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Identification and characterization of GLOBE, a major gene controlling fruit shape and impacting fruit size and marketability in tomato

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Horticulture Research 2021年第1期8卷 1783-1797页

作者： Edgar Sierra-Orozco Reza Shekasteband Eudald Illa-Berenguer Ashley Snouffer Esther van der Knaap Tong Geon Lee Samuel F.Hutton University of Florida Gulf Coast Research and Education Center14625 County Road 672WimaumaFL 33598USA North Carolina State University Department of Horticultural ScienceMountain Horticultural Crops Research and Extension Center455 Research DriveMills RiverNC 28759USA University of Georgia Center for Applied Genetic Technologies111 Riverbend RoadAthensGA 30602USA University of Georgia Department of Horticulture1111 Plant Sciences BldgAthensGA 30602USA

Within large-fruited germplasm,fruit size is influenced by flat and globe *** flat fruits are smaller and retain better marketability,globe fruits are larger and more prone to cuticle *** hybrids are often developed from crosses between flat and globe shaped parents because flat shape is thought to be dominant and fruit size *** objectives of this study were to determine the genetic basis of flat/globe fruit shape in large-fruited fresh-market tomato germplasm and to characterize its effects on several fruit ***-three advanced single plant selections from the Fla.8000×Fla.8111B cross were selectively genotyped using a genome-wide SNP array,and inclusive composite interval mapping identified a single locus on the upper arm of chromosome 12 associated with shape,which we termed globe.A 238-plant F 2 population and 69 recombinant inbred lines for this region from the same parents delimited globe to approximately 392-kilobases.A germplasm survey representing materials from multiple breeding programs demonstrated that the locus explains the flat/globe shape broadly.A single base insertion in an exon of Solyc12g006860,a gene annotated as a brassinosteroid hydroxylase,segregated completely with shape in all populations ***/Cas9 knock out plants confirmed this gene as underlying the globe *** silico analysis of the mutant allele of GLOBE among 595 wild and domesticated accessions suggested that the allele arose very late in the domestication *** measurements in three genetic backgrounds evidenced that globe impacts fruit size and several fruit shape attributes,pedicel length/width,and susceptibility of fruit to weather *** mutant allele of GLOBE appears mostly recessive for all traits except fruit size where it acts additively.

关键词： breeding size shape

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The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

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Horticulture Research 2023年第5期10卷 207-219页

作者： Xiaoya Shi Shuo Cao Xu Wang Siyang Huang Yue Wang Zhongjie Liu Wenwen Liu Xiangpeng Leng Yanling Peng Nan Wang Yiwen Wang Zhiyao Ma Xiaodong Xu Fan Zhang Hui Xue Haixia Zhong Yi Wang Kekun Zhang Amandine Velt Komlan Avia Daniela Holtgräwe Jérôme Grimplet JoséTomás Matus Doreen Ware Xinyu Wu Haibo Wang Chonghuai Liu Yuling Fang Camille Rustenholz Zongming Cheng Hua Xiao Yongfeng Zhou College of Horticulture Qingdao Agricultural UniversityQingdao 266109China State Key Laboratory of Tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Key Laboratory of Horticultural plant Biology Ministry of Education College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China School of Agriculture and Food Science University College DublinBelfieldDublin 4Ireland national Demonstration center for Experimental plant Science Education College of AgricultureGuangxi UniversityNanning 530004China State Key Laboratory of resource Insects Southwest UniversityChongqing 400715China Institute of Horticulture Crops Xinjiang Academy of Agricultural SciencesUrumqi 830091China Beijing Key Laboratory of Grape Science and Enology Institute of BotanyChinese Academy of SciencesXiangshanBeijing 100093China College of Enology Northwest A&F UniversityYangling 712100China SVQV INRAE-University of Strasbourg68000 ColmarFrance genetics and Genomics of plants CeBiTec&Faculty of BiologyBielefeld University33615 BielefeldGermany Unidad de Hortofruticultura Centro de Investigación y Tecnología Agroalimentaria de Aragón(CITA)50059 ZaragozaSpain Institute for Integrative Systems Biology(I2SysBio) Systems Biotech ProgramUniversitat de València-CSICPaterna46908ValenciaSpain Cold Spring Harbor Laboratory Cold Spring HarborNY 11724USA USDA ARS NEA Robert W.Holley center for Agriculture and Health Agricultural Research ServiceIthacaNY 14853USA Fruit Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(Germplasm Resources Utilization)Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit TreeLiaoning ProvinceXingch

Grapevine is one of the most economically important crops ***,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these ***,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long *** T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 *** annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T *** detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease *** though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein *** fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

关键词： breeding crops cultivar

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Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple

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Journal of Integrative plant Biology 2017年第3期59卷 190-204页

