Rapid Genotyping of Soybean Cultivars Using High Throughput Sequencing 英文参考文献.docVIP

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Rapid Genotyping of Soybean Cultivars Using High Throughput Sequencing 英文参考文献.doc

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Rapid Genotyping of Soybean Cultivars Using High Throughput Sequencing 英文参考文献

RapidGenotypingofSoybeanCultivarsUsingHigh ThroughputSequencing KranthiVarala,KankshitaSwaminathan,YingLi,MatthewE.Hudson* DepartmentofCropSciences,UniversityofIllinois,Urbana-Champaign,Illinois,UnitedStatesofAmerica Abstract Soybean (Glycine max) breedinginvolves improvingcommercially grown varietiesby introgressing importantagronomic traitsfrompooryieldingaccessionsand/orwildrelativesofsoybeanwhileminimizingtheassociatedyielddrag.Molecular markers associated with these traits are instrumental in increasing the efficiency of producing such crosses and Single NucleotidePolymorphisms(SNPs)areparticularlywellsuitedforthistask,owingtohighdensityinthenon-genicregions andthusincreasedlikelihoodoffindingatightlylinkedmarkertoagiventrait.ArapidmethodtodevelopSNPmarkersthat candifferentiatespecificlocibetweenanytwoparentsinsoybeanisthushighlydesirable.Inthisstudyweinvestigatesuch aprotocolfordevelopingSNPmarkersbetweenmultiplesoybeanaccessionsandthereferenceWilliams82genome.To restrictsamplingfrequencyreducedrepresentationlibraries(RRLs)ofgenomicDNAweregeneratedbyrestrictiondigestion followedbylibraryconstruction.WechosetosequencefouraccessionsDowling(PI548663),Dwight(PI597386),Komata (PI200492)andPI594538AfortheiragronomicimportanceaswellasWilliams82asacontrol. MseIwaschosentodigest genomicDNAbasedonpredictionsthatitwillcutsparinglyinthemathematicallydefinedhigh-copy-numberregionsofthe genome.AllRRLsweresequencedontheIlluminagenomeanalyzer.ReadswerealignedtotheGlyma1referenceassembly and SNP calls made from the alignments. We identified from 4294 to 14550 SNPs between the four accessions and the Williams82reference.InadditionasmallnumberofSNPs(1142)werefoundbyaligningWilliams82readstothereference assembly(Glyma1)suggestinglimitedgeneticvariationwithintheWilliams82line.TheSNPdataallowedustoestimate geneticdiversitybetweenthefourlinesandWilliams82.RestrictiondigestionofsoybeangenomicDNAwithMseIfollowed byhighthroughputsequencingprovidesarapidandreproduciblemethodfor