Methods for sequence-directed molecular breeding

Abstract

The present invention provides breeding methods and compositions to enhance the germplasm of a plant by the use of direct nucleic acid sequence information. The methods describe the identification and accumulation of preferred nucleic acid sequences in the germplasm of a breeding population of plants.

1 . A method of plant breeding comprising
 determining the sequence of a plurality of nucleic acids within the genome of at least one or more plants in a breeding population;   associating each of the nucleic acid sequences with a numerical value; and   making at least one plant breeding decision for the one or more plants based on the numerical value.   
   
   
       2 . The method of  claim 1 , wherein the plant is selected from the group consisting of a forage crop, oilseed crop, grain crop, fruit crop, ornamental plants, vegetable crop, fiber crop, spice crop, nut crop, turf crop, sugar crop, beverage crop, tuber crop, root crop, and forest crop. 
   
   
       3 . The method of  claim 1 , wherein the numerical value is a nucleic acid sequence effect estimate. 
   
   
       4 . The method of  claim 1 , wherein the numerical value is a breeding value. 
   
   
       5 . The method of  claim 1 , wherein the numerical value is a nucleic acid frequency. 
   
   
       6 . The method of  claim 1 , wherein the phenotypic trait is selected from the group consisting of herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, enhanced nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, sterility, other agronomic traits, traits for industrial uses, or traits for improved consumer appeal. 
   
   
       7 . The method of  claim 1 , wherein the step of making at least one plant breeding decision comprises selecting among breeding populations based on the at least one numerical value. 
   
   
       8 . The method of  claim 1 , wherein the step of making at least one plant breeding decision comprises selecting progeny in one or more breeding populations based on the at least one numerical value. 
   
   
       9 . The method of  claim 1 , wherein the step of making at least one plant breeding decision comprises predicting progeny performance of parental lines and selecting parental lines based on the predicted progeny performance. 
   
   
       10 . The method of  claim 1 , wherein the step of making at least one plant breeding decision comprises selection of a tester for hybrid seed production. 
   
   
       11 . The method of  claim 1 , wherein the step of making at least one plant breeding decision comprises advancing lines in germplasm improvement activities based on the at least one numerical value. 
   
   
       12 . The method of  claim 11 , wherein the germplasm improvement activities are selected from the group consisting of line and variety development, hybrid development, transgenic event selection, making breeding crosses, testing and advancing a plant through self fertilization, purification of lines or sublines, using plant or parts thereof for transformation, using plants or parts thereof for candidates for expression constructs, and using plant or parts thereof for mutagenesis. 
   
   
       13 . The method of  claim 1 , wherein the step of making at least one plant breeding decision comprises selecting for at least one phenotypic trait based on the at least one numerical value associated with another phenotypic trait. 
   
   
       14 . A method of plant breeding, the method comprising
 providing at least two plants wherein sequence information has been determined for at least one nucleic acid for at least one locus for each of the at least two plants;   determining a nucleic acid sequence effect estimate for at least one phenotypic trait for at least two nucleic acid sequences for the at least one locus; and   making at least one plant breeding decision based on the determined nucleic acid effect estimate for the at least one phenotypic trait.   
   
   
       15 . The method of  claim 14 , wherein the plant is selected from the group consisting of a forage crop, oilseed crop, grain crop, fruit crop, ornamental plants, vegetable crop, fiber crop, spice crop, nut crop, turf crop, sugar crop, beverage crop, tuber crop, root crop, and forest crop. 
   
   
       16 . The method of  claim 14 , wherein the phenotypic trait is selected from the group consisting of herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, enhanced nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, sterility, other agronomic traits, traits for industrial uses, or traits for improved consumer appeal. 
   
   
       17 . The method of  claim 14 , wherein the step of making at least one plant breeding decision comprises selecting among breeding populations based on one or more determined nucleic acid effect estimates. 
   
   
       18 . The method of  claim 14 , wherein the step of making at least one plant breeding decision comprises selecting among progeny in one or more breeding populations based on one or more determined nucleic acid effect estimates. 
   
   
       19 . The method of  claim 14 , wherein the step of making at least one plant breeding decision comprises selecting predicting progeny performance of parental lines based on one or more determined nucleic acid effect estimates and selecting among parental lines based on the predicted progeny performance. 
   
   
       20 . The method of  claim 14 , wherein the step of making at least one plant breeding decision comprises selection of a tester for hybrid seed production. 
   
   
       21 . The method of  claim 14 , wherein the step of making at least one plant breeding decision comprises advancing lines in germplasm improvement activities based on one or more determined nucleic acid effect estimates. 
   
   
       22 . The method of  claim 21 , wherein the germplasm improvement activities are selected from the group consisting of line and variety development, hybrid development, transgenic event selection, making breeding crosses, testing and advancing a plant through self fertilization, purification of lines or sublines, using plant or parts thereof for transformation, using plants or parts thereof for candidates for expression constructs, and using plant or parts thereof for mutagenesis. 
   
   
       23 . The method of  claim 14 , wherein the step of making at least one plant breeding decision comprises selecting for at least one phenotypic trait based on the at least one numerical value associated with another phenotypic trait. 
   
   
       24 . A method of plant breeding comprising
 establishing a fingerprint map defining a plurality of loci within the genome of a breeding population;   associating a QTL allele with known map location with a phenotypic trait in a mapping population;   assaying at least one other plant for presence of the QTL allele using at least one nucleic acid sequence for at least one of the plurality of loci associated with the phenotypic trait.   
   
