qtl mapping - wright

Di truyền số lượng QTL Công nghệ sinh học chọn tạo giống các phương pháp xác định Quantitative trait loci bản đồ di truyền số lượng

1 Institute of Agriculture Sciences – Biotechnology Division Trait Mapping (Quantitative Trait Loci) IAS – Biotech Division Robert J. Wright Texas Tech University Trait Mapping Phenotypic/Genotypic Breeding Molecular Genetics Mapping a trait is accomplished by identifying nearby genetic markers, which are linked, with the discrete phenotype. Phenotypic/Genotypic Breeding IAS – Biotech Division – Slide 2 Trait (Phenotype) Heredity Genetic mapping permits the molecular dissection of biological processes in which genetic variation is observed. Genes explaining variation in simple or complex traits can easily be mapped to chromosomes or linkage groups with minimal a priori information. 2 What is a QTL? • A quantitative trait loci (QTL) is the location of a gene(s) that have an effect on a trait. A QTL is depicted as a confidence interval on a genetic map. confidence interval on a genetic map. – Examples of quantitative traits • plant height •grain yield – These traits are typically affected by more than one genes, and also by the environment IAS – Biotech Division – Slide 3 environment . – Thus, QTL mapping is not as simple as mapping a single gene that influences a qualitative trait (such as flower color). Why map QTL ? • To provide knowledge towards a fundamental understanding of heredity and the gene(s) that control individual traits traits • To study individual gene(s), gene actions and interactions • To enable positional cloning of the gene • To improve estimations of breeding value and selection response through IAS – Biotech Division – Slide 4 value and selection response through marker assisted selection (Predictive Breeding) 3 Principles of Mapping QTLs IAS – Biotech Division – Slide 5 Principles of QTL mapping A TGB C D DNA Markers DNA MarkersTarget Gene Candidate Genes B CTG DNA markers that are near a disease resistance gene tend to be inherited to g ethe r (g eneticall y linked ) . IAS – Biotech Division – Slide 6 ……….TCGCCGTTACGTAGC………. ……….TCGCCGTGACGTAGC………. Resistant Allele Susceptible Allele g (g y ) 4 Independent Assortment A a b B a a b b Segregation in a Single Parent Segregation AB Ab aB 25% 25% 25% a b a b A a b B IAS – Biotech Division – Slide 7 ab 25% During gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair (Mendel’s Second Law). Genetic Linkage AB ab Recombination in a Single Parent a b a b A a b B Crossover (recombination) AB Ab aB >25% <25% <25% Parental Type Recombinant Recombinant IAS – Biotech Division – Slide 8 Recombination frequency = total # of meioses # of recombination events x 100 ab aB >25% <25% Parental Type Recombinant 5 Localize Target Gene to a Delimited Region A B TG C D DNA Markers DNA MarkersTarget Gene A B TG C D I II III IV A a B b D d C c R s Score (Genotype) Graphical Genotypes (Recombination) A B C d R 8034 - 3 Resistant Susceptible IAS – Biotech Division – Slide 9 A B C d R 8034 - 3 ab C Ds8034-44 ab C DR8034-78 ab c ds8034-123 Goals QTL Mapping • Identify genomic regions (QTLs) that contribute to phenotypic variation of a trait. • Delineate the QTL location within a confidence interval. • Estimate the effects of the QTL, putative gene action , and contribution IAS – Biotech Division – Slide 10 10 to the phenotypic variance. 