Methods for increasing genetic gain in a breeding population

Abstract

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.

What is claimed is: 
     
         1 . 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. 
   
     
     
         2 . The plant made by the method of  claim 1 , wherein the plant is selected from the group consisting of maize, wheat, barley, rice, sugar beet, sunflower, winter oilseed rape, canola, tomato, pepper, melon, watermelon, broccoli, cauliflower, Brussel sprouts, lettuce, spinach, sugar cane, coffee, cocoa, pine, poplar, eucalyptus, apple tree, and grape. 
     
     
         3 . The plant made by the method of  claim 1 , wherein the plant is maize. 
     
     
         4 . A cell from the plant of  claim 1 . 
     
     
         5 . Seed or progeny from the plant of  claim 1 .