二代测序在农业中SNP筛选0815

二代测序在农业中SNP筛选中的应用贝瑞和康生物技术有限公司NatureGenetics(2010),42(11):1027-1030Genome-widepatternsofgeneticvariationamongelitemaizeinbredlines★六个自交系：Zheng58、5003、478、178、Chang7-2和Mo17★平均测序深度：5.4倍★SNP位点：1,272,134(130,540)★InDel：30178Genome-widepatternsofgeneticvariationamongelitemaizeinbredlines★PAV(presence/absencevariations)大多仅发生一个基因的事件只有一部分存在2-4个临近基因的缺失。BMCGenomics(2012),13(3):RADtagsequencingasasourceofSNPmarkersinCynaracardunculusLCynaracardunculus(2n=2x=34,haploidgenomesize~1.08Gbp)朝鲜蓟花蕾的总苞片及花托可作为蔬菜来食用，根部可作为药物，有增强肝脏机能及利尿作用。ThreeC.cardunculusaccessionsgeneratedsome9.7millionreads(19.4millionpairedends),correspondingto~1Gbpofsequence.with1.2millionreadsachievedforglobeartichoke,2.6millionforcultivatedcardoonand5.9millionforwildcardoonBMCGenomics(2012),13(3)RADtagsequencingasasourceofSNPmarkersinCynaracardunculusLBMCGenomics(2012),13(3）RADtagsequencingasasourceofSNPmarkersinCynaracardunculusLBMCGenomics(2012),13(3)RADtagsequencingasasourceofSNPmarkersinCynaracardunculusL1、atotalof19,762contigs(38.1%)containedreadsfromonlytwogenotypes,with18.3%ofthecontigshavingreadsfromB493×QALandB7262,9.4%fromB493×QALandB6274,and10.4%fromB7262andB6274Denovoassemblyandcharacterizationofthecarrottranscriptomerevealsnovelgenes,newmarkers,andgeneticdiversityBMCGenomics(2011):12:389B493librarygenerateatotalof8,221,411ntwithanaveragelengthof456ntB6274,B7262andB493×QALyield34Mto39Musablereadsof41ntorlongerforeachgenotypeDenovoassemblyandcharacterizationofthecarrottranscriptomerevealsnovelgenes,newmarkers,andgeneticdiversityBMCGenomics(2011):12:389EndospermII/IIIEndospermV/VIGerminatingseedLeafMaleflowersTotalreads21,858,75414,326,64117,374,53719,322,72417,869,625Totalnumberofpositionsmapped36,412,20725,447,31629,038,42432,267,70628,774,682TotalReadsmapped19,924,43613,130,08415,892,92615,749,36116,193,189Percentageofreadsmapped9192918291Denovoassemblyandcharacterizationofthecarrottranscriptomerevealsnovelgenes,newmarkers,andgeneticdiversityBMCGenomics(2011):12:389Denovoassemblyandcharacterizationofthecarrottranscriptomerevealsnovelgenes,newmarkers,andgeneticdiversityBMCGenomics(2011):12:389Rapidgene-basedSNPandhaplotypemarkerdevelopmentinnon-modeleukaryotesusing3’UTRsequencingBMCGenomics(2012),13:18Rapidgene-basedSNPandhaplotypemarkerdevelopmentinnon-modeleukaryotesusing3’UTRsequencingBMCGenomics(2012),13:18cherrycultivars,BingandRainierRapidgene-basedSNPandhaplotypemarkerdevelopmentinnon-modeleukaryotesusing3’UTRsequencingBMCGenomics(2012),13:18A-Carefromprimersamplifyingaregionexpectedtocontain1putativeSNPwhileDcontains2,Ehas3,andFcontains5.Rapidgene-basedSNPandhaplotypemarkerdevelopmentinnon-modeleukaryotesusing3’UTRsequencingBMCGenomics(2012),13:18Boxes1and2representuniquehaplotypesfromBingandRainier，Haplotype1consistsof11readsfromBingand1ofRainierwhilehaplotype2isentirelyRainier.685haplotypes