Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes,however,the utility of this technology for complex plant genomes is unproven.We evaluated the technology ...Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes,however,the utility of this technology for complex plant genomes is unproven.We evaluated the technology for this purpose by sequencing the 3.5-gigabase(Gb)diploid pepper(Capsicum annuum)genome with a single Linked-Read library.Plant genomes,including pepper,are characterized by long,highly similar repetitive sequences.Accordingly,significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus.With a phased assembly approach,we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion.The Supernova software generated a highly ordered,more contiguous sequence assembly than all currently available C.annuum reference genomes.Over 83%of the final assembly was anchored and oriented using four publicly available de novo linkage maps.A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly.The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers,as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes.The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes.This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.展开更多
Despite an increasing awareness of the potential of“orphan”or unimproved crops to contribute to food security and enhanced livelihoods for farmers,coordinated research agendas to facilitate production and use of orp...Despite an increasing awareness of the potential of“orphan”or unimproved crops to contribute to food security and enhanced livelihoods for farmers,coordinated research agendas to facilitate production and use of orphan crops by local communities are generally lacking.We provide an overview of the current knowledge on leafy vegetables with a focus on Gynandropsis gynandra,a highly nutritious species used in Africa and Asia,and highlight general and species-specific guidelines for participatory,genomics-assisted breeding of orphan crops.Key steps in genome-enabled orphan leafy vegetables improvement are identified and discussed in the context of Gynandropsis gynandra breeding,including:(1)germplasm collection and management;(2)product target definition and refinement;(3)characterization of the genetic control of key traits;(4)design of the‘process’for cultivar development;(5)integration of genomic data to optimize that‘process’;(6)multi-environmental participatory testing and end-user evaluation;and(7)crop value chain development.The review discusses each step in detail,with emphasis on improving leaf yield,phytonutrient content,organoleptic quality,resistance to biotic and abiotic stresses and post-harvest management.展开更多
The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide populat...The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land.These conditions require increased efficiency in pepper breeding to deal with these imminent challenges.Through resequencing of inbred lines we have completed a valuable haplotype map(HapMap)for the pepper genome based on single-nucleotide polymorphisms(SNP).The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines.A selection of one marker per gene model was utilized to create the PepperSNP16K array,which simultaneously genotyped 16405 SNPs,of which 90.7%were found to be informative.A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array.Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups.The interspecific population created between Tabasco(C.frutescens chile type)and P4(C.annuum blocky type)produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM.This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper.As a standardized tool for genetic analyses,the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers.Data and information on the array are available through the Solanaceae Genomics Network.展开更多
基金This work was supported by research grants provided by Enza Zaden and Rijk ZwaanLibrary preparation and sequencing costs were provided by 10x GenomicsAdditional support was from the UC Davis Seed Biotechnology Center and USDA-ARS Project#6066-21310-004-00-D.
文摘Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes,however,the utility of this technology for complex plant genomes is unproven.We evaluated the technology for this purpose by sequencing the 3.5-gigabase(Gb)diploid pepper(Capsicum annuum)genome with a single Linked-Read library.Plant genomes,including pepper,are characterized by long,highly similar repetitive sequences.Accordingly,significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus.With a phased assembly approach,we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion.The Supernova software generated a highly ordered,more contiguous sequence assembly than all currently available C.annuum reference genomes.Over 83%of the final assembly was anchored and oriented using four publicly available de novo linkage maps.A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly.The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers,as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes.The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes.This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.
基金This study was supported by the Applied Research Fund of the Netherlands Organization for Science under the Project“Utilizing the genome of the vegetable species Cleome gynandra for the development of improved cultivars for the West and East African markets”(Project Number:W.08.270.350)and the African Orphan Crops Consortium.
文摘Despite an increasing awareness of the potential of“orphan”or unimproved crops to contribute to food security and enhanced livelihoods for farmers,coordinated research agendas to facilitate production and use of orphan crops by local communities are generally lacking.We provide an overview of the current knowledge on leafy vegetables with a focus on Gynandropsis gynandra,a highly nutritious species used in Africa and Asia,and highlight general and species-specific guidelines for participatory,genomics-assisted breeding of orphan crops.Key steps in genome-enabled orphan leafy vegetables improvement are identified and discussed in the context of Gynandropsis gynandra breeding,including:(1)germplasm collection and management;(2)product target definition and refinement;(3)characterization of the genetic control of key traits;(4)design of the‘process’for cultivar development;(5)integration of genomic data to optimize that‘process’;(6)multi-environmental participatory testing and end-user evaluation;and(7)crop value chain development.The review discusses each step in detail,with emphasis on improving leaf yield,phytonutrient content,organoleptic quality,resistance to biotic and abiotic stresses and post-harvest management.
文摘The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land.These conditions require increased efficiency in pepper breeding to deal with these imminent challenges.Through resequencing of inbred lines we have completed a valuable haplotype map(HapMap)for the pepper genome based on single-nucleotide polymorphisms(SNP).The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines.A selection of one marker per gene model was utilized to create the PepperSNP16K array,which simultaneously genotyped 16405 SNPs,of which 90.7%were found to be informative.A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array.Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups.The interspecific population created between Tabasco(C.frutescens chile type)and P4(C.annuum blocky type)produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM.This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper.As a standardized tool for genetic analyses,the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers.Data and information on the array are available through the Solanaceae Genomics Network.
