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

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 

机构地区：[1]Department of Plant Sciences,University of California-Davis,Davis,95616,California,USA [2]Illumina Incorporated,5200 Illumina Way,San Diego,92122,CA,USA [3]TraitGenetics GmbH,Am Schwabeplan 1b,Stadt Seeland OT,Gatersleben,Germany [4]Department of Horticultural Sciences,North Carolina State University,2721 Founders Drive,234 Kilgore Hall,Raleigh,NC 27518,USA

出　　处：《Horticulture Research》2016年第1期157-166,共10页园艺研究（英文）

摘　　要：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.

关 键 词：BREEDING PEPPER LINKAGE 

分 类 号：S64[农业科学—蔬菜学]