作者： Baiquan Ma Liao Liao Qian Peng Ting Fang Hui Zhou Schuyler S. Korban Yuepeng Han Key Laboratory of plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan 430074 China Graduate University of Chinese Academy of Sciences 19A Yuquanlu Beijing 100049 China Sino-African Joint Research center Chinese Academy of Sciences Wuhan 430074 China Department of Biology University of Massachusetts Boston Boston Massachusetts 02184 USA

Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and lo wild apples were genotyped using specific-locus ampli- fied fragment sequencing, and 39,635 single nucleotide polymorphisms with no missing genotypes and evenly distributed along the genome were selected to investi- gate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than culti- vated apples. Linkage disequilibrium （LD） decays were observed quite rapidly in cultivated and wild apples, with an r2-value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribu- tion patterns of LD blocks were detected betweendomesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domes- tication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgres- sion could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.

关键词： Hongya Gu Peking University China

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Germplasm resources and genetic breeding of Paeonia:a systematic review

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Horticulture Research 2020年第1期7卷 1369-1387页

作者： Yong Yang Miao Sun Shanshan Li Qihang Chen Jaime A.Teixeira da Silva Ajing Wang Xiaonan Yu Liangsheng Wang Key Laboratory of plant resources/Beijing Botanical Garden Institute of BotanyChinese Academy of Sciences100093 BeijingChina College of Landscape Architecture Beijing Forestry University100083 BeijingChina Beijing Key Laboratory of Ornamental plants Germplasm Innovation and Molecular Breeding 100083 BeijingChina national Engineering Research center for Floriculture 100083 BeijingChina University of Chinese Academy of Sciences 100049 BeijingChina P.O.Box 7 Miki–cho post officeIkenobe 3011–2Kagawa–ken 761–0799Japan

Members of the genus Paeonia,which consists of globally renowned ornamentals and traditional medicinal plants with a rich history spanning over 1500 years,are widely distributed throughout the Northern *** 1900,over 2200 new horticultural Paeonia cultivars have been created by the discovery and breeding of wild ***,information pertaining to Paeonia breeding is considerably fragmented,with fundamental gaps in knowledge,creating a bottleneck in effective breeding *** review systematically introduces Paeonia germplasm resources,including wild species and cultivars,summarizes the breeding strategy and results of each Paeonia cultivar group,and focuses on recent progress in the isolation and functional characterization of structural and regulatory genes related to important horticultural *** pertaining to the resource protection and utilization,breeding and industrialization of Paeonia in the future are also briefly discussed.

关键词： breeding cultivar globally

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Invitation to Contribute to Frontiers of Agricultural Science and Engineering

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Frontiers of Agricultural Science and Engineering 2016年第3期3卷 191-192页

作者： Xu Liu Xiuxin Deng Shaozhong Kang Zhaohu Li Chinese Academy of Engineering(CAE) Chinese Association of Agricultural Science Societies(CAASS) genetic resource Branch of CAASS Chinese Society of Agricultural Technology China Wild plant Conservation Association CAE Huazhong Agricultural University Chinese Society for Horticultural Science International Society of Citrus center for Agricultural Water Research in China China Agricultural University China Association of Water Conservation in Agriculture and Rural Water Supply China Association of Agricultural Engineering Chinese Agricultural Soil and Water Engineering Society Chinese Committee of Irrigation and Drainage China Agricultural University College Agronomy and Biotechnology China Agricultural University

Colleagues,It is our great pleasure to introduce you to the Frontiers of Agricultural Science and Engineering(FASE),a new international journal launched in *** was founded jointly by the Chinese Academy of Engineering... 详细信息

关键词： FASE Invitation to Contribute to Frontiers of Agricultural Science and Engineering

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Whole genome analyses reveal significant convergence in obsessive-compulsive disorder between humans and dogs

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Science Bulletin 2021年第2期66卷 187-196,M0004页

作者： Xue Cao Wei-Peng Liu Lu-Guang Cheng Hui-Juan Li Hong Wu Yan-Hu Liu Chao Chen Xiao Xiao Ming Li Guo-Dong Wang Ya-Ping Zhang State Key Laboratory of genetic resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Department of Laboratory Animal Science Kunming Medical UniversityKunming 650500China Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650223China Kunming Police Dog base Ministry of Public SecurityKunming 650204China Laboratory for Conservation and Utilization of Bio-resource&Key Laboratory for Microbial resources of the Ministry of Education Yunnan UniversityKunming 650091China center for Excellence in Brain Science and Intelligence Technology Chinese Academy of SciencesShanghai 200031China KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China center for Excellence in Animal Evolution and genetics Chinese Academy of SciencesKunming 650223China

