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A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding

Horticulture Research 2016年第1期3卷 157-166页

作者： Amanda M Hulse-Kemp Hamid Ashrafi Joerg Plieske Jana Lemm Kevin Stoffel Theresa Hill Hartmut Luerssen Charit L Pethiyagoda Cindy T Lawley Martin W Ganal allen van deynze Department of Plant Sciences University of California-DavisDavis95616CaliforniaUSA Illumina Incorporated 5200 Illumina WaySan Diego92122CAUSA TraitGenetics GmbH Am Schwabeplan 1bStadt Seeland OTGaterslebenGermany Department of Horticultural Sciences North Carolina State University2721 Founders Drive234 Kilgore HallRaleighNC 27518USA

The Capsicum genus(Pepper)is a part of the Solanacae *** has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and *** population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available *** conditions require increased efficiency in pepper breeding to deal with these imminent *** 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 *** analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm *** interspecific population created between Tabasco(*** chile type)and P4(*** blocky type)produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 *** publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for *** 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 *** and information on the array are available through the Solanaceae Genomics Network.

关键词： breeding pepper linkage

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A roadmap for breeding orphan leafy vegetable species: a case study of Gynandropsis gynandra (Cleomaceae)

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Horticulture Research 2018年第1期5卷 903-917页

作者： E.O.Deedi Sogbohossou Enoch G.Achigan-Dako Patrick Maundu Svein Solberg Edgar M.S.Deguenon Rita H.Mumm Iago Hale allen van deynze M.Eric Schranz Biosystematics Group Wageningen UniversityPostbus 6476700APWageningenThe Netherlands Laboratory of Genetics Horticulture and Seed SciencesFaculty of Agronomic SciencesUniversity of Abomey-CalaviBP 2549Abomey-CalaviBenin Kenya Resource Center for Indigenous Knowledge(KENRIK) Centre for BiodiversityNational Museums of KenyaMuseum HillP.O.Box 40658Nairobi00100Kenya World Vegetable Center(AVRDC) P.O.Box 42ShanhuaTainan74199Taiwan NGO Hortitechs Developpement 02 BP 1111CotonouBenin Department of Crop Sciences University of IllinoisUrbana-ChampaignIL61801USA Department of Agriculture Nutritionand Food SystemsUniversity of New HampshireDurhamNH03824USA Department of Plant Sciences University of CaliforniaDavisCA95616USA

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 *** 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 *** 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 *** 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.

关键词： breeding crops cultivar

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Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

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Horticulture Research 2018年第1期5卷 890-902页

作者： Amanda M.Hulse-Kemp Shamoni Maheshwari Kevin Stoffel Theresa A.Hill David Jaffe Stephen R.Williams Neil Weisenfeld Srividya Ramakrishnan Vijay Kumar Preyas Shah Michael C.Schatz Deanna M.Church allen van deynze Department of Plant Sciences University of CaliforniaDavisCAUSA USDA-ARS Genomics and Bioinformatics Research Unit RaleighNCUSA Department of Crop and Soil Sciences North Carolina State UniversityRaleighNCUSA 10x Genomics Inc7068 Koll Center ParkwaySuite 401PleasantonCAUSA Department of Computer Science Johns Hopkins UniversityBaltimoreMDUSA

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 *** evaluated the technology for this purpose by sequencing the 3.5-gigabase(Gb)diploid pepper(Capsicum annuum)genome with a single Linked-Read *** genomes,including pepper,are characterized by long,highly similar repetitive ***,significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid *** 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/*** Supernova software generated a highly ordered,more contiguous sequence assembly than all currently available *** reference *** 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 *** 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 *** 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 *** 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.

