Hayes  reported that the degree of linkage equilibrium
according to genetic distance had reflected genetic diversity of past generation.
If these loci are at linkage equilibrium
(DL = 0 and LE = 1), i.e., in a situation of random association between their alleles, the observed haplotype frequencies should equal the expected frequencies, which correspond to the product of the respective allele frequencies.
In population genetics, linkage equilibrium
and linkage disequilibrium describe linkage of alleles at different loci.
The test of linkage equilibrium
revealed no significant values.
This program also computes the linkage equilibrium
between each pair of loci based on a likelihood-ratio test (Slatkin and Excoffier 1996).
After correcting allele frequencies for putative null alleles, a significant deviation from linkage equilibrium
was detected with GENEPOP for only one pair of loci: Med 362 / Med 722 (P < 0.001).
This is especially important for the application of marker-facilitated selection to open-pollinated populations at or near linkage equilibrium
. We recently demonstrated linkage equilibrium
between tightly linked molecular markers and the Ms locus in open-pollinated populations of onion (Gokce and Havey, 2002).
This conclusion gains additional support from the apparent single-locus Hardy-Weinberg equilibrium and two-locus linkage equilibrium
in populations sampled through the hybrid zone.
All other SNP-wise tests, except the above 10 pair-wise tests, showed linkage equilibrium
between the two pair-wise SNP (p [greater than or equal to] 0.10).
These formulas, however, assume linkage equilibrium
and Hardy-Weinberg equilibrium.
Recombination rate between adjacent loci is assumed to be 0.1, thus the condition favors linkage equilibrium
and the central limit theorem.
The (H93 x B99)[F.sub.2] population testcrossed to B73 x Mo17 was expected to have the same mean as its reciprocal population, (B73 x Mo17)[F.sub.2] testcrossed to H93 x B99, if either of two conditions was met (Melchinger, 1988): (i) epistasis was absent; or (ii) epistasis was present but the parental populations were in linkage equilibrium
. The [F.sub.2] populations, having been random mated twice, were expected to be largely at linkage equilibrium