Obsessive-compulsive disorder(OCD)represents a heterogeneous collection of diseases with diverse levels of phenotypic,genetic,and etiologic variability,making it difficult to identify the underlying genetic and biological mechanisms in *** dogs exhibit several OCD-like *** continuous circling as a representative phenotype for OCD,we screened two independent dog breeds,the Belgian Malinois and Kunming Dog and subsequently sequenced ten circling dogs and ten unaffected dogs for each *** population differentiation analyses,we identified 11 candidate genes in the extreme tail of the differentiated regions between cases and *** genes overlap significantly with genes identified in a genome wide association study(GWAS)of human OCD,indicating strong convergence between humans and *** gene expressional analysis and functional exploration,we found that two candidate OCD risk genes,PPP2R2B and ADAMTSL3,affected the density and morphology of dendritic ***,changes in dendritic spine may underlie some common biological and physiological pathways shared between humans and *** study revealed an unprecedented level of convergence in OCD shared between humans and dogs,and highlighted the importance of using domestic dogs as a model species for many human diseases including OCD.

关键词： Obsessive-compulsive disorder Circling behavior Whole genome sequencing genetic convergence Domestic dogs

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bHLH transcription factor SmbHLH92 negatively regulates biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza

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Chinese Herbal Medicines 2020年第3期12卷 237-246页

作者： Jian-hong Zhang Hai-zhou Lv Wan-jing Liu Ai-jia Ji Xin Zhang Jing-yuan Song Hong-mei Luo Shi-lin Chen Engineering Research center of Chinese Medicine resource Ministry of EducationInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China School of Pharmaceutical Sciences Guangzhou University of Chinese MedicineGuangzhou 510006China Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China

Objective:Salvia miltiorrhiza is a valuable herbal medicine with tanshinone and phenolic acid as the main biological active *** biosynthetic regulation of these bioactive compounds is controlled by a set of transcription factors(TFs).The basic helix-loop-helix(bHLH)transcription factor plays an important role in various physiological and biochemical processes in ***,research on bHLH TFs regulating phenolic acid or tanshinone biosynthesis in *** is ***:qRT-PCR was used for gene expression *** subcellular localization of SmbHLH92 was detected by SmbHLHg2-GFP transient transformation into tobacco leaves,and its fluorescence was observed using a confocal laser scanning *** transcriptional activity of SmbHLH92 was confirmed in the AH109 yeast *** interference hairy roots of SmbHLH92-RNAi transgenic lines were obtained through Agrobacterium-mediated genetic *** performance liquid chromatography(UPLC)was used to detect the changes of phenolic acids and ***:SmbHLH92 is a bHLH transcription factor that is highly expressed in the root and phloem of *** subcellular localization and transcriptional activity of SmbHLH92 indicated that SmbHLH92 was located in the nucleus and may be a transcription *** interference(RNAi)of SmbHLH92 in hairy roots of *** significantly increased the accumulation of phenolic acid and *** RT-PCR(RT-qPCR)analysis showed the transcription level of genes encoding the key enzymes involved in the phenolic acid and tanshinone biosynthetic pathways was increased in the hairy roots of the SmbHLH92-RNAi transgenic line,comparing with the control ***:These data indicate that SmbHLH92 is a negative regulator involved in the regulation of phenolic acid and tanshinone biosynthesis in ***.

关键词： phenolic acid Salvia miltiorrhiza bunge SmbHLH92 tanshinone transcription factor

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Towards a scientific rationale for traditional properties of Chinese medicinal plants: “natures” and “flavors”

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Chinese Herbal Medicines 2019年第3期11卷 258-266页

作者： Li-ping Li Ben-gang Zhang Zhao Zhang Xiao-jin Li Guo-ping Wang Hai-long Song Cong-zhao Fan Yang-ming Jiang Tuo Wang Hui-hui Zhao Wei-hong Cui Jiang-shan Lai Xiu-lian Chi Xue-ping Wei Chong-ming Wu Yao-dong Qi Hai-tao Liu Pei-gen Xiao Eimear Nic Lughadha Christine J.Leon Institute of Remote Sensing and Digital Earth Chinese Academy of SciencesBeijing100101China Institute of Medicinal plant Development Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100193China Xinjiang Institute of Chinese and Ethnic Medicine Urumqi830002China State Key Laboratory of Vegetation and Environmental Change Institute of BotanyChinese Academy of SciencesBeijing100093China national resource center for Chinese Materia Medica China Academy of Chinese Medical SciencesState Key Laboratory Breeding Base of Dao-di HerbsBeijing100700China Conservation Science Department Royal Botanic GardensKewRichmondSurreyTW93AEUK Collections Department Royal Botanic GardensKewRichmondSurreyTW93AEUK

