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| 1 | 柑橘果实色素—类胡萝卜素的研究进展显示文摘柑橘果实丰富多彩,广受大众喜爱,外观色泽作为消费者选择看重的果实品质之一,其研究就显得格外重要。类胡萝卜素是柑橘果实呈色的主要贡献者,成为近年来柑橘果实色素研究的重点。类胡萝卜素包括胡萝卜素和叶黄素两大类,不同的色素单体呈现黄到橙红甚至紫红多种颜色,其丰富多样的组成给与柑橘果实丰富的颜色表现。笔者概述了柑橘果实呈色色素的主要来源、内外部及其他影响因素、3条合成途径(番茄红素、胡萝卜素和含氧类胡萝卜素生物合成),并介绍了类胡萝卜素对植物体和人体的生理活性功能,但目前对类胡萝卜素的分解过程以及分解产物存在形式和生理功能的研究较少,有待进一步深入开展。 | 黄贝 王鹏 温明霞 吴韶辉 高伟勤 徐建国 夏仁学 | 2019 | 果树学报2019，36，6： | 17 |
| 2 | 柑橘果实风味组学研究进展显示文摘风味是决定柑橘果实整体品质的重要因素,直接影响消费者的购买意愿。风味组学则是解析风味品质物质基础的组学技术。柑橘风味包含甜味、酸味、香味、苦味、质地和异味等多种属性。本文对柑橘风味组学的产生、研究策略、方法以及研究进展进行了综述和展望。文章提出,柑橘风味组学相关研究重点将更注重消费者偏好性,发掘影响柑橘风味的最主要代谢物,以期在生产中定向培育或利用栽培技术提升和改善柑橘果实品质,助力产业的良性发展。 | 张海朋 彭昭欣 石梅艳 温欢 张红艳 徐娟 | 2021 | 华中农业大学学报2021，40，1： | 16 |
| 3 | Genome sequences of horticultural plants:past,present,and future显示文摘Horticultural plants play various and critical roles for humans by providing fruits,vegetables,materials for beverages,and herbal medicines and by acting as ornamentals.They have also shaped human art,culture,and environments and thereby have influenced the lifestyles of humans.With the advent of sequencing technologies,there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade.The genomes of horticultural plants are highly diverse and complex,often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication.Here we summarize the advances in the genome sequencing of horticultural plants,the reconstruction of pan-genomes,and the development of horticultural genome databases.We also discuss past,present,and future studies related to genome sequencing,data storage,data quality,data sharing,and data visualization to provide practical guidance for genomic studies of horticultural plants.Finally,we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project. | Fei Chen Yunfeng Song Xiaojiang Li Junhao Chen Lan Mo Xingtan Zhang Zhenguo Lin Liangsheng Zhang | 2019 | Horticulture Research2019，6，1： | 16 |
| 4 | Advances in Genomic,Transcriptomic,and Metabolomic Analyses of Fruit Quality in Fruit Crops显示文摘Fruit quality is the main factor determining market competitiveness;it represents the combination of fruit flavor,color,size,and the contents of aromatic and bioactive substances.Research on the genetic basis of fruit quality can provide new information about fruit biology,promote genomic-assisted breeding,and provide technological support for the regulation of fruit quality via habitat selection and/or the control of environmental conditions.High-throughput sequencing is a powerful research method for studying fruit quality traits,and reference genome sequences for many important fruit crops have provided vast amounts of genomic data.To study fruit quality,it is important to select appropriate omics strategies and to analyze omics data meaningfully.Here,we summarize genomic mechanisms of fruit quality formation:gene duplication,transposable element insertion,structural variations and genome methylation in functional genes.We review the genomic,transcriptomic,and metabolomic strategies that have been used to study the genetic basis of fruit quality traits.We also describe some of the genes associated with fruit traits;these genes are a valuable resource for genomics-assisted breeding and are useful models for deciphering the mechanisms of agronomic traits,such as fruit color,size,hardness,aroma components,sugar and acid content.Finally,to maximize the application of omics information,we propose some further directions for research using omics strategies. | Chunmei Zhang Yu-Jin Hao | 2020 | Horticultural Plant Journal2020，6，6： | 11 |
| 5 | 柑橘中挥发性萜类物质代谢研究进展显示文摘柑橘中挥发性物质以萜类为主,不仅影响植株与环境间的信号传递和赋予果实的香气,而且对消费者的感官体验及人体健康有多样的功能。对柑橘中挥发性萜类物质生物学功能、代谢谱的种质及组织特异性、合成途径相关基因及挥发性物质与柑橘分类等研究进展进行了综述。提出目前对柑橘挥发性萜类物质的研究仅限于代谢通路及代谢谱分析;在成分分析上多以游离态为主,糖苷等键合态的分析较少;已明确功能的结构基因及调控基因报道较少,香气品质的形成机理尚有待深入解析。展望未来,基础研究方面应重点揭示柑橘中挥发性萜类物质代谢的进化和演变规律、重要结构基因及转录因子调控机制等;生产应用中关注开发利用现有具特异香味种质、创制特殊香味新品种以及提升香气品质的栽培措施。 | 张海朋 刘翠华 刘园 温欢 施要强 张红艳 徐娟 | 2020 | 园艺学报2020，47，8： | 10 |