   
       25 . The method of  claim 24 , wherein the plant is selected from the group consisting of a forage crop, oilseed crop, grain crop, fruit crop, ornamental plants, vegetable crop, fiber crop, spice crop, nut crop, turf crop, sugar crop, beverage crop, tuber crop, root crop, and forest crop. 
   
   
       26 . The method of  claim 24 , wherein the phenotypic trait is selected from the group consisting of herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, enhanced nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, sterility, other agronomic traits, traits for industrial uses, or traits for improved consumer appeal. 
   
   
       27 . The method of  claim 24 , wherein the method further comprises selecting among breeding populations based on the predicted expression of the phenotypic trait. 
   
   
       28 . The method of  claim 24 , wherein the plant breeding decision comprises selecting among progeny in one or more breeding populations. 
   
   
       29 . The method of  claim 24 , wherein the plant breeding decision comprises predicting progeny performance of parental lines and selecting among parental lines based on the predicted progeny performance. 
   
   
       30 . The method of  claim 24 , wherein the plant breeding decision comprises selection of a tester for hybrid seed production. 
   
   
       31 . The method of  claim 24 , wherein the plant breeding decision comprises advancing lines in germplasm improvement activities. 
   
   
       32 . The method of  claim 31 , wherein the germplasm improvement activities are selected from the group consisting of line and variety development, hybrid development, transgenic event selection, making breeding crosses, testing and advancing a plant through self fertilization, purification of lines or sublines, using plant or parts thereof for transformation, using plants or parts thereof for candidates for expression constructs, and using plant or parts thereof for mutagenesis. 
   
   
       33 . The method of  claim 24 , wherein the method plant breeding decision comprises selecting for at least one phenotypic trait based on the at least one numerical value associated with another phenotypic trait. 
   
   
       34 . The method of  claim 24 , wherein the assayed nucleic acid sequence is an allele-specific tag. 
   
   
       35 . A method of marker assisted breeding comprising
 providing a breeding population comprising at least two plants;   associating at least one phenotypic trait with at least one locus of the genome of the plants of the breeding population, wherein the locus is defined by at least one nucleic acid sequence; and   assaying for the presence of at least one nucleic acid sequence of the at least one locus associated with at least one phenotypic trait in a progeny plant of the breeding population; and   making a plant breeding decision for the one or more progeny of the breeding population.   
   
   
       36 . The method of  claim 35 , wherein the plant is selected from the group consisting of a forage crop, oilseed crop, grain crop, fruit crop, ornamental plants, vegetable crop, fiber crop, spice crop, nut crop, turf crop, sugar crop, beverage crop, tuber crop, root crop, and forest crop. 
   
   
       37 . The method of  claim 35 , wherein the phenotypic trait is selected from the group consisting of herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, enhanced nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, sterility, other agronomic traits, traits for industrial uses, or traits for improved consumer appeal. 
   
   
       38 . The method of  claim 35 , wherein the plant breeding decision comprises selecting among breeding populations. 
   
   
       39 . The method of  claim 35 , wherein the plant breeding decision comprises selecting among progeny in breeding populations. 
   
   
       40 . The method of  claim 35 , wherein the plant breeding decision comprises predicting progeny performance and selecting among parental lines based on the predicted progeny performance. 
   
   
       41 . The method of  claim 35 , wherein the plant breeding decision comprises selection of a tester for hybrid seed production. 
   
   
       42 . The method of  claim 35 , wherein the plant breeding decision comprises advancing lines in germplasm improvement activities. 
   
   
       43 . The method of  claim 42 , wherein the germplasm improvement activities are selected from the group consisting of line and variety development, hybrid development, transgenic event selection, making breeding crosses, testing and advancing a plant through self fertilization, purification of lines or sublines, using plant or parts thereof for transformation, using plants or parts thereof for candidates for expression constructs, and using plant or parts thereof for mutagenesis. 
   
   
       44 . The method of  claim 35 , wherein the plant breeding decision comprises selecting for at least one phenotypic trait based on the at least one numerical value associated with another phenotypic trait. 
   
   
       45 . The method of  claim 35 , wherein the assayed nucleic acid sequence is an allele-specific tag. 
   
   
       46 . A method of selecting a breeding population for use in a breeding program comprising
 providing at least two distinct breeding populations;   using a plurality of breeding values for at least one phenotypic trait for at least two nucleic acids for at least one locus for the breeding populations; and   selecting at least one breeding population based on at least one breeding value.   
   
   
       47 . The method of  claim 46 , wherein the breeding populations comprise plants selected from the group consisting of a forage crop, oilseed crop, grain crop, fruit crop, ornamental plants, vegetable crop, fiber crop, spice crop, nut crop, turf crop, sugar crop, beverage crop, tuber crop, root crop, and forest crop. 
   
   
       48 . The method of  claim 46 , wherein the breeding value is calculated for at least one phenotypic trait selected from the group consisting of herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, enhanced nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, sterility, other agronomic traits, traits for industrial uses, or traits for improved consumer appeal. 
   
   
       49 . The method of  claim 46 , wherein the breeding population is used in germplasm improvement activities. 
   
   
       50 . The method of  claim 49 , wherein the germplasm improvement activities are selected from the group consisting of line and variety development, hybrid development, transgenic event selection, making breeding crosses, testing and advancing a plant through self fertilization, purification of lines or sublines, using plant or parts thereof for transformation, using plants or parts thereof for candidates for expression constructs, and using plant or parts thereof for mutagenesis.