Selection based on optimal haploid value to create elite lines

Abstract

This disclosure concerns methods for estimating the breeding value of plants for the purpose of producing doubled haploid, for example, to identify selection candidates having high breeding values.

What may be claimed is: 
     
         1 . A method for selecting a plant or plant tissue, the method comprising:
 providing a plant that is segregating;   for a plurality of genomic segments in the segregating plant, determining a haploid value (HV) for a trait of interest in each haploid genomic segment, wherein a combined haploid value (CHV) is the combined value of HVs in each haploid genome of a doubled haploid produced from a plant and an optimal haploid value (OHV) is the best CHV that can be produced from a plant;   determining the optimal haploid value (OHV) of the segregating plant;   producing from the segregating plant at least one doubled haploid plant or haploid tissue suitable for making the doubled haploid plant; and   selecting the doubled haploid plant or haploid tissue, if the CHV of the doubled haploid plant or tissue, respectively, approaches the OHV.   
     
     
         2 . The method according to  claim 1 , wherein the method comprises:
 producing and selecting the doubled haploid plant and wherein the selected doubled haploid plant is advanced in a breeding program or utilized as a new elite plant variety.   
     
     
         3 . The method according to  claim 1 , wherein the method comprises:
 producing a plurality of doubled haploid plants or haploid tissues; and   selecting a doubled haploid plant or haploid tissue from the plurality that has a CHV that approaches the OHV.   
     
     
         4 . The method according to  claim 1 , wherein the CHV of the selected plant or tissue is identical to the OHV; the CHV of the selected plant or tissue is substantially identical to the OHV; or the CHV of the selected plant or tissue is closer to the OHV than the CHVs of other doubled haploid plants or haploid tissues produced from the segregating plant. 
     
     
         5 . The method according to  claim 1 , wherein the method comprises selecting the haploid tissue and producing a doubled haploid plant from the haploid tissue. 
     
     
         6 . The method according to  claim 5 , wherein the doubled haploid plant is utilized as a new elite plant variety. 
     
     
         7 . The method according to  claim 6 , wherein a commodity product is produced from the selected plant that is utilized as a new elite plant variety. 
     
     
         8 . A method for producing a progeny plant, the method comprising:
 determining the optimal haploid value (OHV) for each plant in a plurality of plants for a trait of interest;   selecting a first plant from the plurality, wherein the OHV of the first plant is the highest OHV of the plants in the plurality;   producing the progeny plant by crossing the first plant with one or more other plants or by selfing the first plant.   
     
     
         9 . The method according to  claim 8 , wherein the method further comprises:
 determining the combined haploid value (CHV) for the progeny plant for the trait of interest, and selecting the progeny plant if the CHV approaches the OHV of the first plant; and   producing doubled haploids from the selected progeny plant.   
     
     
         10 . The method according to  claim 9 , wherein the method further comprises:
 determining the OHV for the selected progeny plant; and   selecting one of the doubled haploids having a CHV that approaches the OHV of the selected progeny plant from which the doubled haploid was produced.   
     
     
         11 . The method according to  claim 8 , wherein the method is repeated one or more times within a breeding population and thereby increases genetic gain while preserving genetic diversity in the breeding population. 
     
     
         12 . The method according to  claim 11 , wherein the genetic gain is increased by about 0.6 genetic base standard deviations when compared to selection by genomic selection. 
     
     
         13 . The method according to  claim 11 , wherein the genetic diversity is increased by about 2 fold after 2 generations, when compared to selection by genomic selection 
     
     
         14 . The method according to  claim 8 , wherein the genome of the progeny plant is a polyploid genome. 
     
     
         15 . The method according to  claim 8 , wherein the genome of the progeny plant is a diploid genome. 
     
     
         16 . The method according to  claim 1 , wherein determining the OHV comprises determining the highest HV at each of a plurality of genomic segments in the first and second parent and summing together the highest HV for each genomic segment. 
     
     
         17 . The method according to  claim 1 , wherein each selected plant or haploid tissue comprises a desirable trait that is linked to a genetic marker. 
     
     
         18 . The method according to  claim 17 , wherein the desirable trait is a sex-linked trait, a trait that is only detectable after destruction of the plant, a disease resistance trait, or a trait with low heritability. 
     
     
         19 . The method according to  claim 8 , wherein each selected plant comprises a desirable trait that is linked to a genetic marker and the desirable trait is present in only one of the first plant and the other plants crossed with the first plant, if any. 
     
     
         20 . The method according to  claim 17 , wherein the desirable trait is a transgenic event. 
     
