精细定位及其克隆

1、Most of the important morphological ,physiological and agronomical traits are quantitative traits, which are always analyzed by QTL napping . Whats QTL ?Statistic methodQuantitative traitQTL3QTL2QTL1gene1gene3gene2gene7gene6gene5gene4expressionAbundance of available molecular markers facilitate the

2、detection of genetic fundamental of quantitative traitsTwo Steps For QTL AnalysisSTEP 1 : From Phenotype to QTL Primary Mapping Fine mapping STEP 2 : From QTL to Gene QTL-QTG-QTNSTEP 1STEP 2Strategies for Fine Mapping & cloning QTLsStill a challenge work Polygene & minor effect Complicated epistasis

3、es G x ESolution Advanced mapping population Progeny testFine mappingREQUIREMENT Advanced populations Saturated markers Proper methods Populations for primary mappingAdvanced populations for fine mapping Primary result dependent populations NIL,RHL(HIF),QTR Primary result independent populations IL,

4、CSSL,SSSLPrimary result dependent populations NIL (Near Isogonic Line) Advantage: Identical background Easy to detect epistasis Disadvantage Laborious & Long time consumed Primary result dependent populations RHL (Residual Heterozygous Line) Advantage: Identical background one time for maker assista

5、nt selection backcross free Disadvantage Not fit for detecting epistasisPrimary result dependent populations QIR (QTL Isogenic Recombinants) Advantage: easy to construct Disadvantage background interruption Not fit for detecting epistasis121 2 3 4 5 67 8 9 10 111 2 3 4 5 6 7 8 9 1011 121 2 3 4 5 67

6、8 9 10 11 121 2 3 4 5 67 8 9 10 11 12F2ABLRILA new methodGain more attentionWidely used Advantage: Identical background Fit for detecting epistasis provide optimal starting material for the fine-mapping of the mapped loci and for generating improved breeding lines.Disadvantage Difficult to construct

7、 Relative low resolution (dependent on the resolution of the IL library .i.e. the average introgression segment size) Primary result independent populations IL (Introgression Line)CSSL (Chromosome Segment Substitution Line)SSSL (Single Segment Substitution Line)REQUIREMENT Advanced populations Satur

8、ated markers Proper methods ?genomic mine &New genotyping methodfor model plants genomic minee.g. RICE (oryza sativa)SNP :0.65%InDel :0.200.27%SSR :18,828codominantPCR basedCAPSdCAPSSSLPfor other plants - syntenymethods for genotypingNew method for genotyping Microarray-based QTL MappingCONCLUSIONTh

9、e background of the fine mapping populations should be as simple as possible, while the markers are the more the betterREQUIREMENT Advanced populations Saturated markers Proper methods methods for fine mapping Statistic based means Genetic verification Point out the direction for further analysis Ju

10、st a statistic result, need for genetic verificationOverlapping substitution line avoid problems associated with environmental variation and genetic background effects in early generation analysis.Extreme sampling methodThe improvement of genomics facilitate this work?Progeny testingWhy progeny test

11、ing? Very a few recombiners Relative minor effect -hard to distinguish QTL effect to E Also a way for QTL fine mappingKey for fine mapping:Acquire enough recombination events to separate the genes that govern the quantitative trait from closely linked markers. Large population Plenty markersSUMMARYQ

12、TLs cloningDwarf8tb1Gn1a,Hd1,Hd6,Hd3a,Ehd1,PSR1,qUVR10SKC1 etc.Map Based Cloning forward genetics strategyThe improvement of genomics facilitate this work?Candidate gene strategyA reverse genetics method How to choose a candidate Gene?Homology searches.Deficiency-complementation test.Polymorphisms in coding or regulatory regions.Mutational analysis.Expression analysis.A case of QTLph1 Candidate confirmation Transformation