Methods for method for increasing genetic gain in a breeding process are provided. The methods can include (a) providing effects with respect to a trait of interest of a plurality of genome-wide markers in a breeding population (b) selecting from the breeding population a breeding pair, wherein crossing the breeding pair would produce a subsequent progeny population (c) inferring or determining haplotypes based on genotypes with respect to the plurality of genome-wide markers for the breeding pair (d) simulating a cross of the breeding pair to produce a subsequent generation, each member of the progeny generation having a simulated genotype (e) calculating a genetic potential value of the progeny generation (f) repeating steps (b)-(e) one or more times, wherein in each iteration of step (b) employs a different breeding pair (g) ranking each simulated cross and (h) selecting one or more optimal breeding pairs based on the ranking, wherein the optimal breeding pair(s) selected is/are predicted to generate progeny with increased genetic gain. Also provided are methods for choosing breeding pairs predicted to produce progeny having desired phenotypes, methods for increasing the likelihood of producing progeny individual having desired phenotypes, methods for generating progeny individual having desired genotypes and/or phenotypes, progeny produced thereby, and cells, seeds, parts, and tissues cultures thereof.
