Methods for increasing genetic gain in a breeding population

A plant made by the method for generating a plant having a desired genotype, the method comprising:

• (a) providing effects with respect to a trait of interest of a plurality of genome-wide markers in a breeding population comprising a plurality of potential breeding partners;
• (b) selecting from the breeding population a first breeding pair comprising a first breeding partner and a second breeding partner, wherein crossing the first breeding partner and the second breeding partner would produce a segregating progeny population;
• (c) inferring haplotypes with respect to the plurality of genome-wide markers for the first breeding partner and the second breeding partner;
• (d) simulating a cross between the first breeding partner and the second breeding partner to produce a progeny generation, each member of the progeny generation comprising a simulated genotype;
• (e) calculating a genetic potential value of the progeny generation, wherein the genetic potential value of the progeny generation is the mean of the genomic breeding values of the simulated genotypes of the member of the progeny generation;
• (f) repeating steps (b)-(e) one or more times, wherein in each iteration of step (b), the selecting comprises selecting a different first breeding partner, a different second breeding partner, or both from the breeding population;
• (g) ranking each simulated cross of step (d) based on the genetic potential values calculated in step (e);
• (h) selecting one or more breeding pairs based on the ranking of step (g);
• and
• (i) breeding the one or more breeding pairs selected in step (h) to generate a plant having a desired genotype,
• wherein the inferring step, the simulating step, or both are performed by a suitably-programmed computer.