Methods And Systems For Identifying Hybrids For Use In Plant Breeding

Abstract

Exemplary systems for identifying hybrids for use in a plant breeding pipeline are disclosed. One exemplary system includes a computing device configured to access phenotypic data related to a pool of hybrids from a data structure and determine a prediction score for each of the hybrids in the pool of hybrids based on the accessed phenotypic data. The prediction score is indicative of a probability of selection and/or a probability of success of the hybrid based on historical data. The computing device is also configured to select a group of hybrids from the pool of hybrids based on the prediction score, identify a set of hybrids, from the selected group of hybrids, based on one or more factors associated with the hybrids, and then direct the set of hybrids to a validation phase of the plant breeding pipeline for planting and/or testing.

What is claimed is: 
     
         1 . A system for use in identifying hybrids for use in a plant breeding pipeline, the system comprising:
 a data structure including phenotypic data related to a pool of hybrids, each hybrid in the pool of hybrids including one male line and one female line, wherein the male lines and the female lines of the hybrids in the pool of hybrids define a pool of male lines and a pool of female lines; and   a computing device coupled in communication with the data structure and configured to:
 access the phenotypic data related to the pool of hybrids; 
 determine a prediction score for each of the hybrids in the pool of hybrids based on the accessed phenotypic data, the prediction score indicative of a probability of selection and/or a probability of success of the hybrid based on historical data; 
 select a group of hybrids from the pool of hybrids based on the prediction score; 
 identify a set of hybrids, from the selected group of hybrids, based on one or more factors associated with the hybrids; and 
 direct the set of hybrids to a validation phase of the plant breeding pipeline for planting and/or testing. 
   
     
     
         2 . The system of  claim 1 , wherein the computing device is configured to select the group of hybrids based on the prediction score of each of the hybrids in the selected group of hybrids satisfying one or more thresholds. 
     
     
         3 . The system of  claim 1 , wherein the computing device is further configured to identify, based on a user input, the pool of hybrids, prior to determining a prediction score for each of the hybrids in the pool of hybrids. 
     
     
         4 . The system of  claim 1 , wherein the computing device is configured to identify the set of hybrids based, at least in part, on a deviation of the identified set of hybrids from a desired profile for both male and female line distributions. 
     
     
         5 . The system of  claim 4 , wherein the computing device is further configured to identify the set of hybrids (x OPT ) based on a set identification algorithm, which includes:
     x   OPT =arg max λ p Σ i=1   N   x   i   p   i −λ d     m   1 T θ m −λ d     f   1 T θ f −λ h     m   1 T γ m −λ h     f   1 T γ f ; and
   where p i  is indicative of a probability of success; and
   λ p ( b   i   f ) T   y   *   f −λ d ( y   *   f ) T   S   f   y   *   f ,
 
   where b i   f  is a probability of success of the female line, and S f  is a pairwise matrix of homology of the pool of female lines, subject to:
   1 T   y   *   f =1, 0 ≤y   *   f ≤1; and
 
   λ p ( b   i   m ) T   y   *   m −λ d ( y   *   m ) T   S   m   y   *   m  
 
 where b i   m  is a probability of success of the male line, and S f  is a pairwise matrix of homology of the pool of male lines, subject to: 
   
       
         
           
             
               
                 
                   
                     
                       1 
                       T 
                     
                     ⁢ 
                     
                       y 
                       * 
                       m 
                     
                   
                   = 
                   1 
                 
                 , 
                 
                   
                     0 
                     ≤ 
                     
                       y 
                       * 
                       m 
                     
                     ≤ 
                     1 
                   
                   ; 
                   and 
                 
               
               ⁢ 
               
 
               
                 
                   - 
                   
                     
                       γ 
                       m 
                     
                     ( 
                     i 
                     ) 
                   
                 
                 ≤ 
                 
                   
                     
                       ∑ 
                       
                         j 
                         = 
                         1 
                       
                       N 
                     
                     
                       
                         
                           M 
                           h 
                           m 
                         
                         ( 
                         
                           i 
                           , 
                           j 
                         
                         ) 
                       
                       * 
                       
                         x 
                         j 
                       
                     
                   
