Marker-based estimates of identity by descent and alikeness in state among maize inbreds

Molecular markers are useful for determining relationships and similarity among inbreds, especially if the proportion of marker loci with alleles common to inbreds i and j is partitioned into: (1) the probability that marker alleles are identical by descent ((M)f(ij)) and (2) the conditional probability that marker alleles are alike in state, given that they are not identical by descent (θ(ij)). Our objectives were to: develop a method, based on tabular analysis of restriction fragment length polymorphism marker data, for estimating (M)f(ij), θ(ij), and the parental contribution to inbred progeny; validate the accuracy of the method with a simulated data set; and compare the pedigree-based coefficient of coancestry (f(ij)) and (M)f(ij) among a set of maize (Zea mays L.) inbreds. Banding patterns for 73 probe-enzyme combinations were determined among 13 inbreds. Iterative estimation of (M)f(ij), θ(ij) and the parental contribution to progeny was performed with procedures similar to a tabular analysis of pedigree data. Deviations of (M)f(ij) from pedigree-based f(ij) ranged from 0.002 to 0.288, indicating large effects of selection and/or drift during inbreeding for some inbreds. Differences between marker-based estimates and expected values of parental contribution to inbred progeny were as large as 0.205. Results for a simulated set of inbreds indicated that tabular analysis of marker data provides more accurate estimates of (M)f(ij) and θ(ij), than other methods described in the literature. Tabular analysis requires the availability of marker data for all the progenitors of each inbred. When marker data are not available for the parents of a given inbred, (M)f(ij) and θ(ij) may still be calculated if parental contributions to the inbred are assumed equal to their expectations.