GenomicsandAbioticStress Oct11 2012 Outline Introduction genome genomicsGenomemapping sequencingNext generationsequencing applicationsCropgenomicsandabioticstressGWAS itsapplicationinabioticstressComparativegenomicsPhylogeneticandevolutionaryanalysisFuturedirections FunctionalGenomics SystemsBiology Genome 1920byHansWinkler GermanyAblendofthewordsgeneandchromosome OxfordEnglishDictionarytheentiretyofanorganism shereditaryinformation includesboththegenesandthenon codingsequencesoftheDNA RNA Introduction genome TypesofGenomechromosome organizedstructureofhereditaryinformationincells Eukaryoticcells nucleargenomemitochondrialgenomechloroplastgenomeProkaryoticcells Chromosome genomic DNAPlasmid ChromosomeDNA Plasmids Introduction genome Nucleargenome FluorescentIn SituHybridization FISH identificationofHumanChromosomes ChromosomePainting Introduction genome PackingnuclearDNA Histones packingmaterialforeukaryoticnuclearDNA playbothpositiveandnegativerolesingeneexpression Introduction genome Mitochondrialandchloroplastgenome Humanmitochondrialgenome Ricechloroplastgenome Introduction genome HumanGenomeProgram U S DepartmentofEnergy GenomicsandItsImpactonMedicineandSociety A2001Primer 2001 Introduction genome Genomics coinedbyThomasRoderickin1986 referstoanewscientificdisciplineofmapping sequencing andanalyzinggenomes NowGenomicsisundergoingatransitionandexpansionfromthemappingandsequencingofgenomestoanemphasisongenomefunction Introduction genomics Genetic Linkagemapping遗传图谱 Geneticmapping determinethepositionofgenesormarkersrelativetoeachother Alinkagemapisageneticmapshowstherelativedistanceofmarkers Thisdistanceisexpressedintermsofageneticmapunit acentimorgan cM遗传距离 whichisdefinedasthedistancebetweengenesforwhichoneproductofmeiosisin100isrecombinant AlfredSturtevantfirstdevelopedgeneticmapsin1913 Heproposedthatthegreaterthedistancebetweenlinkedgenes thegreatercrossoverbetweenthegenes Arecombinantfrequency RF of1 isequivalentto1cM Butthisequivalenceisonlyagoodapproximationforsmallpercentages GenomeMapping assigningDNAfragmentstochromosomes Physicalmapping物理图谱 Thephysicalpositionsofgenes markers orsequencesonchromosomesGenescanbemappedtochromosomespriortothecompletesequencingbyindependentapproacheslikeFISHandFingerprinting restrictionmappingWholegenomesequencing GenomeMapping 限制酶作图 restrictionmapping GenomeMapping 荧光原位杂交Fluorescenceinsituhybridization FISH 如何整合遗传图与物理图 Strategiesforwholegenomesequencing 简单 快 成本低组装困难 gap 准确 精确度高难度 费用高 周期长 GenomeSequencing HistoryofWholeGenomeSequencing 1995年7月流感嗜血杆菌 haemophilusinfluenzae 第一个细菌基因组全序列 大小为1 8Mb 含1703个基因 Firstcompletegenomesequencefromafree livingorganism GenomeSequencing Science 1995Jul28 269 5223 496 512 2000年12月拟南芥Arabidopsisthaliana第一个植物基因组序列 遗传图谱 物理图谱建立 全基因组为125Mb 基因组测序区段覆盖了全基因组的115 4Mb 共含有25498个基因 GenomeSequencing 2001年2月人类基因组人类基因组共有30亿个碱基对 预测编码基因31000个 比最初预测的10万个编码基因数大大减少 GenomeSequencing 2002年4月 水稻基因组 GenomeSequencing RelativeGenomeSizes PlantGenomesCanBeLargerThanTheHumanGenome GenomeSequencing NewSequencingTechnologiesnextgenerationsequencing NGS IlluminaHiSeqABISOLiDRoche454 NGS Highthroughtput lowcost Sequencingtechnologies NGS Sequencers SangerSequencing 1977 Metzkeretal 2010NatureReviews Genetics Sequencingtechnologies NGS NGSapplications NGSapplications BRIEFINGSINBIOINFORMATICS 2010VOL11 NO5 499 NGSapplications Agriculture LivestockBreeding andBioprocessing growdisease insect anddrought resistantcrops breedhealthier moreproductive disease resistantfarmanimals growmorenutritiousproduce developbiopesticides incorporateediblevaccinesincorporatedintofoodproducts U S DepartmentofEnergyGenomePrograms GenomicsandItsImpactonScienceandSociety 2003 AnticipatedBenefitsofGenomeResearch 农业领域 NGSapplications AnticipatedBenefitsofGenomeResearch 人类健康 U S DepartmentofEnergyGenomePrograms GenomicsandItsImpactonScienceandSociety 2003 HumanhealthandMedicine improveddiagnosisofdiseaseearlierdetectionofgeneticpredispositionstodiseasegenetherapyandcontrolsystemsfordrugspersonalized customdrugs NGSapplications AnticipatedBenefitsofGenomeResearch 微生物应用 MicrobialGenomics rapidlydetectandtreatpathogens disease causingmicrobes inclinicalpractice developnewenergysources biofuels monitorenvironmentstodetectpollutants protectcitizenryfrombiologicalandchemicalwarfare cleanuptoxicwastesafelyandefficiently U S DepartmentofEnergyGenomePrograms GenomicsandItsImpactonScienceandSociety 2003 NGSapplications Applicationsofgenomicsincropimprovement DiscoveryofmolecularmarkerspopulationgeneticsHighthroughputgenotyping GBS germplasmdiversityGenomicresourceandvariationQTLmapping GWAS Mappingbysequencing mappingIdentificationofcandidategenesgenediscoveryTransgenicbreeding MarkerassistedbreedingbreedingGenomeselectionEvolutionofcrops domesticationandselection evolution NGSapplications ImprovementsNeeded J S Boyer PlantProductivityandEnvironment Science Vol 218 October29 1982pp 443 448 Cropgenomicsandabioticstress HowtoImproveCrops Genomicsallowstheidentificationofthegenesandgenenetworksresponsiblefo