricultural SciencesInner Mongolia HohhotChina

Pheromone receptors(PRs)are key proteins in the molecular mechanism of pheromone recognition,and exploring the functional differentiation of PRs between closely related species helps to understand the evolution of moth mating systems.Pheromone components of the agricultural pest Mythimna loreyi have turned into(Z)-9-tetradecen-1-yl acetate(Z9-14:OAc),(Z)-7-dodecen-1-yl acetate(Z7-12:OAc),and(Z)-11-hexadecen-1-yl acetate,while the composition differs from that of M.separata in the genus Mythimna.To understand the molecular mechanism of pheromone recognition,we sequenced and analyzed antennal transcriptomes to identify 62 odorant receptor(OR)genes.The expression levels of all putative ORs were analyzed using differentially expressed gene analysis.Six candidate PRs were quantified and functionally characterized in the Xenopus oocytes system.MlorPR6 and MlorPR3 were determined to be the receptors of major and minor components Z9-14:OAc and Z7-12:OAc.MlorPR1 and female antennae(FA)-biased MlorPR5 both possessed the ability to detect pheromones of sympatric species,including(Z,E)-9,12-tetradecadien-1-ol,(Z)-9-tetradecen-1-ol,and(Z)-9-tetradecenal.Based on the comparison of PR functions between M.loreyi and M.separata,we analyzed the differentiation of pheromone recognition mechanisms during the evolution of the mating systems of 2 Mythimna species.

关键词： antennal transcriptome Mythimna loreyi pheromone receptor sex pheromone Xenopus oocyte

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An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs

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Science China(Life Sciences) 2024年第6期67卷 1133-1154页

作者： Yang Zhang Mengyao Wang Zhenguo Li Xuan Yang Keqin Li Ao Xie Fang Dong Shihan Wang Jianbing Yan Jianxiao Liu National Key laboratory of Crop genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Key laboratory of Smart Farming for Agricultural Animals Huazhong Agricultural UniversityWuhan 430070China Hubei Key laboratory of Agricultural Bioinformatics Huazhong Agricultural UniversityWuhan 430070China College of Informatics Huazhong Agricultural UniversityWuhan 430070China College of Life Sciences Nankai UniversityTianjin 300071China

Detecting genes that affect specific traits(such as human diseases and crop yields)is important for treating complex diseases and improving crop quality.A genome-wide association study(GWAS)provides new insights and directions for understanding complex traits by identifying important single nucleotide polymorphisms.Many GWAS summary statistics data related to various complex traits have been gathered recently.Studies have shown that GWAS risk loci and expression quantitative trait loci(e QTLs)often have a lot of overlaps,which makes gene expression gradually become an important intermediary to reveal the regulatory role of GWAS.In this review,we review three types of gene-trait association detection methods of integrating GWAS summary statistics and e QTLs data,namely colocalization methods,transcriptome-wide association study-oriented approaches,and Mendelian randomization-related methods.At the theoretical level,we discussed the differences,relationships,advantages,and disadvantages of various algorithms in the three kinds of gene-trait association detection methods.To further discuss the performance of various methods,we summarize the significant gene sets that influence highdensity lipoprotein,low-density lipoprotein,total cholesterol,and triglyceride reported in 16 studies.We discuss the performance of various algorithms using the datasets of the four lipid traits.The advantages and limitations of various algorithms are analyzed based on experimental results,and we suggest directions for follow-up studies on detecting gene-trait associations.

关键词： gene-trait association GWAS eQTL colocalization transcriptome-wide association study(TWAS) Mendelian randomization(MR)

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Exploring noncoding variants in genetic diseases:from detection to functional insights

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Journal of genetics and Genomics 2024年第2期51卷 111-132页

作者： Ke Wu Fengxiao Bu Yang Wu Gen Zhang Xin Wang Shunmin He Mo-Fang Liu Runsheng Chen Huijun Yuan Institute of Rare Diseases West China Hospital of Sichuan UniversityChengduSichuan 610041China Key laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiang 310024China Key laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key laboratory of Molecular Biology State Key Laboratory of Cell BiologyShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China

Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.

