Estimation of coefficient of coancestry using molecular markers in maize

Summary

The coefficient of coancestry (f_AB) between individuals A and B is the classical measure of genetic relationship. f_AB is determined from pedigree records and is the probability that random alleles at the same locus in A and B are copies of the same ancestral allele or identical by descent (ibd). Recently, the proportion of molecular marker variants shared between A and B (S_AB) has been used to measure genetic relationship. But S_AB is an upwardly-biased estimator of f_AB, especially between distantly-related lines. f_AB, S_AB, and adjusted (to remove bias) estimates of molecular marker similarity (f ^M_AB ) were compared. RFLP banding patterns at 46 probe-restriction enzyme combinations were obtained for 23 maize inbred lines derived from the Iowa Stiff Stalk Synthetic (BSSS) maize (Zea mays L.) population, and for 4 non-BSSS lines. f ^M_AB was estimated as ${\text{f}}_{{\text{AB}}}^{\text{M}} = \left[ {{\text{S}}_{{\text{AB}}} - \tfrac{1}{2}\left( {\delta _{{\text{A}}{\text{.}}} + \delta _{{\text{B}}{\text{.}}} } \right)} \right]/\left[ {1 - \tfrac{1}{2}\left( {\delta _{{\text{A}}{\text{.}}} + \delta _{{\text{B}}{\text{.}}} } \right)} \right]$, where δ _A (or δ _B) was the average proportion of RFLP variants shared between inbred A (or inbred B) and the non-BSSS lines. The average f_AB among 253 pairwise combinations of BSSS lines was 0.212, whereas the average S_AB was 0.397. The average f ^M_AB was 0.162, indicating that the upward bias in S_AB was effectively removed. S_AB and f_AB were significantly different (α = 0.05) in 76.3% of the comparisons, whereas 24.9% of the f ^M_AB values differed significantly from f_AB. The latter result suggests that selection and/or drift were present during inbred line development and that f_AB may not be an accurate measure of the true proportion of ibd alleles between two lines. Cluster analyses based on S ^M_AB and f ^M_AB grouped lines according to pedigree, although several exceptions were noted. The presence of shared molecular marker variants between unrelated lines must be considered when setting S_AB-based minimum distances for varietal protection. Under simplified conditions, more than 250 molecular marker loci are necessary to obtain sufficiently precise estimates of coefficient of coancestry using molecular markers.