Cross Assist: Online software to identify efficient cross combinations, integrating rosaceous crop genomics, genetics, and breeding

Cross Assist (www.rosaceae.org/breeders_toolbox/cross_assist) is a decision-support tool for breeders to plan crosses. This software was developed as a component of the RosBREED project’s Breeding Information Management System to support U.S. breeders of crops in the Rosaceae family, and the underlying database is housed on the Genome Database for Rosaceae. Cross Assist identifies efficient pairwise parental combinations from a breeder’s available parent pool. This efficiency is determined by the number of seedlings needed to result in a target number predicted to each perform within specified trait thresholds. Efficient crosses achieve all trait thresholds with relatively few seedlings. The software uses available information on the breeding value of each candidate parent to predict how well resulting seedlings would perform. Calculations can be made on three increasing levels of breeding value information. The first method, “Phenotype”, uses only phenotypic information in the database. “+Pedigree” adds information provided by pedigree – estimated breeding value. “+Ped+DNA” further adds information provided by functional genotypes for Mendelian trait loci and QTLs. Where such additional information is not available, calculations behind the latter two methods revert to use of phenotypes only. Users supply two specifications as input: target number of seedlings and target trait thresholds. Cross Assist’s output provides a list of crosses, sorted initially by the estimated number of seedlings required. Further functionalities are being added, such as incorporation of linkage information, output addressing the trait loci involved and their available DNA tests, and integration with our sister software, Seedling Select.