| 6 | Genome-wide Characterization of cis-acting Elements in the Promoters of Key Carotenoid Pathway Genes from the Main Species of Genus Citrus显示文摘Carotenoids are indispensable for both human health and plant survival.Citrus,is one of the fruit crops richest in carotenoid compounds,with approximately 115 kinds of carotenoids;tremendous diversity in carotenoids composition and concentration exists among various species,showing different colors from nearly white to crimson.The carotenoid biosynthetic pathway and the key carotenogenic genes have been identified in citrus;however,the underlying regulatory mechanisms remain unclear.In this study,among the main species of genus Citrus(primitive,wild,and cultivated),we detected carotenoids in flavedo using High-Performance Liquid Chromatography,and analyzed variations in cis-acting elements in the promoters of key carotenoid pathway genes.Intriguingly,both carotenoid composition and content were generally increased during the evolution of citrus,and the corresponding variations in the promoters were identified,including the gain or loss of critical environmental stress-responsive elements and hormone-responsive elements,which are closely associated with carotenoid enhancement.In addition,pummelo has the most heat-responsive elements,but the Mangshan mandarin does not have this element in the promoters of PSY,which is highly related to their geographical origin and indicate that temperature is a critical environmental signal influencing carotenoid accumulation.Moreover,the abscisic acid-responsive motif was rich in almost all the seven species,but the ethylene-responsive motif was deficient,which demystified the unique phytohormone regulation mechanism of carotenoid accumulation in citrus.Overall,our study provides new insights into the molecular regulatory mechanism of carotenoid enhancement in the evolution of citrus,which can facilitate breeding and cultivation efforts to improve the nutritional quality and esthetic value in citrus and hopefully other fruit crops. | Kaijie Zhu Qingjiang Wu Yue Huang Junli Ye Qiang Xu Xiuxin Deng | 2020 | Horticultural Plant Journal2020，6，6： | 8 |
| 7 | Genomic analysis reveals the genetic diversity,population structure,evolutionary history and relationships of Chinese pepper显示文摘Chinese pepper,mainly including Zanthoxylum bungeanum and Zanthoxylum armatum,is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses.Numerous cultivars of Chinese pepper have been developed in China through long-term domestication.To better understand the population structure,demographic history,and speciation of Chinese pepper,we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genomewide genotyping-by-sequencing(GBS)approach.Our analysis provides genetic evidence of multiple splitting events occurring between and within species,resulting in at least four clades in Z.bungeanum and two clades in Z.armatum.Despite no evidence of recent admixture between species,we detected substantial gene flow within species.Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene(including the Penultimate Glaciation and the Last Glacial Maximum)and recent domestication events together shaped the demography and evolution of Chinese pepper.Our analyses also suggest that southeastern Gansu province is the most likely origin of Z.bungeanum in China.These findings provide comprehensive insights into genetic diversity,population structure,demography,and adaptation in Zanthoxylum. | Shijing Feng Zhenshan Liu Yang Hu Jieyun Tian Tuxi Yang Anzhi Wei | 2020 | Horticulture Research2020，7，1： | 6 |
| 8 | CitGVD:a comprehensive database of citrus genomic variations显示文摘Citrus is one of the most important commercial fruit crops worldwide.With the vast genomic data currently available for citrus fruit,genetic relationships,and molecular markers can be assessed for the development of molecular breeding and genomic selection strategies.In this study,to permit the ease of access to these data,a web-based database,the citrus genomic variation database(CitGVD,http://gffzz1758061741e3440chko9k5xcq0wqp695o.ffgz.tsg.suse.edu.cn/home)was developed as the first citrusspecific comprehensive database dedicated to genome-wide variations including single nucleotide polymorphisms(SNPs)and insertions/deletions(INDELs).The current version(V1.0.0)of CitGVD is an open-access resource centered on 1,493,258,964 high-quality