查看更多>>摘要：Although revisiting the discoveries and implications of genetic variations using phased genomics is critical,such efforts are still lacking.Somatic mutations represent a crucial source of genetic diversity for breeding and are especially remarkable in heterozygous perennial and asexual crops.In this study,we focused on a diploid sweet orange(Citrus sinensis)and constructed a haplotype-resolved genome using high fidelity(HiFi)reads,which revealed 10.6％new sequences.Based on the phased genome,we elucidate significant genetic admixtures and haplotype differences.We developed a somatic detection strategy that reveals hidden somatic mutations overlooked in a single reference genome.We generated a phased somatic variation map by combining high-depth whole-genome sequencing(WGS)data from 87 sweet orange somatic varieties.Notably,we found twice as many somatic mutations relative to a single reference genome.Using these hidden somatic mutations,we separated sweet oranges into seven major clades and provide insight into unprecedented genetic mosaicism and strong positive selection.Furthermore,these phased genomics data indicate that genomic heterozygous variations contribute to allele-specific expression during fruit development.By integrating allelic expression differences and somatic mutations,we identified a somatic mutation that induces increases in fruit size.Applications of phased genomics will lead to powerful approaches for discovering genetic variations and uncovering their effects in highly heterozygous plants.Our data provide insight into the hidden somatic mutation landscape in the sweet orange genome,which will facilitate citrus breeding.
查看更多>>摘要：The subfamily Agavoideae comprises crassulacean acid metabolism(CAM),C3,and C4 plants with a young age of speciation and slower mutation accumulation,making it a model crop for studying CAM evolution.However,the genetic mechanism underlying CAM evolution remains unclear because of lacking genomic information.This study assembled the genome of Agave hybrid NO.11648,a constitutive CAM plant belonging to subfamily Agavoideae,at the chromosome level using data generated from high-throughput chromosome conformation capture,Nanopore,and Illumina techniques,resulting in 30 pseudo-chromosomes with a size of 4.87 Gb and scaffold N50 of 186.42 Mb.The genome annotation revealed 58 841 protein-coding genes and 76.91％repetitive sequences,with the dominant repetitive sequences being the I-type repeats(Copia and Gypsy accounting for 18.34％and 13.5％of the genome,respectively).Our findings also provide support for a whole genome duplication event in the lineage leading to A.hybrid,which occurred after its divergence from subfamily Asparagoideae.Moreover,we identified a gene duplication event in the phosphoenolpyruvate carboxylase kinase(PEPCK)gene family and revealed that three PEPCK genes(PEPCK3,PEPCK5,and PEPCK12)were involved in the CAM pathway.More importantly,we identified transcription factors enriched in the circadian rhythm,MAPK signaling,and plant hormone signal pathway that regulate the PEPCK3 expression by analysing the transcriptome and using yeast one-hybrid assays.Our results shed light on CAM evolution and offer an essential resource for the molecular breeding program of Agave spp.
Christian DujakVeredas Coleto-AlcudiaMaria José Aranzana
29-42页
查看更多>>摘要：Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program.Here,we focus on two apple fruit quality traits:shape and size.We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection,which serves as a representative sample of the genetic variability present in European-cultivated apples.The data were then employed for genome-wide association studies(GWAS)using the FarmCPU and the BLINK models.The analysis identified 59 SNPs associated with fruit size and shape traits(35 with FarmCPU and 45 with BLINK)responsible for 71 QTNs.These QTNs were distributed across all chromosomes except for chromosomes 10 and 15.Thirty-four QTNs,identified by 27 SNPs,were related for size traits,and 37 QTNs,identified by 26 SNPs,were related to shape attributes.The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes,among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11.RNA-seq data revealed low or null expression of these genes in the oblong cultivar"Skovfoged"and higher expression in the flat"Grand'mere."The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation.In conclusion,this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes,providing valuable insights that could enhance the efficiency of future breeding programs.