                   - 
                   
                     h 
                     i 
                     m 
                   
                   - 
                 
                 ≤ 
                 
                   
                     γ 
                     m 
                   
                   ( 
                   i 
                   ) 
                 
               
             
           
         
         
           where γ m (i) define a desired profile for heterotic diversity for the male lines; M h   m  is indicative of an incidence matrix from progenies to pool of male lines; and h i   m  is indicative of an average of the probability scores for the hybrids for the male line; and
   −γ f ( i )≤Σ j=1   N   M   h   f ( i,j )* x   j   −h   i   f ≤γ f ( i ); and
 
 
         
         where γ f (i) define a desired profile for heterotic diversity for the male lines; M h   f  is indicative of an incidence matrix from progenies to the pool of female lines; and h i   f  is indicative of an average of the probability scores for the hybrids for the female line; and
   −θ m ( i )≤Σ j=1   N   M   m ( i,j )* x   j   −y   i   m ≤θ m ( i ); and
 
 
         where M m  is indicative of the incidence matrix associated with the pool of male lines; and θ m (i) defines deviation; and
   −θ f ( i )≤Σ j=1   N   M   f ( i,j )* x   j   −y   i   f ≤θ f ( i ); and
 
 
         where M f  is indicative of an incidence matrix associated with the pool of female lines; and θ f (i) defines deviation; and 
       
       
         
           
             
               
                 
                   α 
                   
                     T 
                     k 
                   
                   l 
                 
                 ( 
                 i 
                 ) 
               
               ≤ 
               
                 
                   ∑ 
                   
                     j 
                     = 
                     1 
                   
                   N 
                 
                 
                   
                     
                       M 
                       
                         T 
                         k 
                       
                     
                     ( 
                     
                       i 
                       , 
                       j 
                     
                     ) 
                   
                   * 
                   
                     x 
                     j 
                   
                 
               
               ≤ 
               
                 
                   α 
                   
                     T 
                     k 
                   
                   h 
                 
                 ( 
                 i 
                 ) 
               
             
           
         
         where M T     k    is indicative of the incidence matrix from hybrid trait T k ; and α T     k     l (i) and α T     k     h (i), define lower (l) and upper (h) portfolio bounds for trait T k . 
       
     
     
         6 . The system of  claim 4 , wherein the one or more factors include line distribution, heterotic diversity, and/or market segmentation. 
     
     
         7 . The system of  claim 1 , wherein the one or more factors includes one or more of: line distribution for male lines, line distribution for female lines, heterotic diversity for male lines, heterotic diversity for female lines, trait(s) or trait profiles, market segmentation, risk, product cost, trait availability/readiness; and
 wherein the computing device is configured to identify the set of hybrids further based on a desired profile for said one or more factors.   
     
     
         8 . The system of  claim 1 , wherein the phenotypic data includes historical phenotypic data related to a plurality of hybrids and/or lines and historical selections for each hybrid in the plurality of hybrids; and
 wherein the computing device is further configured to:
 generate a prediction model based on the historical phenotypic data and the historical selections, wherein the plurality of hybrids and/or lines are associated with plant material of a type consistent with a plant type of the pool of hybrids; and 
 determine the prediction score for each of the hybrids in the pool of hybrids further based on the prediction model. 
   
     
     
         9 . The system of  claim 1 , further comprising the plant breeding pipeline coupled in communication with the computing device;
 wherein the plant breeding pipeline includes a cultivation and testing phase and the validation phase;   wherein the computing device is configured to receive at least a portion of the phenotypic data included in the data structure from the cultivation and testing phase of the plant breeding pipeline and to store the at least a portion of the phenotypic data included in the data structure; and   wherein a plant derived from at least one hybrid of the set of hybrids is planted in a growing space of the validation phase of the plant breeding pipeline, after the set of hybrids are directed to the validation phase of the plant breeding pipeline.   
     
     
         10 . The system of  claim 1 , wherein a plant derived from at least one hybrid of the set of hybrids is planted in a growing space of the plant breeding pipeline, after the set of hybrids are directed to the validation phase of the plant breeding pipeline. 
     
     
         11 . The system of  claim 1 , further comprising a growing space including one or more plants, wherein the one or more plants are based on the identified set of hybrids.