6 Factors critical to successful QTL mapping 1. Good genetic map 2. Good phenotyping 3. Rigorous statistical/genetic analysis 4. Validation of QTL IAS – Biotech Division – Slide 11 1 to 3 absolutely critical for genetic analysis; 1 to 4 are all critical for implementation in breeding I. Good Genetic Mapping – Critically look at your map – Identify/remove poor marker loci (disequilibrium and missing data) – Identify alleles mapped as independent loci – Conduct graphical assessment of map quality – Investigate alignment with published maps IAS – Biotech Division – Slide 12 7 Constructing a Genetic Map •DNA Markers – Restriction Fragment Length Polymorphism (RFLP) – Amplified Fragment Length Polymorphism (AFLP) – Simple Sequence Repeats (SSR) – Single Nucleotide Polymorphism (SNP) – Insertion/Deletion Mutations (INDEL) • To be a informative genetic marker, the DNA marker must meet two criteria: – The marker must differentiate between the parents (Polymorphic). IAS – Biotech Division – Slide 13 – The marker must be precisely transmitted to the progeny (Mendelian Segregation). P1 x P2 F1 F2 F1 x P1 (or P2) F1 Selection of the Experimental Lineage F2 F3 BC1 DHL (Backcross) (Doubled haploid line) Created to minimize the confounding effect of heterogeneity of the parental genotypes (i.e. a li i t ti ll h ) IAS – Biotech Division – Slide 14 RIL (Recombinant inbred line) With polymorphic molecular markers and linkage maps as tools, mapping QTL is simply a matter of growing and evaluating large populations of plants, and of applying the appropriate statistical tools. pure li ne i s no t gene ti ca ll y h omogeneous ) . 8 Stringent Computational Analysis • Data Analysis – Marker loci density • 10-20 cm for genome wide linkage analysis • 50-200 kb for genome wide association studies – Pre-selection of marker type • PCR based • Codominant – Significant thresholds • Sufficiently high to avoid false linkages – Maximum linkage IAS – Biotech Division – Slide 15 Maximum linkage • >35 or >40 cm – Computational software •Mapmaker •Jointmap • Map Manager QT Critically look at your map!! IAS – Biotech Division – Slide 16 9 Scoring Marker Loci (3) P Genotypes are scored as: 1 P Homozygote (AA) Aa (2) aa (3) AA (1) P 1 P 2 1 – P 1 Homozygote (AA) 2 – Heterozygote (Aa) 3 – P 2 Homozygote (aa) 4 – P 2 Allele no P 1 (_a) 5 – P 1 Allele no P 2 (A_) IAS – Biotech Division – Slide 17 Scoring Marker Loci AFLP IAS – Biotech Division – Slide 18 10 Dominant Markers (P 1 and P 2 ) a nt AA aa Aa A_A_ A_A_ A_A_ aa aaA_ F 1 F 2 P 2 P 1 Domin a P 1 AA aa Aa AA_a _a_a _aAA _a _a_a F 1 F 2 P 2 P 1 a nt 535 555555335 IAS – Biotech Division – Slide 19 Domin a P 2 144 144441444 Dominant and Codominant Markers AA aa A a AA A a A a A a A a AA aa aa A a F 1 F 2 P 2 P 1 t IAS – Biotech Division – Slide 20 Codominan t 132 122221332 [...]... (Fine) Mapping pAR145 pAR295 A 2232 G 7569 P 7-2 b A 1967 pAR 731 G1099a A1638 IAS – Biotech Division – Slide 66 33 High-Resolution Mapping & Cloning Genetic Map BAC Clones Physical Map pAR070 A1215b pAR237 pAR026a G1262 A1550d P1 0-2 0 P 2-1 6 A1328 A1742a P 9-3 b pAR721 G1161b p pAR145 pAR295 pAR145 pAR295 A 2232 504 kb G 7569 P 7-2 b A 1967 1.2 cM pAR 731 G1099a R-Gene G1099a A1638 P 1-3 4a A1638 CSREES-NRI-200 3-0 0696:... Linked QTLs pAR070 A1215b pAR237 pAR026a G1262 Recurrent A1550d P1 0-2 0 P 2-1 6 A1328 A1742a P 9-3 b pAR721 G1161b pAR145 pAR295 Donor G1099a A1638 P 1-3 4a Flower Color Leaf Color IAS – Biotech Division – Slide 68 34 Fine -Mapping (Substitution Mapping) pAR070 A1215b p pAR237 pAR026a G1262 A1550d P1 0-2 0 P 2-1 6 A1328 A1742a P 9-3 b pAR721 G1161b pAR145 pAR295 G1099a A1638 P 1-3 4a pAR145 pAR295 A 2232 G 7569 P 7-2 b... D02 3.32 26.9 -2 .74 -0 .85 0.31 RA (Qb6b) P1 2-2 0a 5 3.07 22.4 0.52 -3 .46 -6 .65 D Qb6c pAR827 D04 3.53 19.4 -1 .78 -2 .40 1.35 R (Qb6d) pAR723 14 3.01 16.3 1.53 -1 .99 -1 .30 D B12 pAR043 14 50.46 94.2 -3 .66 3.49 -0 .95 D Percentage of variation explained (PVE) is the percentage of phenotypic variation that is explained by the homozygous II Additive effects: the I Dominant deviation: effects of QTL It’s calculated... – Slide 61 QTLs Mapped in Multiple Generations Table 1 Biometrical parameters of individual QTLs conferring resistance to Black Root Rot (BRR) of cotton Positionb LOD BNL1693NAU1072 BNL1693NAU1072 BNL1693NAU1072 6.01 2.74 5.8 -8 .86 -0 .8 0.09 5.01 5.75 19.1 -1 5.14 2.18 -0 .14 6.11 3.93 7.2 -1 1.0 -2 .44 0.22 BNL2690NAU0921 BNL2690NAU0921 2.01 2.86 10.3 -9 .83 1.56 -0 .16 3.01 3.94 8.2 -1 0.63 -3 .36 0.32 BNL3442BNL1034... 