Linkage, recombination and gene mapping. Why are linkage relationships important?

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1 Transmission patterns of linked genes Linkage, recombination and gene mapping Why are linkage relationships important? Linkage and independent assortment - statistical tests of hypotheses Recombination mapping visible markers - detection - calculation of genetic distance - genetic maps vs physical maps - correcting map distances 1

2 Transmission patterns of linked genes alleles of genes on the same chromosome tend to be inherited as a group, especially when close together new combinations of alleles at different loci are produced by recombination A a B b No Recombination AB AB ab ab A a With Recombination B b AB Ab ab ab Transmission patterns of linked genes alleles of genes on the same chromosome tend to be inherited as a group, especially when close together new combinations of alleles at different loci are produced by recombination *for a given pair of loci, product of most meioses will be non-recombinant (parental) *recombination detectable only in individuals heterozygous at all loci in crosses, identify linked loci by non-mendelian ratios - 2 common classes (parentals) - 2 uncommon classes (recombinants) 2

3 Bateson and Punnet s discovery of genetic linkage flower color: purple (P) or red (p) pollen shape: long(l) or round (l) both were autosomal with complete dominance but, dihybrid crosses produced anomalous F 2 ratios Bateson and Punnet s data do not fit the expected F 2 ratio 2 χ dof = Σ (observed number - expected number)2 (expected number) = ( ) 2 + ( ) 2 + ( ) 2 + ( ) = = degrees of freedom = 4-1 = 3 critical value = 782, p << 005 3

4 Drosophila melangaster: autosomal, recessive traits: ebony body (e) spineless bristle (sp) testcross: e/+ sp/+ & x e/e sp/sp % % gamete & gamete phenotype exp f obs f e sp e sp e sp + + e sp e + e sp + sp ebony spineless wild type ebony spineless -independent assortment AaBb types of gametes?? pr(ab) = pr (ab) = pr(ab) = pr(ab) = ¼ 4

5 testcross: e/+ sp/+ & x e/e sp/sp % % gamete & gamete phenotype exp f obs f e sp e sp ebony spineless 250 e sp + + wild type 250 e sp e + ebony 250 e sp + sp spineless parentals recombinants determining the recombination distance between genes: RF = frequency of recombination RF = number of recombinant offspring total number of offspring RF = ( )/1000 RF = 130/1000 = 013 map distance = RF x 100 = map units (cm) 013 x 100 = 13 mu 5

6 Notation: initial (null) hypothesis is that genes are unlinked e/e; sp/sp or e/+; sp/+ for genes known to be linked e sp/e sp or e sp/ + + or e +/+ sp % gamete & gamete phenotype exp f obs # e sp e sp ebony spineless e sp + + wild type e sp e + ebony e sp + sp spineless obs e + tot exp e + tot sp sp tot tot

7 testing for linkage with the chi-square test H 0 : genes are assorting independently 2 χ dof = (observed number - expected number)2 Σ (expected number) 2 χ 1 = ( ) 2 (71-256) 2 (59-244) 2 ( ) = = 5423 p <<< 005 % gamete & gamete phenotype exp f obs # e sp e sp ebony spineless e sp + + wild type e sp e + ebony e sp + sp spineless effects of sample size! Chi-square = < p < 010 7

8 Mapping function: f i = (e -m m i )/i! m = mean number of crossovers i = actual number of crossovers f i = frequency of i th crossover class but, only know the no-crossover class (i = 0) (e -m m 0 )/0! = e -m RF = ½ (1 - e -m ) solve for m m/2 = corrected map distance 8

9 mapping cross with visible markers: > 3 loci test cross: heterozygous female, homozygous recessive male linkage if two common offspring types determine parental genotypes calculate RF values (map distances) for pairs of genes determine gene order (map) 9

10 % gametes & gametes progeny phenotype #progeny jv str pi jv + + javelin 294 jv str pi + str pi striped, pink 287 jv str pi jv str pi javelin, striped, pink 140 jv str pi wild type 139 parentals recombinant jv str pi + + pi pink 66 jv str pi jv str + javelin, striped 65 jv str pi jv + pi javelin, pink 4 jv str pi + str + striped 5 double crossover Take-home points spatial arrangement of genes - gene interactions - genome evolution -crop improvement transmission patterns of linked genes - most offspring will inherit the allele combinations present in their parents - recombination is rare, detect numerically from testcross progeny - parental allele combinations (on the chromosome) - genetic distance between linked loci - gene order (genetic map) - test with chi-square linkage analysis is limited to genes that are close together (non-linear relationship between estimated and actual distance); mapping functions can improve estimates of genetic distance 10

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