关键词： Capsicum pepper insertion

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基于辣椒基因组测序探究辣味在种群中的进化

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辣椒杂志 2014年第2期12卷 40-50页

作者： Seungill Kim Minkyu Park Seon-In Yeom Yong-Min Kim Je Min Lee Hyun-Ah Lee Eunyoung Seo Jaeyoung Choi Kyeongchae Cheong Ki-Tae Kim Kyongyong Jung Gir-Won Lee Sang-Keun Oh Chungyun Bae Saet-Byul Kim Hye-Young Lee Shin-Young Kim Myung-Shin Kim Byoung-Cheorl Kang Yeong Deuk Jo Hee-Bum Yang Hee-Jin Jeong Won-Hee Kang Jin-Kyung Kwon Chanseok Shin Jae Yun Lim June Hyun Park Jin Hoe Huh June-Sik Kim Byung-Dong Kim Oded Cohen Ilan Paran Mi Chung Suh Saet Buyl Lee Yeon-Ki Kim Younhee Shin Seung-Jae Noh Junhyung Park Young Sam Seo Suk-Yoon Kwon Hyun A Kim Jeong Mee Park Hyun-Jin Kim Sang-Bong Choi Paul W Bosland Gregory Reeves Sung-Hwan Jo Bong-Woo Lee Hyung-Taeg Cho Hee-Seung Choi Min-Soo Lee Yeisoo Yu Yang Do Choi Beom-Seok Park allen van deynze Hamid Ashrafi Theresa Hill Woo Taek Kim Hyun-Sook Pai Hee Kyung Ahn Inhwa Yeam James J Giovannoni Jocelyn K C Rose Iben Sφrensen Sang-Jik Lee Ryan W Kim Ik-Young Choi Beom-Soon Choi Jong-Sung Lim Yong-Hwan Lee Doil Choi 刘峰张西露 Department of Plant Science Seoul National University Plant Genomics and Breeding Institute Seoul National University Department of Agricultural Biotechnology Seoul National University Department of Bioinformatics and Life Science Soongsil University Vegetable Breeding Research Center Seoul National University Agricultural Research Organization Institute of Plant Science Volcani Center Bet DaganIsrael. Agricultural Research Organization Institute of Plant Science Volcani Center Bet DaganIsrael Department of Bioenergy Science and Technology Chonnam National University Genomics Genetics Institute GreenGene BioTech Inc. Codes Division Insilicogen Inc. Ginseng Resources Research Laboratory Korea Ginseng Corporation Korea Research Institute of Bioscience and Biotechnology Division of Bioscience and Bioinformatics Myongji University Department of Plant and Environmental Sciences New Mexico State University Chile Pepper Institute New Mexico State University Seeders Inc. Department of Biological Sciences Seoul National University Arizona Genomics Institute University of Arizona Agricultural Genome Center National Academy of Agricultural Science Rural Development Administration Seed Biotechnology Center University of California Davis Davis California USA Department of Systems Biology Yonsei University Department of Horticulture and Breeding Andong National University US Department of Agriculture-Agricultural Research Service Robert W. Holley Center Ithaca New York USA Boyce Thompson Institute for Plant Research Cornell University Ithaca New York USA Department of Plant Biology Cornell University Ithaca New York USA Biotechnology Institute Nongwoo Bio Yeoju Korea Genome Center University of California Davis Davis California USA National Instrumentation Center for Environmental Management Seoul National University Seoul Korea 湖南省蔬菜研究所

辣椒(Capsicum annuum)是美洲最古老的驯化作物之一,在全世界被广泛种植。本研究对CM334(墨西哥地方品种)进行了全基因组测序和组装(覆盖度为186.6×),同时还对另外两个栽培种和一个野生种分别进行了重测序和从头(de novo)测序。结果表... 详细信息

辣椒(Capsicum annuum)是美洲最古老的驯化作物之一,在全世界被广泛种植。本研究对CM334(墨西哥地方品种)进行了全基因组测序和组装(覆盖度为186.6×),同时还对另外两个栽培种和一个野生种分别进行了重测序和从头(de novo)测序。结果表明辣椒基因组大小约为番茄的4倍,辣椒基因组上存在大量gypsy转座子和花椰菜病毒家族元件的积累。结合转录组综合分析认为,辣椒素合成酶基因表达模式的改变及新功能化是导致辣椒素生物合成的原因,研究还发现辣椒与番茄在乙烯合成及果实成熟调控方面存在明显不同的分子模式。辣椒参考基因组的发布为辣椒营养品质和药用价值的改善提供了重要平台。

关键词：基因组测序辣椒素参考基因 Capsicum 转座子辣椒果实分子模式生物合成基因表达模式基因组大小

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