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A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa

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Horticulture Research 2023年第10期10卷 250-261页

作者： Shaofang He Duanyang Weng Yipeng Zhang Qiusheng Kong Keyue Wang Naliang Jing Fengfeng Li yuebin Ge Hui Xiong Lei Wu De-yu Xie Shengqiu Feng xiaqing yu Xuekui Wang Shaohua Shu Zhinan Mei College of Plant Science&Technology Huazhong Agricultural UniversityWuhan 430070China Wuhan Carboncode Biotechnologies Co. Ltd.Wuhan 430070China Sinopharm Zhonglian Pharmaceutical Co. Ltd.Wuhan 430070China College of Horticulture&Forestry Huazhong Agricultural UniversityWuhan 430070China School of Pharmaceutical Science South-Central Minzu UniversityWuhan 430074China Department of Plant and Microbial Biology North Carolina State UniversityRaleighNC 27695USA College of Horticulture Nanjing Agricultural UniversityNanjing 210095China

Chaenomeles speciosa(2n=34),a medicinal and edible plant in the Rosaceae,is commonly used in traditional Chinese *** date,the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal ***,we report the use of an integrative approach involving PacBio HiFi(third-generation)sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of *** genome comprised 650.4 Mb with a contig N50 of 35.5 *** these,632.3 Mb were anchored to 17 pseudo-chromosomes,in which 12,4,and 1 pseudo-chromosomes were represented by a single contig,two contigs,and four contigs,*** pseudo-chromosomes had telomere repeats at both ends,and four had telomere repeats at a single *** sequences accounted for 49.5%of the genome,while a total of 45515 protein-coding genes have been *** genome size of *** was relatively similar to that of Malus *** or contracted gene families were identified and investigated for their association with different plant metabolisms or biological *** particular,functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids,two abundant pentacyclic triterpenoids in the fruits of *** together,this telomere-to-telomere and chromosome-level genome of *** not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues,but also promotes understanding of the evolution of the Rosaceae.

关键词： value. insight metabolism

Mapping of fruit apex shape related QTLs across multi-genetic backgrounds in cucumber(Cucumis sativus L.)

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Horticultural Plant Journal 2022年第3期8卷 328-340页

作者： Pinyu Zhu Yongjiao Meng Kaijing Zhang Xueyan Wang Kun Liang Tuantuan Wang Jian Xu Xiaodong Qin Zhe Wu Chunyan Cheng xiaqing yu Chuntao Qian Qunfeng Lou Jinfeng Chen Ji Li State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China College of Engineering/Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology&Equipment Nanjing Agricultural UniversityNanjing 210031China College of Agriculture Anhui Science and Technology UniversityFengyang 233100China

The shape of fruit apex is critical to appearance quality in cucumber(Cucumis sativus L.),of which the genetic basis was poorly understood,and the use of marker-assisted breeding for fruit apex improvement is not available *** this study,the variation of fruit apex in different cucumber ecotypes was evaluated by fruit apex angle(variation coefficient from 7.1%to 15.7%)and fruit apex index(variation coefficient from 8.8%to 22.6%).Fruit apex associated QTLs were mapped by using 145 F_(2:3) families and 155 F_(2:6) population that were derived from the cross of different ecotype *** of the mapping populations were conducted in four experiments in 2 *** majoreffect QTLs,Bfal4.1,Bfai4.1,Bfad6.1 and Bfai6.1 were consistently and reliably detected across two environments which could explain 11.6%-33.6%phenotypic variations(R^(2))in the F_(2:3) *** major-effect QTLs,Ofai4.1(R^(2)=13.4%-15.5%),Ofal4.1(R^(2)=10.7%-12.8%),and Ofad6.1(R^(2)=11.6%-12.4%)were stably detected in the F_(2:6) population in two ***4.1,Bfal4.1,Ofai4.1 and Ofal4.1 were integrated to be consensus QTL fa4.1,within which 11 candidate genes were ***6.1 and Bfad6.1 were integrated to be consensus QTL *** interaction analysis showed that Bfai6.1 has epistatic effect with *** study revealed two reliable major-effect fruit apex related QTLs across multi-genetic backgrounds and environments in *** possible candidate genes regulating the shape of fruit apex,and the relationship between cell division and fruit apex morphogenesis were discussed.

