ParentChecker: a computer program for automated inference of missing parental genotype calls and linkage phase correction

ParentChecker is a user-friendly tool that uses the segregation patterns of progeny to infer missing genotype information of parental lines that have been used to construct a mapping population. It can also be used to automate correction of linkage phase errors in genotypic data that are in ABH format.ParentChecker efficiently improves genetic mapping datasets for cases where parental information is incomplete by automating the process of inferring missing genotypes of inbred mapping populations and can also be used to correct linkage phase errors in ABH formatted datasets.Lack of knowledge of the parental phase of all alleles segregating in mapping populations can impinge on the accuracy of genetic maps. Recombinant inbred line (RIL) populations developed from two inbred lines are a powerful resource for construction of genetic linkage maps. However, it is not uncommon to observe segregation of markers in RILs that are observed to be fixed in the putative inbred parents of the RIL, and conversely, to observe markers that are polymorphic in the two RIL parents, but fixed in the RIL population. This indicates that the real parents used in the cross to develop the RIL population are different than the available "off parents". This situation probably has two primary causes: 1) where one or both parents were not completely inbred at the time the population was initiated, or 2) from the existence of residual genetic variation within one or both parental lines. This observation is not surprising given that ten or more years can pass between the time when a RIL population is initiated with a cross between two parent plants and the time when it is genotyped along with the presumed parental lines. In both scenarios, one plant of an inbred line was used for the initial hybrid, while another closely related plant of the same inbred line was used for genotyping years later. Thus for case 1) where the original parent plant was heterozygous (Aa) at some fraction of its genome at