Recombination experiments with inversion heterozygotes

Recombination suppression in chromosomal inversion heterozygotes is a well-known but poorly understood phenomenon. Surprisingly, recombination suppression extends far outside of inverted regions where there are no intrinsic barriers to normal chromosome pairing, synapsis, double-strand break formation, or recovery of crossover products. The interference hypothesis of recombination suppression proposes heterozygous inversion breakpoints possess chiasma-like properties such that recombination suppression extends from these breakpoints in a process analogous to crossover interference. This hypothesis is qualitatively consistent with chromosome-wide patterns of recombination suppression extending to both inverted and uninverted regions of the chromosome. The present study generated quantitative predictions for this hypothesis using a probabilistic model of crossover interference with gamma-distributed inter-event distances. These predictions were then tested with experimental genetic data (..., Stock Construction: Inbred lines carrying the standard arrangement and four different cosmopolitan paracentric inversions In(3R)C, In(3R)K, In(3R)Mo, and In(3R)P were drawn from the Drosophila melanogaster Genetic Reference Panel (DGRP). Inversions were identified by polytene chromosome squashes of third instar larva salivary glands and confirmed with PCR amplification of inversion breakpoints. Focal third chromosomes were isolated by balancer chromosome assisted extraction and placed on a common, standard arrangement genetic background for the X, Y, mitochondrial, and second chromosomes (from DGRP line 399).
Three dominant phenotypic markers (Gl1, Sb1, and Dr1) were selected due to their position relative to inversion breakpoints. These markers were introgressed onto both the standard and inverted arrangements followed by repeated backcrossing for a minimum of ten generations. Two exceptions were made, Dr1 on In(3R)Mo and Sb1 on In(3R)P, because >10,000 meioses failed to produce des..., These are classical single interval (two marker) recombination experiments in Drosophila melanogaster. The experiment was conducted in the presence of heterozygous chromosomal inversions so some classes of recombinants are rare. Genotypes have number identifiers that correspond to the Drosophila melanogaster Reference Panel line number from whence the gene arrangement originated.
The experiments are balanced (i.e., full factorial design) except for two inversion-marker combinations. In these two instances, recombination can still be measured in half-balanced design (cis-trans design). In this case, the untested genotypes have \"-----\" entered to draw a distinction from the real observation of \"0\" recording the absence of recombination when tested.
Data are raw counts of F2 individuals in four possible phenotypic class (two non-recombinant classes and two complementary recombinant classes). The phenotypic classes can be classified as non-recombinant or recombinant based on F1 genotype (sp...