Objective: According to theory of Chinese medicine property, the ecological environment shapes properties(natures and flavors) of Chinese materia medica(CMM) and there are close relationships between certain natures and flavors. However, to date these observations have not been validated scientifically in the context of the whole flora of a region. The present study aims to address this ***: We collected geographical distributions of 3637 vascular plant species native to the Xinjiang region of northwest China, of which around 812 are medicinal plants. The CMM property characters of these medicinal plants were also collected. All medicinal plants were then analyzed in the occurrence of their natures(cold, cool, neutral, warm, and hot) and flavors(sweet, bitter, sour, salty, and pungent). Possible correlations between these properties and environmental factors, notably climate, as well as correlations with plant species richness of the wider native flora of Xinjiang were then investigated using permutation test and ***: Cold species(38.5%) were more numerous than warm(21.0%) and neutral(22.3%), while bitter species(43.3%) were more numerous than pungent(25.6%), sweet(22.4%) and sour(6.7%) ones. Species with bitter flavor were most commonly also cold(48.6%) in nature, sour flavor usually coincided with cold(44.2%) or cool nature(26.0%), whereas pungent or sweet species tended to be warm(34.4%, 28.4%) or neutral(27.8%, 28.4%). The percentages of species of cold/cool nature, bitter flavor were higher in mountainous regions, and the percentages of warm/neutral and pungent/sweet/sour were higher in basins. The percentages of species of cold/cool, bitter were positively correlated with actual evapotranspiration(AET),and also plant species richness but had a bell-shaped relationship with potential evapotranspiration(PET),whereas the inverse situation was shown for warm/neutral and pungent/sweet/sour ***: Analysis of the data in Xinjiang

关键词： flavor nature Chinese materia medica theory of Chinese medicine property Xinjiang region

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Molecular Markers for genetic Diversity Studies in African Leafy Vegetables

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Advances in Bioscience and Biotechnology 2016年第3期7卷 188-197页

作者： Emmanuel O. Omondi Thomas Debener Marcus Linde Mary Abukutsa-Onyango Fekadu F. Dinssa Traud Winkelmann Institute of Horticultural Production Systems Woody Plant and Propagation Physiology Leibniz Universit&auml t Hannover Hannover Germany Institute for plant genetics Molecular Plant Breeding Leibniz Universit&auml t Hannover Hannover Germany Department Horticulture Jomo Kenyatta University of Agriculture & Technology (JKUAT) Juja Kenya AVRDC - The World Vegetable center Eastern and Southern Africa Arusha Tanzania

African leafy vegetables are becoming important crops in tackling nutrition and food security in many parts of sub-Saharan Africa, since they provide important micronutrients and vitamins, and help resource-poor farm families bridge lean periods of food shortage. genetic diversity studies are essential for crop improvement programmes as well as germplasm conservation efforts, and research on genetic diversity of these vegetables using molecular markers has been increasing over time. Diversity studies have evolved from the use of morphological and biochemical markers to molecular markers. Molecular markers provide valuable data, since they detect mostly selectively neutral variations at the DNA level. They are well established and their strengths and limitations have been described. New marker types are being developed from a combination of the strengths of the basic techniques to improve sensitivity, reproducibility, polymorphic information content, speed and cost. This review discusses the principles of some of the established molecular markers and their application to genetic diversity studies of African leafy vegetables with a main focus on the most common Solanum, Amaranthus, Cleome and Vigna species.

关键词： AFLPs Allozymes Amaranthus Cleome ISSRs Microsatellites RAPDs SNPs Solanum SSRs Vigna

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Integrated phenotypic,phylogenomic,and evolutionary analyses indicate the earlier domestication of Geng upland rice in China

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Molecular plant 2022年第10期15卷 1506-1509页

作者： Zhi Luo Hui Xia Zhigui Bao Lei Wang Yu Feng Ting Zhang Jie Xiong Liang Chen Lijun Luo College of plant Sciences&Technology Huazhong Agricultural UniversityWuhanChina Shanghai Agrobiological Gene center ShanghaiChina 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 SciencesShenzhenChina CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengduChina Key Laboratory of Grain Crop genetic resources Evaluation and Utlization Ministry of Agriculture and Rural AffairsShanghaiChina Shanghai OE Biotech.Co. Ltd.ShanghaiChina School of Agriculture and Biology Shanghai Jiao Tong UniversityShanghaiChina

Dear Editor,Ensuring food security with finite resources and environmental impacts is a new challenge in sustainable agriculture(Yu et al.,2022).It is therefore essential to develop suitable rice varieties for resource-saving and environmentally friendly cultivation(Luo et al.,2019;Yu et al.,2022).Upland rice,which evolves many green characters for rice sustainable cultivation(e.g.,drought resistance,the usage efficiency of nitrate,the good capacity of direct seeding,etc.),is therefore an important germplasm in rice breeding(Luo et al.,2019).However,the origination and evolution of upland rice,as well as its green genetic resource,remain mysterious(Xia et al.,2019).

关键词： breeding drought upland

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