Lesson 6: Genetic Linkage and Mapping in Eukaryotes Terms

syntenic genes

genes located on the same chromosome

genetic linkage

when two syntenic genes are so close to each other that the alleles are unable to assort independently

homologous recombination

process that occurs as a result of crossing over in prophase I of meiosis

recombinant/nonparental chromosomes

chromosomes that come about by the reshuffling of alleles residing on recombining chromosomes

nonrecombinant/parental chromosomes

homologous chromosomes that don’t undergo crossing over during meiosis retain all of the same alleles that they had

genetic linkage mapping

plots the positions of genes in chromosomes

recombination frequency

identifies rates of recombination for a given pair of syntenic genes (# of recombinants/total # of progeny)

map unit/centiMorgan

1 m.u. or 1 cM of distance between linked genes=1% recombination

two-point test-cross analysis

dihybrid F1 fly where dihybrid fly is crossed to a pure breeding mate w/ recessive phenotypes

three-point test-cross analysis

analysis allows geneticists to efficiently map three-linked genes simultaneously

double recombinants (crossovers)

occurrence of two crossovers between homologous chromosomes in a particular region, may involve two, three, or all four chromatids

interference (I)

a reduction in the observed number of double crossovers relative to the number expected if the two single crossovers happened independently of one another (I=1-c)

coefficient of chromosome (c)

the value that is produced when observed double recombinants are divided by expected double recombinants (observed double recombinants/expected double recombinants)

negative intereference

when an experiment generates more double recombinants than expected (I<0)

mapping function

correlates map distance and recombination frequency between gene pairs

recombination hotspots

a chromosome region w/ a recombination rate that is higher than average for the # of nucleotide base pairs

recombination coldspot

a chromosome region w/ a recombination rate that is lower than average for the # of nucleotide base pairs present

genetic markers

DNA sequence polymorphisms that provide thousands of signposts on every chromosome to assist in gene mapping and linkage analysis

linkage groups

clusters of syntenic genes that are linked to one another and then to assignment of chromosomal locations to linkage groups

variable number tandem repeat (VNTR)

clusters of varying numbers of repetitive DNA sequences of more than 10 bae pairs each that are variable among individuals (can be used as genetic markers)

single nucleotide polymorphisms (SNPs)

much more commonly used than VNTRs as genetic markers, they are DNA sequence variants in which one base pair is substituted by another base pair usually located in noncoding parts of the genome

restriction endonucleases (enzymes)

DNA-cutting enzymes that can recognize and cut specific segments of DNA

restriction fragment length polymorphisms (RFLP)

a type of genetic marker related to SNPs, result from a change in DNA sequence

restriction fragments

DNA fragments that are cut from restriction enzymes

haplotype

syntenic SNPs that are close together in a small region of a chromosome constitute a set of closely linked variants

allelic phase

particular combination of alleles of linked genes on each parental chromosome

lod score

statistical value representing the probability of genetic linkage between genes (>3 means genetic linkage is likely, <-2 means genetic linkage isn’t likely)

theta value

likelihood of genetic linkage for many different recombination frequencies

genome-wide association studies (GWAS)

studies designed to detect and locate the genes that as a group influence the form/appearance of traits produced by multiple genes

linkage disequilibrium

nonrandom relationship between alleles of very closely linked genes