关键词： Cucumber Fruit apex Variation QTL Candidate gene

High Throughput Sequencing of circRNAs in Tomato Leaves Responding to Multiple Stresses of Drought and Heat

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Horticultural Plant Journal 2020年第1期6卷 34-38页

作者： Rong Zhou xiaqing yu Carl-Otto Ottosen Tongmin Zhao Department of Food Science Aarhus UniversityArslev DK-5792Denmark Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu Province Institute of Vegetable CropJiangsu Province Academy of Agricultural SciencesNanjing 210014China National Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China

Our aim is to study the roles of a new emerging group of non-coding RNAs, circRNAs, in tomato(Solanum lycopersicum L.) plants grown at the combination of drought and heat, two of the most usual stress conditions known to frequently happen in field. Tomato seedlings from cultivar‘Jinling Meiyu’ were treated without stresses(control), at water shortage, high temperature and subjected the multiple stresses. In total, 467 circRNAs were identified with 87.82% from exon using high throughput sequencing technology. Among the circRNAs, 70 were from chr1 with the range from 23 to 49 from the other chromosomes. In detail, 156 circRNAs were shared in the four libraries, while 21, 17 and 36 circRNAs were only shown in drought, heat and multiple stresses libraries, respectively. Through a differential expression analysis, four, seven and nine circRNAs were differentially regulated in tomato at drought, heat and multiple stresses as compared with control. These circRNAs played roles on photosynthesis, starch and sucrose metabolism, RNA transport, RNA degradation, spliceosome, ribosome, etc. Our study underlined the potential role of circRNAs involved in the abiotic stress response in tomato, which might pave the way for studying biological roles of circRNAs responding to multiple stresses in plants.

关键词： Solanum lycopersicum circRNAs High throughput sequencing High temperature Water shortage

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葫芦科作物多倍化研究进展

南京农业大学学报 2022年第5期45卷 874-882页

作者：虞夏清陈劲枫南京农业大学作物遗传与种质创新国家重点实验室江苏南京210095

多倍化是物种形成与作物驯化的重要驱动力之一。多倍化能够在短期内极大丰富物种多样性,因此被广泛应用于作物的遗传改良。利用多倍化开展的作物品种改良已在西瓜、黄瓜、甜瓜等重要葫芦科作物中获得成功。近期研究发现,多倍体通常具有... 详细信息

多倍化是物种形成与作物驯化的重要驱动力之一。多倍化能够在短期内极大丰富物种多样性,因此被广泛应用于作物的遗传改良。利用多倍化开展的作物品种改良已在西瓜、黄瓜、甜瓜等重要葫芦科作物中获得成功。近期研究发现,多倍体通常具有明显的环境适应性优势,在全球气候问题日益严峻的今天,利用多倍化提高葫芦科作物的环境适应能力已成为葫芦科作物育种的重要内容之一。根据基因组组成的不同,多倍体可分为同源多倍体和异源多倍体,以往的葫芦科作物研究多数只关注于同源多倍体,对于异源多倍体的认识与研究存在明显不足,有待进一步开发与利用。随着基因组测序技术的发展以及多种组学和分子生物学技术的快速发展,植物多倍化研究取得了许多重要的进展,为葫芦科作物多倍化相关机制研究提供了前所未有的机会。本文系统综述了近年来葫芦科作物多倍化研究现状,探讨多倍化在葫芦科作物育种中的发展与未来,为葫芦科作物以及其他作物的遗传育种提供参考。

关键词：葫芦科多倍体表型组学育种

Comparative Cyto-molecular Analysis of Repetitive DNA Provides Insights into the Differential Genome Structure and Evolution of Five Cucumis Species

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Horticultural Plant Journal 2019年第5期5卷 192-204页

作者： Shuqiong Yang Chunyan Cheng Xiaodong Qin xiaqing yu Qunfeng Lou Ji Li Chuntao Qian Jinfeng Chen State Key Lab of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing210095China Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province School ofAgricultural EngineeringNanyang Normal UniversityNanyang473061China