30 15 Mapping Traits as QTLs Empire B2 Chromosome 20 pAR988 pGH239 pAR335b G1219 pAR137a M1 6-1 50 Empire B2b6 Chromosome 20 Empire B2b6 Chromosome 5 Empire B2b6 LGD04 (34.4 cM) pAR179x pAR988 A1318a pGH239 pAR335b P 5-5 7 pVNC163a A1695b A1318b pAR335a PXP 1-9 a pAR 1-2 8 G1219 Empire B2b6 LGD02 A1666 M1 6-4 0 pAR648 pAR566 pAR044b P1 2-2 0a A1701b pAR430 pAR137a M1 6-1 50 pAR125 pAR377 pAR610 A1429 pAR 3-3 7 pAR827... acre-1 Lint boll -1 Total R Boll Acre-1 2 Parameter Component Intercept 0.951 2 _ 0.00 -1 Boll plant 6.43 6 43 -1 Plants acre 0.374 0 374 1.51 Total R 0.376 2 0.750 IAS – Biotech Division – Slide 43 Replicated Trial Biological Replication Var A Check 98032 98241 99342 992312 00283 002 3-1 002 3-1 00283 Var B Check 99342 002 3-1 002 3-9 992312 98241 00283 Rep 1 Var A Check Var B Rep 2 Check 98241 002 3-9 ... 3.94 8.2 -1 0.63 -3 .36 0.32 BNL3442BNL1034 Markers flanking the QTL likelihood peak 2.01 3.02 8.5 -9 .08 11.15 -1 .23 Data Set QTL F2 BRR5.1 LG.A5 F2:3 BRR5.1 LG.A5 F2-adjusted BRR5.1 LG.A5 Intervala Locus F2:3 BRR9.1 LG.A9 F2-adjusted BRR9.1 LG.A9 F2:3 BRR13.1 LG.A13 % Var Mode of QTL actionc a d d/a a b Position of the QTL likelihood peak (centi-Morgan from top) c Biometrical parameters were calculated... PXP 2-4 1 A1701b S295 Chromosome 14 (7.9 cM) pAR 3-4 1 pGH559b pGH510a pAR137b pAR377 pAR610 A1429 pAR 3-3 7 Empire B3 Chromosome 20 Empire B2b6 Chromosome 14 (11.4 cM) pAR043 pAR129 p 7 b pAR723b pAR 3-2 4b G1012 A1580 pAR 3-4 1 pAR1005 pGH559b pGH510a pAR043 pAR723 pAR 3-2 4b pAR451b G1012 A1580 pAR129 pAR545 pAR545 (14.8 cM) Wright et al., (1998) Genetics 149:198 7-1 996 IAS – Biotech Division – Slide 31 QTLs... to describe the QTLs Xcm Race 2 (4) 2 (4) 18 (7) Empire B2b6 2 (4) 18 (7) 18 (7) 18 (7) 18 (7) S295 18 (2, 4, 7) Population Empire B2 Empire B3 Probable gene Nearest DNA Gene identity marker L.G LOD PVE a d d/a action B2 G1219 20 103.12 98.0 -3 .51 3.56 -1 .01 D B3 pGH510a 20 23.21 88.2 -2 .70 -1 .11 0.41 AR B3 pGH510a 20 10.56 53.4 -0 .75 -0 .01 0.01 A B2 G1219 20 53.36 92.2 -3 .60 3.50 -0 .97 D Qb6a A1666... explain the phenotypic variation of the trait The bar along the linkage group indicates the 90% (1-LOD) likelihood interval (1 LOD) lik lih d i t l for the QTL, and whiskers indicate 99% (2-LOD) likelihood interval IAS – Biotech Division – Slide 58 29 Mapping QTLs • The critical factor to successfully mapping quantitative traits is a detailed understanding of the traits and the precision in which individuals . (Recombination) A B C d R 8034 - 3 Resistant Susceptible IAS – Biotech Division – Slide 9 A B C d R 8034 - 3 ab C Ds803 4-4 4 ab C DR803 4-7 8 ab c ds803 4-1 23 Goals QTL Mapping • Identify genomic regions (QTLs) that. B2b6 LGD02 A1666 M1 6-4 0 pAR648 pAR566 pAR044b (34.4 cM) Mapping Traits as QTLs Empire B3 Chromosome 20 A1701b pAR377 pAR610 A1429 pAR 3-3 7 pAR 3-4 1 pGH510a pGH559b PXP 2-4 1 pAR137b pAR137a M1 6-1 50 pAR125 A1701b pAR377 pAR610 pAR 3-3 7 A1429 pAR 3-4 1 pAR1005 (7.9. 20 pAR988 pGH239 pAR335b G1219 pAR137a M1 6-1 50 Empire B2b6 Chromosome 5 P1 2-2 0a pAR 1-2 8 PXP 1-9 a pAR335a A1318b pAR179x Empire B2b6 Chromosome 20 pAR988 A1318a pAR335b pGH239 G1219 P 5-5 7 pVNC163a A1695b Empire