查看更多>>摘要：Sugars are the main drivers of strawberry sweetness,and understanding their genetic control is of critical importance for breeding.Large-scale genome-wide association studies were performed in two populations totaling 3399 individuals evaluated for soluble solids content(SSC)and fruit yield.Two stable quantitative trait loci(QTL)on chromosome 3B and 6A for SSC were identified.Favorable haplotypes at both QTL for SSC decreased yield,though optimal allelic combinations were identified with reduced impacts on yield.Metabolites in the starch and sucrose metabolism pathway were characterized and quantified for 23 contrasting genotypes in leaves,white fruit,and red fruit.Variations in sucrose concentrations/efflux indicated genetic variation underlying sucrose accumulation and transportation during fruit ripening.Integration of genome-wide association studies and expression quantitative locus mapping identified starch synthase 4(FxaC_10g00830)and sugar transporter 2-like candidate genes(FxaC_21g51570)within the respective QTL intervals.These results will enable immediate applications in genomics-assisted breeding for flavor and further study of candidate genes underlying genetic variation of sugar accumulation in strawberry fruit.
查看更多>>摘要：Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease.However,whether this recruitment is regulated by quantitative trait loci(QTL)is unclear.The role of QTL in recruiting specific bacteria against bacterial wilt(BW)is an important question of practical significance to disease management.Here,to identify QTL controlling BW resistance,Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193.The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers.Rhizosphere bacterial composition of R06112,S55193,and resistant individuals EB158(with the QTL)and susceptible individuals EB327(without QTL)from BC2F1 generation were assessed by Illumina sequencing-based analysis,and the activation of plant immunity by the bacterial isolates was analyzed.Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10,namely EBWR10,and nsLTPs as candidate genes confirmed by RNA-Seq.EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus.pp.A SynCom of three isolated Bacillus.pp trains significantly reduced the disease incidence,changed activities of CAT,PPO,and PAL and concentration of NO,H2O2,and O2-,activated SA and JA signaling-dependent ISR,and displayed immune activation against Ralstonia solanacearum in eggplant.Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria,which jointly promote the suppression of BW.This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.
查看更多>>摘要：In the era of rapid advancements in high-throughput omics technologies,the visualization of diverse data types with varying orders of magnitude presents a pressing challenge.To bridge this gap,we introduce DataColor,an all-encompassing software solution meticulously crafted to address this challenge.Our aim is to empower users with the ability to handle a wide array of data types through an assortment of tools,while simultaneously streamlining parameter selection for rapid insights and detailed enhancements.DataColor stands as a robust toolkit,encompassing 23 distinct tools coupled with over 600 parameters.The defining characteristic of this toolkit is its adept utilization of the color spectrum,allowing for the representation of data spanning diverse types and magnitudes.Through the integration of advanced algorithms encompassing data clustering,normalization,squarified layouts,and customizable parameters,DataColor unveils an abundance of insights that lay hidden within the intricate relationships embedded in the data.Whether you find yourself navigating the analysis of expansive datasets or embarking on the quest to visualize intricate patterns,DataColor stands as the comprehensive and potent solution.We extend the availability of DataColor to all users at no cost,accessible through the following link:https://github.com/frankgenome/DataColor.
查看更多>>摘要：The completion of the first telomere-to-telomere(T2T)genome assembly of Penthorum chinense Pursh(PC),a prominent medicinal plant in China,represents a significant achievement.This assembly spans a length of 257.5 Mb and consists of nine chromosomes.PC's notably smaller genome size in Saxifragales,compared to that of Paeonia ostii,can be attributed to the low abundance of transposable elements.By utilizing single-copy genes from 30 species,including 28 other Superrosids species,we successfully resolved a previously debated Superrosids phylogeny.Our findings unveiled Saxifragales as the sister group to the core rosids,with both being the sister group to Vitales.Utilizing previously characterized cytochrome P450(CYP)genes,we predicted the compound classes that most CYP genes of PC are involved in synthesizing,providing insight into PC's potential metabolic diversity.Metabolomic and transcriptomic data revealed that the richest sources of the three most noteworthy medicinal components in PC are young leaves and flowers.We also observed higher activity of upstream genes in the flavonoid synthesis pathway in these plant parts.Additionally,through weighted gene co-expression network analysis,we identified gene regulatory networks associated with the three medicinal components.Overall,these findings deepen our understanding of PC,opening new avenues for further research and exploration.