The genus Cucumis, includes the cucumber(2n = 14), melon(2n = 24), and other wild species, which is a good model for studying genome organization and evolution due to their variation in genome size and basic chromosome number. In this study, five Cucumis species with different geographical origins and basic chromosome numbers(i.e., C. sativus, C. hystrix, C. melo, C. anguria, and C. metuliferus) were used to identify and characterize the repetitive DNA in detail using a phylogenetic method. Comparative cyto-molecular genetic analysis of repetitive DNA was carried out using a graph-based clustering method, construction of Neighbor-Joining tree and fluorescence in situ hybridization(FISH).The results revealed that the five Cucumis species had differences in the repeat content of their genome, as well as in the composition of repetitive DNA and their genomic proportions. Three species from subgenus Melo showed a decreased tendency in both repeat types and genomic proportions, while two species from subgenus Cucumis also showed a decreased tendency in repeat types, but an increased tendency in genomic proportions. Phylogenic analysis of Cucumis Ty1/Copia, Ty3/Gypsy, and 45 S rDNA ITS regions revealed that C. sativus, C. hystrix, and C. melo were closely related species, which C. sativus and C. hystrix were closer, while C. anguria and C. metuliferus were closer to each other and further from the other three species. Differential accumulation and elimination of different repeat types divergently shaped the genomic architecture of these five Cucumis species, contributing to the genome’s evolution and diversification. Overall, these results enhance our understanding of the genomes of these five Cucumis species, and contribute to a more holistic view of genome evolution and phylogenetics of this genus.

关键词： Cucumis repetitive sequence comparative genomics FISH phylogenetic evolution

A leaf shape mutant provides insight into PINOID Serine/Threonine Kinase function in cucumber(Cucumis sativus L.)

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Journal of Integrative Plant Biology 2019年第9期61卷 1000-1014页

作者： Mengfei Song Feng Cheng Jing Wang Qingzhen Wei Wenyuan Fu xiaqing yu Ji Li Jinfeng Chen Qunfeng Lou State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China

Optimizing leaf shape is a major challenge in efforts to develop an ideal plant type. Cucumber leaf shapes are diverse;however, the molecular regulatory mechanisms underlying leaf shape formation are unknown. In this study, we obtained a round leaf mutant(rl) from an ethyl methanesulfonate-induced mutagenesis population. Genetic analysis revealed that a single recessive gene, rl, is responsible for this mutation. A modified Mut Map analysis combined linkage mapping identified a single nucleotide polymorphism within a candidate gene,Csa1 M537400, as the mutation underlying the ***1 M537400 encodes a PINOID kinase protein involved in auxin transport. Expression of Csa1 M537400 was significantly lower in the rl mutant than in wild type, and it displayed higher levels of IAA(indole-3-acetic acid) in several tissues. Treatment of wild-type plants with an auxin transport inhibitor induced the formation of round leaves,similar to those in the rl mutant. Altered expression patterns of several auxin-related genes in the rl mutant suggest that rl plays a key role in auxin biosynthesis,transport, and response in cucumber. These findings provide insight into the molecular mechanism underlying the regulation of auxin signaling pathways in cucumber,and will be valuable in the development of an ideal plant type.

关键词： red Cucumis sativus L Kinase function PINOID

欧洲温室型黄瓜品质性状杂种优势及配合力分析

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南京农业大学学报 2022年第3期45卷 483-492页

作者：王慧臧柯昕陈劲枫虞夏清南京农业大学作物遗传与种质创新国家重点实验室江苏南京210095

[目的]本文旨在通过对欧洲温室型黄瓜品质性状进行杂种优势和配合力分析,辅助选择综合性状优异的亲本和杂交组合,为培育优良无刺的黄瓜新品种提供参考。[方法]以6个欧洲温室型黄瓜的高代自交系为试验材料,采用完全双列杂交方法(Griffing... 详细信息