genomic variations and 84 phenotypes of 346 organisms curated from in-house projects and public resources.CitGVD integrates closely related information on genomic variation annotations,related gene annotations,and details regarding the organisms,incorporating a variety of built-in tools for data accession and analysis.As an example,CitGWAS can be used for genome-wide association studies(GWASs)with SNPs and phenotypic data,while CitEVOL can be used for genetic structure analysis.These features make CitGVD a comprehensive web portal and bioinformatics platform for citrus-related studies.It also provides a model for analyzing genome-wide variations for a wide range of crop varieties. | Qiang Li Jingjing Qi Xiujuan Qin Wanfu Dou Tiangang Lei Anhua Hu Ruirui Jia Guojin Jiang Xiuping Zou Qin Long Lanzhen Xu Aihong Peng Lixiao Yao Shanchun Chen Yongrui He | 2020 | Horticulture Research2020，7，1： | 4 |
| 9 | Genome of a citrus rootstock and global DNA demethylation caused by heterografting显示文摘Grafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years.Citrus plants,with a seed-to-seed cycle of 5–15 years,are among the fruit crops that were probably domesticated by grafting.Poncirus trifoliata,a widely used citrus rootstock,can promote early flowering,strengthen stress tolerance,and improve fruit quality via scion–rootstock interactions.Here,we report its genome assembly using PacBio sequencing.We obtained a final genome of 303 Mb with a contig N50 size of 1.17Mb and annotated 25,680 protein-coding genes.DNA methylome and transcriptome analyses indicated that the strong adaptability of P.trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes.Heterografting by using sweet orange as scion and P.trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock.Single-base methylome analysis indicated that P.trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs(sRNAs)in scions compared to the level observed with autografting,implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting.Taken together,the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology. | Yue Huang Yuantao Xu Xiaolin Jiang Huiwen Yu Huihui Jia Chunming Tan Gang Hu Yibo Hu Muhammad Junaid Rao Xiuxin Deng Qiang Xu | 2021 | Horticulture Research2021，8，1： | 4 |
| 10 | 柚子基因组比较分析以及祖先染色体重构显示文摘柚子(Citrus grandis Osbeck)全基因组测序完成为柑橘植物乃至整个芸香科植物提供了研究机会。本研究通过对柚子基因组结构分析,鉴定柚子基因组中存在的由多倍化产生的重复基因,构建了葡萄基因组和柚子基因组之间与多倍化、物种分化相关联的同源共线性基因列表,为柚子基因组进化和基因功能演化提供了重要的比较基因组学数据资源;通过与外类群葡萄保留的同源染色体区域进行比较,发现柚子基因组在多倍化之后发生了大量的片段化重组;利用葡萄基因组保留有较完整的染色体结构相对于真双子叶六倍体(ECH),结合葡萄和柚子基因组之间的同源关系,推断出柚子祖先基因组结构。本研究对理解柚子基因组乃至柑橘植物基因组以及其进化提供了重要的比较基因组学的基础。 | 袁嘉庆 王金朋 王希胤 | 2020 | 河北农业大学学报2020，43，1： | 2 |
| 11 | Comparative population genomics dissects the genetic basis of seven domestication traits in jujube显示文摘Jujube(Ziziphus jujuba Mill.)is an important perennial fruit tree with a range of interesting horticultural traits.It was domesticated from wild jujube(Ziziphus acidojujuba),but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood.Here,we report a comprehensive genome variation map based on the resequencing of 350 accessions,including wild,semi-wild and cultivated jujube plants,at a>15×depth.Using the combination of a genome-wide association study(GWAS)and selective sweep analysis,we identified several candidate genes potentially involved in regulating seven domestication traits in jujube.For fruit shape and kernel shape,we integrated the GWAS approach with transcriptome profiling data,expression analysis and the transgenic validation of a candidate gene to identify a causal gene,ZjFS3,which encodes an ethyleneresponsive transcription factor.Similarly,we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS.In the selective sweep analysis,we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits.This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube. | Mingxin Guo Zhongren Zhang Yanwei Cheng Sunan Li Peiyin Shao Qiang Yu Junjie Wang Gan Xu Xiaotian Zhang Jiajia Liu Linlin Hou Hanxiao Liu Xusheng Zhao | 2020 | Horticulture Research2020，7，1： | 2 |