查看更多>>摘要：The phytohormone ethylene is well known for its important role in the ripening of climacteric fruit,such as tomato(Solanum lycopersicum).However,the role and mode of action of other plant hormones in climacteric fruit ripening regulation are not fully understood.Here,we showed that exogenous GA treatment or increasing endogenous gibberellin content by overexpressing the gibberellin synthesis gene SlGA3ox2 specifically in fruit tissues delayed tomato fruit ripening,whereas treatment with the GA biosynthesis inhibitor paclobutrazol(PAC)accelerated fruit ripening.Moreover,exogenous ethylene treatment cannot completely reverse the delayed fruit ripening phenotype.Furthermore,exogenous GA treatment of ethylene signalling mutant Never ripe(Nr)or SlEBF3-overexpressing lines still delayed fruit ripening,suggesting that GA involved in fruit ripening partially depends on ethylene.Transcriptome profiling showed that gibberellin affect the ripening of fruits by modulating the metabolism and signal transduction of multiple plant hormones,such as auxin and abscisic acid,in addition to ethylene.Overall,the results of this study provide new insight into the regulation of gibberellin in fruit ripening through mediating multiple hormone signals.
查看更多>>摘要：Huanglongbing(HLB)primarily caused by Candidatus Liberibacter asiaticus(CLas)has been threatening citrus production globally.Under HLB conditions,an excessive accumulation of the polysaccharide callose in citrus phloem occurs,leading to phloem blockage and starch accumulation in leaves.The callose production is controlled by callose synthases(CalS),which have multiple members within plants.However,the knowledge of callose production in the citrus upon infection with CLas is limited.In this study,we firstly identified 11 CalSs in the Citrus sinensis genome through bioinformatics and found the expression pattern of CsCalS11 exhibited a positive correlation with callose deposition in CLas-infected leaves(correlation coefficient of 0.77,P ≤ 0.05).Knockdown of CsCalS11 resulted in a reduction of callose deposition and starch accumulation in CLas-infected citrus.Interestingly,we observed significantly higher concentrations of abscisic acid(ABA)in HLB-infected citrus leaves compared to uninfected ones.Furthermore,the expressions of CsABI5,CsPYR,and CsSnRK2 in the ABA pathway substantially increased in citrus leaves upon CLas infection.Additionally,the expression of CsCalS11 was significantly upregulated in citrus leaves following the application of exogenous ABA.We confirmed that CsABI5,a pivotal component of the ABA signaling pathway,regulates CsCalS11 expression by binding to its promoter using yeast one-hybrid assay,dual luciferase assay,and transient expression in citrus leaves.In conclusion,our findings strongly suggest that the CsABI5-CsCalS11 module plays a crucial role in regulating callose deposition through the ABA signaling pathway during CLas infection.The results also revealed new function of the ABA signaling pathway in plants under biotic stress.
查看更多>>摘要：Solanum habrochaites(SH),a wild species closely related to'Ailsa Craig'(AC),is an important germplasm resource for modern tomato breeding.Trichomes,developed from epidermal cells,have a role in defense against insect attack,and their secretions are of non-negligible value.Here,we found that the glandular heads of type VI trichomes were clearly distinguishable between AC and SH under cryo-scanning electron microscopy,the difference indicating that SH could secrete more anti-insect metabolites than AC.Pest preference experiments showed that aphids and mites preferred to feed near AC compared with SH.Integration analysis of transcriptomics and metabolomics data revealed that the phenylpropanoid biosynthesis pathway was an important secondary metabolic pathway in plants,and SH secreted larger amounts of phenylpropanoids and flavonoids than AC by upregulating the expression of relevant genes in this pathway,and this may contribute to the greater resistance of SH to phytophagous insects.Notably,virus-induced silencing of Sl4CLL6 not only decreased the expression of genes downstream of the phenylpropanoid biosynthesis pathway(SlHCT,SlCAD,and SlCHI),but also reduced resistance to mites in tomato.These findings provided new genetic resources for the synthesis of phenylpropanoid compounds and anti-insect breeding in S.habrochaites and a new theoretical basis for the improvement of important traits in cultivated tomato.
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