GENE3200 - Pedigree Mapping (class 13)

quantifying recombination

-if cross-overs occur at random on a chromosome, recombination rate should reflect physical distance

-recombination frequency between two loci, A and B: R_ab = (# recombinant progeny)/(# progeny scored)

map distance

-the percent recombination

-R_ab x 100

-map distance measured in cM (centiMorgans) or m.u. (map units)(cM = m.u.)

for a pair of linked genes…

parental phenotype pairs appear more frequently in F2s than recombinant phenotypes

humans cross over…

2-4 times per chromosome

double crossovers…

can only be observed among 3 or more loci

progeny classes…

can be identified from offspring frequency

using mapping from a phenotype → casual genes

-trait of interest that varies in a population: genetic disorder, adaptive phenotype

-you want to know what are the underlying genes

-use a linkage map and ask which markers (ex. loci) associate with the trait of interest (forward genetic approach)

-need individuals that vary in both the trait and the markers → then you can look for linkage

two things that are needed to identify recombinants (mapping requirements)

-double heterozygote parent

-scorable gamete genotypes in offspring

identifying individuals that allow us to score recombination

-one caveat to calculating recombination frequency is that we can only use scorable offspring in whom we can be certain whether recombination occurred

-this most often shows up in x-linked crosses where female offspring may have the same phenotype, but have different genotypes

scorable offspring…

are testcross progeny that by their phenotype alone (or genotype if it is given) their phased genotype can be deduced

we can use pedigrees to calculate recombination frequencies

-recombination frequency - the percentage of recombinant offspring produced from a cross

-if we can identify the recombinants in a pedigree, we can find the recombination frequency

scoring the phase of alleles in a double heterozygote’s offspring steps

identify whether the mapping requirements are met (which parent(s) are dihybrid, which offspring are scorable), identify recombinants, calculate RF

fine scale genetic maps

-there are very few polymorphic visible markers

-there’s essentially an unlimited number of polymorphic molecular markers (= molecular loci)

-single nucleotide polymorphisms (SNPs)

-SNP loci are easily scored (molecular methods)

-large number of SNP loci in the genome (in humans, 1 SNP every 100-300 bp) →15 million SNPs

SNPs

-usually only two alleles at a SNP locus (four are possible in a population)

-SNP alleles usually have no phenotype (thus no dominance)

-SNP alleles follow Mendel’s rules

mapping mendelian traits using SNP loci

-the key to mapping is to infer recombination in double heterozygotes

-examine individuals with heterozygous genotype for trait, in which inheritance of heterozygous SNP loci can be followed

-look for linkage between the trait locus and SNP 1, then SNP 2, then SNP 3, then SNP 4…

-goal is to find aa SNP as close as possible to trait locus