| 12 | Structural variation and parallel evolution of apomixis in citrus during domestication and diversification显示文摘Apomixis,or asexual seed formation,is prevalent in Citrinae via a mechanism termed nucellar or adventitious embryony.Here,multiple embryos of a maternal genotype form directly from nucellar cells in the ovule and can outcompete the developing zygotic embryo as they utilize the sexually derived endosperm for growth.Whilst nucellar embryony enables the propagation of clonal plants of maternal genetic constitution,it is also a barrier to effective breeding through hybridization.To address the genetics and evolution of apomixis in Citrinae,a chromosome-level genome of the Hongkong kumquat(Fortunella hindsii)was assembled following a genome-wide variation map including structural variants(SVs)based on 234 Citrinae accessions.This map revealed that hybrid citrus cultivars shelter genome-wide deleterious mutations and SVs into heterozygous states free from recessive selection,which may explain the capability of nucellar embryony in most cultivars during Citrinae diversification.Analyses revealed that parallel evolution may explain the repeated origin of apomixis in different genera of Citrinae.Within Fortunella,we found that apomixis of some varieties originated via introgression.In apomictic Fortunella,the locus associated with apomixis contains the FhRWP gene,encoding an RWP-RK domain-containing protein previously shown to be required for nucellar embryogenesis in Citrus.We found the heterozygous SV in the FhRWP and CitRWP promoters from apomictic Citrus and Fortunella,due to either two or three miniature inverted transposon element(MITE)insertions.A transcription factor,FhARID,encoding an AT-rich interaction domain-containing protein binds to the MITEs in the promoter of apomictic varieties,which facilitates induction of nucellar embryogenesis.This study provides evolutionary genomic and molecular insights into apomixis in Citrinae and has potential ramifications for citrus breeding. | Nan Wang Xietian Song Junli Ye Siqi Zhang Zhen Cao Chenqiao Zhu Jianbing Hu Yin Zhou Yue Huang Shuo Cao Zhongjie Liu Xiaomeng Wu Lijun Chai Wenwu Guo Qiang Xu Brandon S.Gaut Anna M.G.Koltunow Yongfeng Zhou Xiuxin Deng | 2022 | National Science Review2022，9，10： | 1 |
| 13 | 湖南省主栽柑橘品质及贮藏性的比较显示文摘为综合评价湖南省柑橘主栽品种的果实品质和贮藏性,该文从湖南省不同主产区分别采摘4个主栽柑橘品种‘宫川’温州蜜柑、‘辛女’椪柑、冰糖橙和‘纽荷尔’脐橙,分别贮藏于通风库和冷库中,对果实性状(大小、果形指数、色泽、种子数)、品质[出汁率、可滴定酸(titratable acid,TA)、可溶性固形物(total soluble solids,TSS)、维生素C(vitamin C,V_(C))和贮藏性(呼吸强度、发病率和失水率)]进行比较研究。结果表明,贮藏期间,果实TA含量呈下降趋势,果实发病率和失水率随贮藏时间的延长而逐渐上升,TSS和V_(C)含量有轻微变化。相关性分析表明,TA与发病率和失水率呈负相关。此外,低温更适合‘宫川’和‘辛女’果实的贮藏,但不适合冰糖橙和‘纽荷尔’长时间贮藏。研究结果将有助于4个主要柑橘品种的特性评价,并为柑橘产业提供有益的指导。 | 郭静 金燕 廖满余 张芬 李娜 朱亦赤 龙晴柔 盛玲 | 2023 | 食品研究与开发2023，44，14： | 0 |
| 14 | Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes显示文摘Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus.Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased,with the available genomes of varying accuracy and completeness.We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species;Citrus australis(round lime)using highly accurate PacBio HiFi long reads,complemented with Hi-C scaffolding.Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C.australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness(BUSCO).Repeat analysis showed that more than 50% of the genome contained interspersed repeats.Among them,LTR elements were the predominant type(21.0%),of which LTR Gypsy(9.8%)and LTR copia(7.7%)elements were the most abundant repeats.A total of 29464 genes and 32009 transcripts were identified in the genome.Of these,28222 CDS(25753 genes)had BLAST hits and 21401 CDS(75.8%)were annotated with at least one GO term.Citrus specific genes for antimicrobial peptides,defense,volatile compounds and acidity regulation were identified.The synteny analysis showed conserved regions between the two haplotypes with some structural variations in Chromosomes 2,4,7 and 8.This chromosome scale,and haplotype resolved C.australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species. | Upuli Nakandala Ardashir Kharabian Masouleh Malcolm WSmith Agnelo Furtado Patrick Mason Lena Constantin Robert J.Henry | 2023 | Horticulture Research2023，10，5： | 0 |
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