Methods and compositions for predicting unobserved phenotypes (pup)

A method for predicting a phenotype in a plant of a predicted population, the method comprising:

• (a) determining marker effects for a plurality of markers in a genotyped and phenotyped reference population, wherein the reference population comprises a linkage disequilibrium (LD) panel;
• (b) genotyping one or more plants of the predicted population with respect to the plurality of markers, wherein each of the one or more plants of the predicted population is a descendant of two parents, each of which is at least 80% genetically identical to a member of the reference population;
• (c) summing the marker effects for each of the one or more plants of the predicted population based on the genotyping of step (b);
• and
• (d) predicting the phenotype of the one or more plants of the predicted population based on the marker effects summed in step (c).

A method for generating a plant with a phenotype of interest, the method comprising:

• (a) determining marker effects for a plurality of markers in a genotyped and phenotyped reference population, wherein the reference population comprises:
• (i) an F2 generation produced by crossing two parental plants to produce an F1 generation and then intercrossing, backcrossing, and/or selfing the F1 generation;
• and/or
• (ii) an F3 or subsequent generation, wherein the F3 or subsequent generation is produced by intercrossing, backcrossing, selfing, and/or producing double haploids from the F2 generation and/or a subsequent generation;
• and/or
• (iii) a reference network comprising a plurality of members generated by:
• (1) selecting a plurality of different parental lines;
• (2) crossing the plurality of different parental lines to produce a plurality of F1 generations;
• (3) intercrossing, backcrossing, and/or selfing the F1 generation;
• and/or making a double haploid from F1 to produce a plurality of distinct F2 generations, and optionally singly or sequentially intercrossing, backcrossing, selfing, and/or producing double haploids from the plurality of distinct F2 generations to produce distinct F3 and, optionally, subsequent generations;
• (4) pooling some or all of the members of the distinct F2, F3, or subsequent generations to generate the reference network, wherein each member of the reference network derives its genome from two of the parental lines;
• and/or
• (iv) a linkage disequilibrium (LD) panel;
• (b) genotyping one or more plants of a predicted population with respect to the plurality of markers, wherein the each of the one or more plants of the predicted population is a descendant of two parents each of which is at least 80% genetically identical to at least one of the two plants that comprise or where employed to generate the reference population;
• (c) summing the marker effects for each of the one or more plants of the predicted population based on the genotype determined in step (b) to generate a genetic score for each of the one or more plants of the predicted population;
• (d) predicting phenotypes of the one or more plants of the predicted population based on the genetic scores generated in step (c);
• (e) selecting one or more of the one or more plants of the predicted population based on the predicting step that are predicted to have a phenotype of interest, and
• (f) growing the selected one or more plants of the predicted population,
• wherein a plant with a phenotype of interest is generated.

A method for estimating genetic similarity between a first and a second population, the method comprising:

• (a) providing a first and a second population, wherein:
• (i) the first population comprises individuals that are F2 or subsequent generation progeny produced by crossing a first parent and a second parent to produce a first F1 generation, and then intercrossing, backcrossing, selfing, and/or producing double haploids from the first F1 generation to produce the F2 generation, and optionally, further intercrossing, backcrossing, selfing, and/or producing double haploids from the F2 generation and any subsequent generations to produce the first population;
• and
• (ii) the second population comprises individuals that are F2 or subsequent generation progeny produced by crossing a third parent and a fourth parent to produce a second F1 generation, and then intercrossing, backcrossing, selfing, and/or producing double haploids from the second F1 generation to produce the F2 generation, and optionally, further intercrossing, backcrossing, selfing, and/or producing double haploids from the F2 generation and any subsequent generations to produce the second population;
• (b) genotyping the first, second, third, and fourth parents with respect to a plurality of pre-determined markers;
• (c) calculating first, second, third, and fourth percent genetic similarities, wherein:
• (i) the first percent genetic similarity is the percentage of allele sharing across all of the pre-determined markers of the first parent with respect to the third parent;
• (ii) the second percent genetic similarity is the percentage of allele sharing across all of the pre-determined markers of the first parent with respect to the fourth parent;
• (iii) the third percent genetic similarity is the percentage of allele sharing across all of the pre-determined markers of the second parent with respect to the third parent;
• and
• (iv) the fourth percent genetic similarity is the percentage of allele sharing across all of the pre-determined markers of the second parent with respect to the fourth parent;
• (d) determining a first mean percentage genetic similarity comprising the mean percentage genetic similarity of the first percent genetic similarity and the third percent genetic similarity;
• (e) determining a second mean percentage genetic similarity comprising the mean percentage genetic similarity of the second percent genetic similarity and the fourth percent genetic similarity;
• and
• (f) selecting the greater of the first mean percentage genetic similarity and the second mean percentage genetic similarity, wherein the greater of the two mean percentage genetic similarities provides an estimate of the genetic similarity between a first and a second population.