基因组分析揭示番茄育种的历史

番茄（Solanum lycopersicum）适应性广，产量高，营养丰富，风味独特，栽培方式多样，是世界范围内广泛种植的第一大蔬菜作物。2012年全球产量达到1.62亿吨（联合国粮农组织（FAO）统计），产值超过550亿美元。番茄也是植物遗传、发育和生理研究的重要模式系统。番茄起源于南美洲的安第斯山脉，随着人类迁移和驯化逐渐传到中美洲和墨西哥一代，16世纪传到欧洲，在随后的几百年中番茄被传播到世界各地，在这一过程中受到不同的人工选择，产生了丰富的变异类型。番茄果实大小的变化是驯化的一个重要特征，今天人们食用的大果栽培番茄是由野生醋栗番茄（Solanum pimpinellifolium）驯化而来，野生番茄果实非常小，只有1~2g 重，经过人工的长期驯化，现代栽培番茄的果重是其祖先的100多倍。然而，番茄果实变大的人工驯化过程一直未有全面的研究，人类选择如何改变番茄基因组仍是知之甚少。

The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development

Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement.Optimal collection,preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection.Here we use the high-throughput genotyping-by-sequencing(GBS)technology to characterize the United States National Plant Germplasm System(NPGS)collection of cucumber(Cucumis sativus L.).The GBS data,derived from 1234 cucumber accessions,provided more than 23 K high-quality single-nucleotide polymorphisms(SNPs)that are well distributed at high density in the genome(~1 SNP/10.6 kb).The SNP markers were used to characterize genetic diversity,population structure,phylogenetic relationships,linkage disequilibrium,and population differentiation of the NPGS cucumber collection.These results,providing detailed genetic analysis of the U.S.cucumber collection,complement NPGS descriptive information regarding geographic origin and phenotypic characterization.We also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies(GWAS).Finally,we developed a molecularly informed,publicly accessible core collection of 395 accessions that represents at least 96%of the genetic variation present in the NPGS.Collectively,the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection,and will provide a valuable resource for genetic analyses,gene discovery,crop improvement,and germplasm preservation.

A key‘foxy’aroma gene is regulated by homologyinduced promoter indels in the iconic juice grape‘Concord’

‘Concord’,the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L.,possesses a special‘foxy’aroma predominantly resulted from the accumulation of methyl anthranilate(MA)in berries.This aroma,however,is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V.vinifera.Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key‘foxy’aroma gene,anthraniloyl-CoA:methanol acyltransferase(AMAT),that is responsible for MA biosynthesis.We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in‘Concord’and other V.labrusca-derived grapes.These promoter variants,all with direct and inverted repeats,were further confirmed in more than 1,300 Vitis germplasm.Moreover,functional impact of these indels was validated in transgenic Arabidopsis.Superimposed on the promoter regulation,large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V.vinifera grapes.Elucidation of the AMAT genetic regulation advances our understanding of the‘foxy’aroma trait and makes it genetically trackable and amenable in grapevine breeding.

Kiwifruit Genome Database(KGD):a comprehensive resource for kiwifruit genomics

Kiwifruit(Actinidia spp.)plants produce economically important fruits containing abundant,balanced phytonutrients with extraordinarily high vitamin C contents.Since the release of the first kiwifruit reference genome sequence in 2013,large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.To efficiently store,analyze,integrate,and disseminate these large-scale datasets to the research community,we constructed the Kiwifruit Genome Database(KGD;http://kiwifruitgenome.org/).The database currently contains all publicly available genome and gene sequences,gene annotations,biochemical pathways,transcriptome profiles derived from public RNA-Seq datasets,and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies.A set of user-friendly query interfaces,analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit,which include JBrowse,a popular genome browser,and the NCBI BLAST sequence search tool.Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology(GO)term and pathway enrichment analysis.

Comparative transcriptome analyses shed light on carotenoid production and plastid development in melon fruit

Carotenoids,such asβ-carotene,accumulate in chromoplasts of various fleshy fruits,awarding them with colors,aromas,and nutrients.The Orange(CmOr)gene controlsβ-carotene accumulation in melon fruit by posttranslationally enhancing carotenogenesis and repressingβ-carotene turnover in chromoplasts.Carotenoid isomerase(CRTISO)isomerizes yellow prolycopene into red lycopene,a prerequisite for further metabolism intoβ-carotene.We comparatively analyzed the developing fruit transcriptomes of orange-colored melon and its two isogenic EMS-induced mutants,low-β(Cmor)and yofi(Cmcrtiso).The Cmor mutation in low-βcaused a major transcriptomic change in the mature fruit.In contrast,the Cmcrtiso mutation in yofi significantly changed the transcriptome only in early fruit developmental stages.These findings indicate that melon fruit transcriptome is primarily altered by changes in carotenoid metabolic flux and plastid conversion,but minimally by carotenoid composition in the ripe fruit.Clustering of the differentially expressed genes into functional groups revealed an association between fruit carotenoid metabolic flux with the maintenance of the photosynthetic apparatus in fruit chloroplasts.Moreover,large numbers of thylakoid localized photosynthetic genes were differentially expressed in low-β.CmOR family proteins were found to physically interact with light-harvesting chlorophyll a–b binding proteins,suggesting a new role of CmOR for chloroplast maintenance in melon fruit.This study brings more insights into the cellular and metabolic processes associated with fruit carotenoid accumulation in melon fruit and reveals a new maintenance mechanism of the photosynthetic apparatus for plastid development.