[目的]本文旨在通过对欧洲温室型黄瓜品质性状进行杂种优势和配合力分析,辅助选择综合性状优异的亲本和杂交组合,为培育优良无刺的黄瓜新品种提供参考。[方法]以6个欧洲温室型黄瓜的高代自交系为试验材料,采用完全双列杂交方法(GriffingⅣ)配制15个杂交组合,分析12个品质性状的杂种优势、配合力、遗传参数以及性状间的相关性。[结果]黄瓜瓜长、瓜横径、果形指数、维生素C含量、可溶性糖含量等9个性状存在正向杂种优势,瓜把长表现为最大负向杂种优势,可以有效利用改善欧洲温室型黄瓜的外观和内在品质。瓜横径、果肉硬度和可溶性蛋白含量表现为显性方差大于加性方差,瓜长、维生素C含量、可溶性糖含量等8个性状遗传力较高并表现为加性作用,宜在早期世代选育。相关性研究表明,欧洲温室型黄瓜的外观品质与内在品质存在相关性,瓜长与维生素C含量、可溶性糖含量、可溶性蛋白含量显著正相关,果肉厚与可溶性糖含量、可溶性蛋白含量显著正相关,其相关性在选育过程中应加以利用。配合力分析结果显示,自交系20055S、20062S和20011S在大部分品质性状上都具有较好的一般配合力效应,有较高的育种价值;20055S×20062S、20062S×20011S和20011S×20014S分别是综合性状表现优异的长果型组合、中长果型组合和短果型组合,都可作为品质优良的无刺类黄瓜推广应用。[结论]欧洲温室型黄瓜品质性状存在杂种优势;20055S、20062S和20011S是优异亲本,20055S×20062S、20062S×20011S和20011S×20014S是优势杂交组合,应用前景较好。

关键词：欧洲温室型黄瓜品质性状杂种优势配合力遗传参数相关性

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肠道微生物对甲状腺碘代谢的潜在调控机制

中华核医学与分子影像杂志 2022年第3期42卷 181-185页

作者：郁霞青吕中伟李丹同济大学附属第十人民医院核医学科上海200072

碘是人体必需的微量元素,胃肠道摄入是人体获取碘的主要途径。肠道包含的万亿数量级的微生物对于人体物质能量代谢及基因信息调控有着十分重要的影响。肠道微生物或其代谢产物可通过循环系统作用于甲状腺(即"肠-甲状腺轴"),对甲状腺的... 详细信息

碘是人体必需的微量元素,胃肠道摄入是人体获取碘的主要途径。肠道包含的万亿数量级的微生物对于人体物质能量代谢及基因信息调控有着十分重要的影响。肠道微生物或其代谢产物可通过循环系统作用于甲状腺(即"肠-甲状腺轴"),对甲状腺的碘代谢进行潜在调控。该文综述了肠道微生物对肠内碘摄取的影响及其对甲状腺细胞表面钠/碘同向转运体(NIS)表达及活性的调控,探讨了肠道微生物参与甲状腺碘代谢的潜在调控机制。肠道微生物影响甲状腺碘代谢的直接因素包括脂多糖、短链脂肪酸、微生物肽段或蛋白质等,通过影响核因子kappa B通路、参与组蛋白乙酰化修饰或抗原抗体反应等方式影响甲状腺NIS的表达或活性;间接因素包括肠道微生物改变细胞内环境,从而通过调控甲状腺特异转录因子的水平及调节促甲状腺激素及其受体介导的信号通路等方式影响甲状腺细胞内外碘离子的转运。

关键词：宏基因组胃肠道代谢碘甲状腺发展趋势

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多倍化与植物新表型关联性的研究进展

园艺学报 2023年第9期50卷 1854-1866页

作者：裴芸虞夏清赵晓坤张万萍陈劲枫南京农业大学园艺学院作物遗传与种质创新国家重点实验室南京210095 贵州大学农学院贵州大学蔬菜研究院贵阳550025

系统分析和讨论了全基因组复制(Whole genome duplications,WGD)与植物新表型(形态器官“巨大性”、开花期变异、次生代谢物增加、农艺性状优化、抵御胁迫能力增强等)的形成关系及其在进化中的贡献和意义,展望了未来多倍体研究的发展方... 详细信息

系统分析和讨论了全基因组复制(Whole genome duplications,WGD)与植物新表型(形态器官“巨大性”、开花期变异、次生代谢物增加、农艺性状优化、抵御胁迫能力增强等)的形成关系及其在进化中的贡献和意义,展望了未来多倍体研究的发展方向,为多倍体植物进化创新研究和新型多倍体作物分子育种提供重要参考。

关键词：多倍体表型创新适应性进化物种多样性