关键词： Noncoding variation genetic disease Research approach Challenge

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Single-cell transcriptomic atlas of goat ovarian aging

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Journal of Animal Science and Biotechnology 2024年第1期15卷 146-161页

作者： Dejun Xu Shuaifei Song Fuguo Wang Yawen Li Ziyuan Li Hui Yao Yongju Zhao Zhongquan Zhao Chongqing Key laboratory of Herbivore Science College of Animal Science and TechnologySouthwest UniversityChongqing 400715China

Background The ovaries are one of the first organs that undergo degenerative changes earlier in the aging process,and ovarian aging is shown by a decrease in the number and quality of oocytes.However,little is known about the molecular mechanisms of female age-related fertility decline in different types of ovarian cells during aging,especially in goats.Therefore,the aim of this study was to reveal the mechanisms driving ovarian aging in goats at single-cell resolution.Results For the first time,we surveyed the single-cell transcriptomic landscape of over 27,000 ovarian cells from newborn,young and aging goats,and identified nine ovarian cell types with distinct gene-expression signatures.Functional enrichment analysis showed that ovarian cell types were involved in their own unique biological processes,such as Wnt beta-catenin signalling was enriched in germ cells,whereas ovarian steroidogenesis was enriched in granulosa cells(GCs).Further analysis showed that ovarian aging was linked to GCs-specific changes in the antioxidant system,oxidative phosphorylation,and apoptosis.Subsequently,we identified a series of dynamic genes,such as AMH,CRABP2,THBS1 and TIMP1,which determined the fate of GCs.Additionally,FOXO1,SOX4,and HIF1A were identified as significant regulons that instructed the differentiation of GCs in a distinct manner during ovarian aging.Conclusions This study revealed a comprehensive aging-associated transcriptomic atlas characterizing the cell typespecific mechanisms during ovarian aging at the single-cell level and offers new diagnostic biomarkers and potential therapeutic targets for age-related goat ovarian diseases.

关键词： Goat Granulosa cells Ovarian aging Single-cell transcriptomic

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Heat-inducible SlWRKY3 confers thermotolerance by activating the SlGRXS1 gene cluster in tomato

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Horticultural Plant Journal 2024年第2期10卷 515-531页

作者： Ying Wang Wenxian Gai Liangdan Yuan Lele Shang Fangman Li Zhao Gong Pingfei Ge Yaru Wang Jinbao Tao Xingyu Zhang Haiqiang Dong Yuyang Zhang National Key laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops Huazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan laboratory WuhanHubei 430070China

High temperature stress is one of the major environmental factors that affect the growth and development of plants. Although WRKY transcription factors play a critical role in stress responses, there are few studies on the regulation of heat stress by WRKY transcription factors,especially in tomato. Here, we identified a group I WRKY transcription factor, SlWRKY3, involved in thermotolerance in tomato. First, SlWRKY3 was induced and upregulated under heat stress. Accordingly, overexpression of SlWRKY3 led to an increase, whereas knock-out of SlWRKY3 resulted in decreased tolerance to heat stress. Overexpression of SlWRKY3 accumulated less reactive oxygen species(ROS), whereas knock-out of SlWRKY3 accumulated more ROS under heat stress. This indicated that SlWRKY3 positively regulates heat stress in tomato. In addition,SlWRKY3 activated the expression of a range of abiotic stress-responsive genes involved in ROS scavenging, such as a SlGRXS1 gene cluster.Further analysis showed that SlWRKY3 can bind to the promoters of the SlGRXS1 gene cluster and activate their expression. Collectively, these results imply that SlWRKY3 is a positive regulator of thermotolerance through direct binding to the promoters of the SlGRXS1 gene cluster and activating their expression and ROS scavenging.

关键词： Tomato WRKY transcription factor SlWRKY3 Thermotolerance SlGRXS1 gene cluster Abiotic stress

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Distant cousins come to ABP1’s rescue

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Science China(Life Sciences) 2024年第1期67卷 219-220页

作者： Andre Kuhn Dolf Weijers laboratory of Biochemistry Wageningen UniversityStippeneng 46708WE Wageningenthe Netherlands

There are few plant processes that are not in one way or another influenced by the auxin signaling molecule.The many roles auxin plays in plants have inspired a range of investigations towards understanding its mechanisms of action.In recent years and decades,genetic analysis in the flowering plant Arabidopsis has been immensely successful in bringing a nuclear response mechanism to light(reviewed in Weijers and Wagner,2016).This system,the nuclear auxin pathway(NAP),acts by regulating gene expression,and when its components are mutated,growth and development is strongly disturbed(Weijers and Wagner,2016).