The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening

Fleshy fruit ripening is governed by multiple external and internal cues and accompanied by changes in color,texture,volatiles,and nutritional quality traits.While extended shelf-life and increased phytonutrients are desired,delaying ripening via genetic or postharvest means can be accompanied by reduced nutritional value.Here we report that the high pigment 1(hp1)mutation at the UV-DAMAGED DNA BINDING PROTEIN 1(DDB1)locus,previously shown to influence carotenoid and additional phytonutrient accumulation via altered light signal transduction,also results in delayed ripening and firmer texture,resulting at least in part from decreased ethylene evolution.Transcriptome analysis revealed multiple ethylene biosynthesis and signaling-associated genes downregulated in hp1.Furthermore,the hp1 mutation impedes softening of the pericarp,placenta,columella as well as the whole fruit,in addition to reduced expression of the FRUITFUL2(FUL2)MADS-box transcription factor and xyloglucan endotransglucosylase/hydrolase 5(XTH5).These results indicate that DDB1 influences a broader range of fruit development and ripening processes than previously thought and present an additional genetic target for increasing fruit quality and shelf-life.

Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat(Eriobotrya japonica)fruit

Loquat(Eriobotrya japonica)fruit accumulates lignin during postharvest storage under chilling conditions(0℃),while low-temperature conditioning(LTC;5℃for 6 days followed by transfer to 0℃)or heat treatment(HT;40℃for 4 h followed by transfer to 0℃)can alleviate lignification.Here we compared transcriptome profiles of loquat fruit samples under LTC or HT to those stored at 0℃at five time points from day 1 to day 8 after treatment.High-throughput transcriptome sequences were de novo assembled into 53,319 unique transcripts with an N50 length of 1306 bp.A total of 2235 differentially expressed genes were identified in LTC,and 1020 were identified in HT compared to 0℃.Key genes in the lignin biosynthetic pathway,including EjPAL2,EjCAD1,EjCAD3,4CL,COMT,and HCT,were responsive to LTC or HT treatment,but they showed different expression patterns during the treatments,indicating that different structural genes could regulate lignification at different treatment stages.Coexpression network analysis showed that these candidate biosynthetic genes were associated with a number of transcription factors,including those belonging to the AP2,MYB,and NAC families.Gene ontology(GO)enrichment analysis of differentially expressed genes indicated that biological processes such as stress responses,cell wall and lignin metabolism,hormone metabolism,and metal ion transport were significantly affected under LTC or HT treatment when compared to 0℃.Our analyses provide insights into transcriptome responses to postharvest treatments in loquat fruit.

The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening

Snake gourd(Trichosanthes anguina L.),which belongs to the Cucurbitaceae family,is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world.Although progress has been made in its genetic improvement,the organization,composition,and evolution of the snake gourd genome remain largely unknown.Here,we report a high-quality genome assembly for snake gourd,comprising 202 contigs,with a total size of 919.8 Mb and an N50 size of 20.1 Mb.These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date.The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0%of the genome consists of repetitive sequences.Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor~33–47 million years ago.The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species.In addition,fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.

Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple(Malus×domestica)

Apple cultivars with durable resistance are needed for sustainable management of fire blight,the most destructive bacterial disease of apples.Although studies have identified genetic resistance to fire blight in both wild species and cultivated apples,more research is needed to understand the molecular mechanisms underlying host–pathogen interaction and differential genotypic responses to fire blight infection.We have analyzed phenotypic and transcriptional responses of‘Empire’and‘Gala’apple cultivars to fire blight by infecting them with a highly aggressive E.amylovora strain.Disease progress,based on the percentage of visual shoot necrosis,started showing significant(p<0.001)differences between‘Empire’and‘Gala’4 days after infection(dai).‘Empire’seems to slow down bacterial progress more rapidly after this point.We further compared transcriptome profiles of‘Empire’and‘Gala’at three different time points after fire blight infection.More genes showed differential expression in‘Gala’at earlier stages,but the number of differentially expressed genes increased in‘Empire’at 3 dai.Functional classes related to defense,cell cycle,response to stress,and biotic stress were identified and a few co-expression gene networks showed particular enrichment for plant defense and abiotic stress response genes.Several of these genes also co-localized in previously identified quantitative trait locus regions for fire blight resistance on linkage groups 7 and 12,and can serve as functional candidates for future research.These results highlight different molecular mechanisms for pathogen perception and control in two apple cultivars and will contribute toward better understanding of E.amylovora-Malus pathosystem.