     
         21 . A method for producing an elite double haploid plant, the method comprising:
 crossing a first parent plant and a second parent plant to produce a population of F 1  plants;   producing a population of doubled haploids from at least one of the F 1  plants; and   selecting an elite doubled haploid plant from the population, wherein the selected double haploid has a combined haploid value (CHV) that approaches the highest possible optimal haploid value (OHV) for segregating individuals that can be produced from the breeding cross.   
     
     
         22 . The method according to  claim 1 , wherein the selected plant has a CHV greater than the mean CHV of the population of doubled haploids. 
     
     
         23 . The method according to  claim 21 , wherein the first parent plant comprises an allele of interest, wherein the second parent plant does not comprise the allele of interest, and wherein the selected plant also comprises the allele of interest. 
     
     
         24 . The method according to  claim 23 , wherein the allele of interest is a transgenic event. 
     
     
         25 . A method for producing an elite double haploid plant, the method comprising:
 providing a first diploid parent plant and a plurality of candidate second diploid parental plants;   predicting genotypes that can be produced from crosses between the first parent plant and each of the candidate parental plants;   determining the optimal haploid value (OHV) for each of the predicted genotypes;   selecting the candidate second parental plant that is predicted in a cross with the first parent plant to produce the genotype having the highest OHV;   crossing the first parent plant with the selected second parental plant to produce an F 1  plant;   producing haploid plants or tissues from the F 1  plant;   determining the combined haploid value (CHV) for each of the haploid plants or tissues;   selecting at least one haploid plant or tissue having a CHV that approaches the OHV of the F 1  plant; and   producing a population of doubled haploids from each of the selected haploid plants or tissues.   
     
     
         26 . A method for introducing a desired trait into an elite plant variety, the method comprising:
 (a) crossing a first parent plant of an elite plant variety with a second parent plant of a different variety that comprises a desired trait to produce an F 1  plant;   (b) determining the optimal haploid value (OHV) for the F 1  plant;   (c) producing haploids from the F 1  plant;   (d) selecting a haploid that has a combined haploid value (CHV) that approaches the optimal haploid value (OHV), wherein the CHV is the sum of the haploid values for each of a plurality of genome segments in the plant, and the desired trait;   (e) producing a population of doubled haploids from the selected haploid; and   (f) performing steps (a) through (e) one or more times in succession, to produce the selected or higher backcross progeny plant that comprises the desired trait.   
     
     
         27 . A method for introducing one or more desired traits into an elite plant variety, the method comprising:
 (a) crossing a first parent plant of an elite plant variety with a second parent plant of a different variety that comprises one or more desired traits to produce an F 1  plant, wherein the first and second parent plant genome comprise several desired traits on a number (n) of alleles x n , wherein the set of alleles is (x 1 , x 2 , . . . x n );   (b) assigning a weight w n  to the introgression of each of alleles x n , such that the set of weights for each allele is (W 1 , w 2 , . . . w n );   (c) determining the introgression-weighted optimum haploid value (OHVi) of the F 1  plant, wherein the OHVi includes the overall weight placed on combined introgression of the alleles (iEmphasis), calculated as:
   OHV i =OHV+ i Emphasis( w   1   x   1   ,w   2   x   2   , . . . w   n x n ); 
   (d) producing one or more haploids from the F 1  plant;   (e) selecting at least one haploid that has a combined haploid value (CHV) that approaches the OHVi, wherein the CHV is the sum of the haploid values for each of a plurality of genome segments in the plant, and the desired trait; and   (f) producing one or more doubled haploid from each of the one or more selected haploids.   
     
     
         28 . The method of  claim 27 , wherein the method comprises producing a plurality of haploids from the F 1  progeny plant, producing a population of doubled haploids from each of the haploids, and selecting at least one double haploid that has a CHV that approaches the OHVi. 
     
     
         29 . The method of  claim 27 , wherein each of w n =[desired frequency of the introgression allele (x n )]−[actual frequency of the introgression allele (x n )]. 
     
     
         30 . The method of  claim 1 , wherein the plants are alfalfa, apple, banana, bean, broccoli, castorbean, citrus, clover, coconut, coffee, cucumber, Douglas fir,  Eucalyptus , Loblolly pine, linseed, melon, oat, olive, palm, pea, peanut, pepper, poplar,  Radiata  pine, sorghum, Southern pine, strawberry, sugarbeet, sugarcane, sunflower, sweetgum, tea, tobacco, tomato, turf,  Arabidopsis thaliana , barley, maize, cotton, rapeseed/canola, rice, rye, soybean, or wheat plants. 
     
     
         31 . The method of  claim 30 , wherein the plants are wheat plants. 
     
     
         32 . The method of  claim 30 , wherein the plants are maize plants.