Lecture 14 - Complex Traits and QTL Maping Doerge (2001) Nature Genetics Reviews 3:43-52 Neale, chapter 18 Liu, chapters 13-14.

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Presentation transcript:

Lecture 14 - Complex Traits and QTL Maping Doerge (2001) Nature Genetics Reviews 3:43-52 Neale, chapter 18 Liu, chapters 13-14

Figures from Lander and Schork, Science, 265-September 1994-pp2037

QTL Mapping Mapping population Markers and a map Phenotypes (trait measurements) QTL mapping software

Distribution of Phenotypic Values Continuous Catagorical Binary

Pitch Canker Phenotypes Fusiform Rust Phenotypes SusceptibleResistant SmallRoughLarge

QTL Mapping - Basic Approaches Single-factor mapping Interval mapping

X A1 Q1 B1 A1 Q1 B1 A2 Q2 B2 A2 Q2 B2 Genotypic value= 20 Genotypic value= 4 A1 Q1 B1 A2 Q2 B2 A2 Q2 B2 A2 Q2 B2 X A1 Q1 B1 A2 Q2 B2 A2 Q2 B2 A2 Q2 B2 A1 Q1 B2 A2 Q2 B2 A2 Q2 B1 A2 Q2 B2 Genotypic value= 12 Genotypic value= A1-A2 = (12+12) -(4+4) = 16 B1-B2 = (12+4) -(12+4) = 0 Genotypic Value Q1= 10 Q2 =2 Q = additive

Edwards et al. 1987, Genetics, Single factor QTL mapping

Advantages of Single Factor QTL Mapping No map needed Standard stat packages, SAS

Disdvantages of Single Factor QTL Mapping Map position not precisely determined Biased estimates of a and d Phenotypic effect overestimated Multiple testing

Interval Mapping Fig 21.1 from Falconer and Mackay. Pg 364 Recombination frequencies between two marker loci, M and N, and a QTL, A M1 N1A1 M2 N2A2 c2 c1 c

Table Falconer and Mackay

Advantages of Interval QTL Mapping More precise location of QTL Better estimates of %PVE

Disdvantages of Interval QTL Mapping Computationally demanding Custom software

ewsg lwsg vol% emfa lmfa ecwc lcwc DETECTION VERIFICATION RELATED UNRELATED Aco_1 0.0 PtIFG_3012_ PtIFG_2150_A PtIFG_2885_B 20.1 estPtIFG_8569_a 29.5 PtIFG_2538_B 30.2 PtIFG_2564_A 40.3 PtIFG_1A7_A 42.6 estPtIFG_9022_a 43.1 PtIFG_2536_ PtIFG_1A7_D 46.8 estPtIFG_48_a 58.3 estPaINRA_PAXY13_a 59.5 estPtIFG_464_a 62.2 PtIFG_1633_a 66.0 PtIFG_48_ estPtIFG_8939_a PtIFG_3006_ PtIFG_1918_h PtIFG_1623_A 90.9 estPtIFG_66_a PtIFG_1626_a 95.4 PtIFG_2986_A PtIFG_1D11_A PtIFG_1165_a Pgd_ estPpaINRA_AS01C10-1_a LG 2 PtIFG_2006_C 0.0 estPtIFG_1934_a 0.3 PtIFG_2145_1 3.4 PtIFG_2068_A 7.8 PtIFG_2897_d 10.4 PtIFG_975_ estPtIFG_8500_a 18.8 PtIFG_138_B 24.1 estPtNCS_22C5_a 30.1 PtIFG_2588_ estPtNCS_C612F_a 33.8 PtIFG_2718_ PtIFG_2745_ PtIFG_1918_ estPtIFG_8612_a 64.2 PtIFG_2090_ PtIFG_1636_ PtIFG_2988_ PtIFG_2718_ estPtIFG_2889_a 95.7 PtIFG_2889_ estPtIFG_8781_a PtIFG_2145_ PtIFG_2145_ PtIFG_1D9_ LG 3 C4H-1 Pta14A 9 SAMS-1 DETECTION VERIFICATION RELATED UNRELATED DETECTION VERIFICATION RELATED UNRELATED PtIFG_2819_12 PtIFG_653_d PtIFG_2086_13 PtIFG_1626_c PtIFG_2697_A PtIFG_2006_A estPtINCS_20G2_a estPtIFG_9053_a estPtIFG_8843_a PtUME_Ps3_A estPtIFG_8537_a estPtIFG_2253_a estPpINR_AS01G01_a estPtIFG_1576_a PtIFG_2253_A PtIFG_2782_31 PtIFG_1457_b estPtIFG_9198_a estPtIFG_8496_a PtIFG_2146_31 PtIFG_2441_1 estPtIFG_107_a PtIFG_2931_b estPtNCS_6N3E_a PtIFG_2393_1 PtIFG_2931_A PtIFG_851_1 LG 1 LAC GlyHMT PtNCS_CAD-08_b SCALE 0 cM 10 cM Brown et al Genetics164:

What can be learned from a QTL mapping experiment Estimate of number of genes controlling complex trait Location of genes in the genome Estimates of a and d Estimate of %PVE