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago （Mya）, respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima ×C. moschata interspecific F1 hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.

Unraveling a genetic roadmap for improved taste in the domesticated apple

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.

Plant Genome Editing Database (PGED): A Call for Submission of Information about Genome-Edited Plant Mutants

Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large or entire chromosome deletions in the genomes of plants and animals (Zhou et al., 2014;Adikusuma et al., 2017).

Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency

In response to phosphate(Pi) deficiency, it has been shown that micro-RNAs(miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long noncoding RNAs(lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond,systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic(TM) of miRNA399,accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress.Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields

Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.

Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

Melon(C.melo L.)is an economically important vegetable crop cultivated worldwide.The melon collection in the U.S.National Plant Germplasm System(NPGS)is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding.Here we use the genotyping-by-sequencing(GBS)technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist.Population structure and genetic diversity analyses suggested that C.melo ssp.melo was firstly introduced from the centers of origin,Indian and Pakistan,to Central and West Asia,and then brought to Europe and Americas.C.melo ssp.melo from East Asia was likely derived from C.melo ssp.agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp.melo accessions from other geographic regions.We developed a core collection of 383 accessions capturing more than 98%of genetic variation in the germplasm,providing a publicly accessible collection for future research and genomics-assisted breeding of melon.Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection.Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits.This study provides insights into melon origin and domestication,and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes

In response to infestation with larvae of the Guatemalan tuber moth （Tecia solanivora）, some Solanum tuberosum （potato） varieties exhibit an overcompensa- tion response, whereby the total dry mass of uninfested tubers is increased. Here, we describe early responses, within the first few days, of T. solanivora feeding, in the Colombian potato variety Pastusa Suprema. Non- targeted metabolite profiling showed significant second- ary metabolism changes in T. solanivora-infested tubers, but not in uninfested systemic tubers. In contrast, changes in primary metabolism were greater in unin- fested systemic tubers than in the infested tubers, with a notable 80% decline in systemic tuber sucrose levels within 1 d of T. solanivora infestation. This suggested either decreased sucrose transport from the leaves or increased sink strength, i.e., more rapid sucrose to starch conversion in the tubers. Increased sucrose synthesis was indicated by higher rubisco activase and lower starch synthase gene expression in the leaves of infested plants. Elevated sink strength was demonstrated by 45% more total starch deposition in systemic tubers of T. solanivord- infested plants compared to uninfested control plants. Thus, rather than investing in increased defense of uninfested tubers, Pastusa Suprema promotes deposition of photoassimilates in the form of starch as a response to T. solanivora infestation.

An R2R3-type myeloblastosis transcription factor MYB103 is involved in phosphorus remobilization

The members of myeloblastosis transcription factor(MYB TF)family are involved in the regulation of biotic and abiotic stresses in plants.However,the role of MYB TF in phosphorus remobilization remains largely unexplored.In the present study,we show that an R2R3 type MYB transcription factor,MYB103,is involved in phosphorus(P)remobilization.MYB103 was remarkably induced by P deficiency in cabbage(Brassica oleracea var.capitata L.).As cabbage lacks the proper mutant for elucidating the mechanism of MYB103 in P deficiency,another member of the crucifer family,Arabidopsis thaliana was chosen for further study.The transcript of its homologue AtMYB103 was also elevated in response to P deficiency in A.thaliana,while disruption of AtMYB103(myb103)exhibited increased sensitivity to P deficiency,accompanied with decreased tissue biomass and soluble P concentration.Furthermore,AtMYB103 was involved in the P reutilization from cell wall,as less P was released from the cell wall in myb103 than in wildtype,coinciding with the reduction of ethylene production.Taken together,our results uncover an important role of MYB103 in the P remobilization,presumably through ethylene signaling.

Transcriptomes of developing fruit of cultivated and wild tomato species

Tomato(Solanum lycopersicum)is one of the world’s most extensively cultivated crops,and has been the subject of hundreds of years of breeding and selection.Nevertheless,the genetic variability available for the breeding and improvement of tomato within the confines of the species is limited.This has been described as a“genetic bottleneck”(Miller and Tanksley 1990)and is due to the domestication history of the crop,particularly the transfer of select germplasm from South America to Europe in the 1500 s,followed by selections and return to the New World,again of limited germplasm(Knapp and Peralta 2016).