Artificial selection method and reagents

Abstract

The present invention provides methods for estimating the breeding value of individuals in populations such as those having small effective population size (Ne) e.g., to identify selection candidates having high breeding values, wherein the methods comprise inferring one or more genotypes for one or more markers at a locus or QTL to be the same as for an ancestor or founder or a subset of ancestors and/or founders from which a corresponding chromosome segment is derived and estimating the breeding value of the individual based on the inferred genotype(s).

1 - 2 . (canceled) 
     
     
         3 . A method of artificial selection comprising genotyping an individual in a current population for the presence or absence of one or more informative markers in one or a plurality of chromosome segments, inferring genotype(s) of each chromosome segment to be the same as for one or more ancestors and/or founders from which the chromosome segment(s) are derived, and estimating the breeding value of the individual based on the inferred genotype(s), wherein each ancestor or founder is an ancestor or founder providing a significant long term genetic contribution to the current population and wherein the genotype(s) of the one or more ancestors and/or founders for one or more informative markers are substantially known, wherein the individual is a plant and the population is a population of plants having a small effective population size. 
     
     
         4 . The method according to claim  1 , wherein said method comprises:
 (i) optionally, determining a minimum set of ancestors and/or founders representative of the current population;   (ii) optionally, genotyping one or more ancestors and/or founders for known markers;   (iii) genotyping an individual in a current population for the presence or absence of one or more informative markers in one or a plurality of chromosome segments;   (iv) optionally, tracing the lineages of the one or plurality of chromosome segments back to one or more ancestors and/or founders from which they are derived;   (v) inferring genotypes of each chromosome segment to be the same as for one Or more ancestors and/or founders from which the chromosome segments are derived; and   (vi) estimating the breeding value of the individual based on the inferred genotypes.   
     
     
         5 . The method according to claim  2 , further comprising tracing the lineage of the one or more chromosome segment(s) back to one or more ancestors and/or founders from which they are derived such as by tracing individual chromosome segments in members of the current population back to the key ancestors and/or founders by a process comprising tracing chromosome segments in selection candidates of the current population to one or more immediate ancestors and/or founders using a small number of markers and tracing the chromosome segments in the immediate ancestors and/or founders to corresponding chromosome segments in one or more key ancestors and/or founders, and preferably comprising tracing the chromosome segments in the immediate ancestors and/or founders back to the chromosome segments in the key ancestors and/or founders using markers. 
     
     
         6 - 7 . (canceled) 
     
     
         8 . The method according to claim  1 , wherein said method comprises:
 (i) genotyping an individual in a current population for the presence or absence of one or more informative markers in one or a plurality of chromosome segments;   (ii) optionally, determining a minimum set of ancestors and/or founders representative of the current population;   (iii) tracing the lineages of the plurality of chromosome segments back to one or more ancestors and/or founders from which they are derived;   (iv) optionally, genotyping one or more ancestors and/or founders for known markers;   (v) inferring genotypes of each chromosome segment to be the same as for one or more ancestors and/or founders from which the chromosome segments are derived; and   (vi) estimating the breeding value of the individual based on the inferred genotypes.   
     
     
         9 - 12 . (canceled) 
     
     
         13 . The method according to claim  1 , wherein the markers within each chromosome segment are in linkage disequilibrium. 
     
     
         14 . The method according to claim  1 , wherein the markers are selected from an allele, haplotype, haplogroup, locus, quantitative trait locus, polymorphism such as single nuclear polymorphisms (SNPs), STRs and combinations thereof. 
     
     
         15 . The method of  claim 14 , wherein the markers are SNPs. 
     
     
         16 . The method according to claim  1 , further comprising inferring the pedigree of the individual from markers that are used to trace chromosome segments. 
     
     
         17 . (canceled) 
     
     
         18 . The method according to claim  1 , further comprising characterizing the ancestors and/or founders by genotyping one or more ancestors and/or founders for known markers. 
     
     
         19 . The method according to claim  1 , further comprising identifying the ancestors and/or founders such as by determining a minimum set of ancestors and/or founders representative of the current population. 
     
     
         20 . (canceled) 
     
     
         21 . The method according to claim  1 , wherein the genome sequences of the key ancestors and/or founders are known and wherein said method comprises inferring genome sequences of individuals in the current population. 
     
     
         22 - 42 . (canceled) 
     
     
         43 . The method of  claim 14 , wherein the markers are STRs and the STRs are microsatellites. 
     
     
         44 . The method of claim  1 , wherein the ancestors and/or founders contribute at least 0.1% of the total genetic variance to the current population. 
     
     
         45 . The method of claim  1 , wherein the ancestors and/or founders contribute at least 0.5% of the total genetic variance to the current population. 
     
     
         46 . The method of claim  1 , wherein the ancestors and/or founders contribute at least 1.0% of the total genetic variance to the current population. 
     
     
         47 . The method of claim  1 , wherein the genotype of the ancestor and/or founder is known for all informative marker(s) for which genotype information is missing from the determined genotype of the individual in the current population.