关键词： bringing disturbed Arabidopsis

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Plant gene co-expression defines the biosynthetic pathway of neuroactive alkaloids

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Molecular Plant 2024年第3期17卷 372-374页

作者： Fang Liu' Alisdair R.Fernie Youjun Zhang Key laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of Sciences100101 BeijingChina Max Planck Institute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center for Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria University of Chinese Academy of Sciences 100049 BeijingChina

Transcriptomes comprise gene co-expression clustersor modules,showcasing distinct patterns of coordinated expression among groups of genes across independent biological samples(Serin et al.,2016).The"guilt-by-association"hypothesis suggests the functional importance of these clusters;for example,co-expressed genes associated with metabolism typically contain genes encoding several enzymes associated with the same pathways.

关键词： metabolism alkaloids

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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 conditions.Here we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot length.expression of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing conditions.Levels 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 treatments.Reduced shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in shoots.Shoot extension by OsUGT75A is achieved mainly by promotion of cell elongation.An elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice accessions.OsUGT75A acts to increase seedling emergence under deep-sowing conditions.

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

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Dynamics and genetic regulation of macronutrient concentrations during grain development in maize

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Journal of Integrative Agriculture 2024年第3期23卷 781-794页

作者： Pengcheng Li Shuangyi Yin Yunyun Wang Tianze Zhu Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Chenwu Xu Zefeng Yang Jiangsu Key laboratory of Crop genetics and Physiology/Key laboratory of Plant Functional Genomics Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Agricultural CollegeYangzhou UniversityYangzhou 225009China Jiangsu Co-lnnovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009China

Nitrogen(N), phosphorus(P), and potassium(K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality. The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown. In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination. We then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations. Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients. Unconditional quantitative trait locus(QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively. Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations. By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRMZM2G371058 encoding a Doftype zinc finger DNA-binding family protein, which was associated with the N concentration, and GRMZM2G113967encoding a CBL-interacting protein kinase, which was related to the K concentration. The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

关键词： maize nutrient concentration unconditional QTL mapping conditional QTL mapping dynamic trait

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Identification of LRRC46 as a novel candidate gene for high myopia

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Science China Life Sciences 2024年

作者： Lingxi Jiang Chao Dai Yao Wei Bo Zhao Qi Li Zhengzheng Wu Liang Zou Zimeng Ye Zhenglin Yang Lulin Huang Yi Shi Sichuan Provincial Key laboratory for Human Disease gene Study and the Center for Medical genetics Department of Laboratory Medicine Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Department of Ophthalmology Sichuan Provincial People's Hospital University of Electronic Science and Technology of China School of Food and Bioengineering Chengdu University School of Medicine University of Sydney Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026) Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital Jinfeng laboratory

High myopia(HM) is the primary cause of blindness, with the microstructural organization and composition of collagenous fibers in the cornea and sclera playing a crucial role in the biomechanical behavior of these tissues. In a previously reported myopic linkage region,MYP5(17q21–22), a potential candidate gene, LRRC46(c.C235T, p.Q79X), was identified in a large Han Chinese pedigree. LRRC46 is expressed in various eye tissues in humans and mice, including the retina, cornea, and sclera. In subsequent cell experiments, the mutation(c.C235T) decreased the expression of LRRC46 protein in human corneal epithelial cells(HCE-T). Further investigation revealed that Lrrc46–/–mice(KO) exhibited a classical myopia phenotype. The thickness of the cornea and sclera in KO mice became thinner and more pronounced with age, the activity of limbal stem cells decreased, and microstructural changes were observed in the fibroblasts of the sclera and cornea. We performed RNA-seq on scleral and corneal tissues of KO and normal control wild-type(WT) mice, which indicated a significant downregulation of the collagen synthesis-related pathway(extracellular matrix, ECM) in KO mice. Subsequent in vitro studies further indicated that LRRC46, a member of the important LRR protein family, primarily affected the formation of collagens. This study suggested that LRRC46 is a novel candidate gene for HM, influencing collagen protein VIII(Col8a1) formation in the eye and gradually altering the biomechanical structure of the cornea and sclera, thereby promoting the occurrence and development of HM.

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