4.1Linkage: basic diploid eukaryotic chromosome mapping

Linkage discovery Bateson and Punnet (early XX c.): Purple flowers and long pollen PPLL Red flowers and round pollen ppll F2 Purple long (P_L_) 4831 Purple round (P_ll ) 390 Red long (ppL_ ) 393 Red round (ppll ) 1338 TOTAL 6952 Expected 9 3991 3 1303 1 435

Linkage in Drosophila T. H. Morgan pr/pr +: purple/red vg/vg+ : vestigial winds/normal pr pr vg vg X pr+ pr+ vg+ vg+ Test cross pr pr vg vg X pr+ pr vg+ vg Expected porportion1:1:1:1 pr + vg 151 pr vg+ 154 pr vg 1195 pr + vg + 1339 TOTAL 2839 Repulsion Coupling

Linkage in Drosophila (II) Crossing with alternated alleles: pr+ pr+ vg vg X pr pr vg+ vg+ F1 pr+ pr vg+ vg X pr pr vg vg pr + vg 965 pr vg + 1067 pr vg 146 pr + vg + 157 TOTAL 2335

Linked alleles tend to be inherited together

Crossing over produces new allelic combinations

Linkage detection

For linked genes, recombinant frequencies are less than 50 percent

Linked genes notation Genotype and allele location in chromosomes can be displayed Double heterozigote Aa Bb (linked) AB / ab (coupling) Ab / aB (repulsion) A B a b Coupling A b a B Repulsion

Recombination frequency Morgan y Sturtevant (1911): recombination frequencies can be used for making maps, since they reflect the genes separation distances. pr pr ct ct X pr+ pr+ ct+ ct+ Test cross pr ct/ pr ct X pr+ ct+ / ct pr pr + ct/ ct pr 21 pr ct + / ct pr 23 pr ct / ct pr 165 pr + ct + / ct pr 191 TOTAL 400 Recombinants Parentals RF=recombinants/total

Linkage maps pr ct 11 cM pr + ct/ ct pr 21 Recombinants TOTAL 400 Recombinants Parentals RF=recombinants/total FR= (21+23)/400=0.11 X100: 11 maps units or centimorgans (cM) pr ct 11 cM

Three point cross vermillion: vermillion eyes, v crossveinless: no veins in wings, cv cut: cut end wings, ct P: v+ cv ct / v+ cv ct X v cv+ ct+ / v cv+ ct+ Test: v cv ct / v cv ct X v+ cv ct / v cv+ ct+ v cv+ ct+ 580 v+ cv ct 592 v cv ct+ 45 v+ cv+ ct 40 v cv ct 89 v+ cv+ ct+ 94 v cv+ ct 3 v+ cv ct+ 5 TOTAL 1448 Parentals Rec. cv-v Rec. cv-ct Rec. v-ct

Recombination frequencies FR v-cv=(45+40+89+94)/1448=18.5 cM FR v-ct=(89+94+3+5)/1448=13.2 cM FR ct-cv=(40+45+3+5)/1448= 6.4 cM Linked genes (FR<50 cM) ct cv v 13.2 cM 6.4 cM 18.5 cM

Coefficient of coincidence and interference cv-ct = 0.064 ct-v = 0.132 ct cv v 13.2 cM 6.4 cM Positive interference: when the occurrence of one crossover reduces the probability that a second one will occur in the same region.

Steps to perform a three point maps Determine phenotypes and numbers of progeny Determine parental genotypes Determine the no recombinant phenotypic classes no recombinants and double ones (more and less frequent) Determine the central locus Determine the order Determine the location of crossovers that led to phenotypic classes Determine the recombination frequencies Construct the map Determine the coefficient of coincidence and the interference