Abstract: A computer-implemented method of preparing a set of differentially informative methylated positions (DIMPs) or differentially informative methylated regions (DIMRs) from a sample methylome of an animal or plant having a phenotypic characteristic different from a wild-type of the same species of animal or plant, and the characteristic is associate with differences in methylation of the genome, comprises: providing a computer with the sample methylome, and a reference methylome of the wild-type of the same species of animal or plant; calculating with the computer a divergence between a plurality of cytosine positions of the sample methylome and the reference methylome; and selecting with the computer a set of DIMPs or DIMRs. Each DIMP or DIMR is selected based on an approximation of the energy required to produce the divergence between methylation levels of the plurality of cytosine positions of the sample methylome as compared to the wild-type methylome.

Abstract: The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Abstract: The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Abstract: The present disclosure provides methods for obtaining plants that exhibit useful traits or that are useful for plant breeding by suppression of plastidic MSH1 in the presence of mitochondrial-targeted MSH1 in plants. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for suppression of plastidic MSH1 in the presence of mitochondrial-targeted MSH1 are also provided.

Abstract: A computer-implemented method of preparing a set of differentially informative methylated positions (DIMPs) or differentially informative methylated regions (DIMRs) from a sample methylome of an animal or plant having a phenotypic characteristic different from a wild-type of the same species of animal or plant, and the characteristic is associate with differences in methylation of the genome, comprises: providing a computer with the sample methylome, and a reference methylome of the wild-type of the same species of animal or plant; calculating with the computer a divergence between a plurality of cytosine positions of the sample methylome and the reference methylome; and selecting with the computer a set of DIMPs or DIMRs. Each DIMP or DIMR is selected based on an approximation of the energy required to produce the divergence between methylation levels of the plurality of cytosine positions of the sample methylome as compared to the wild-type methylome.

Abstract: The present invention provides methods for obtaining plants that exhibit useful traits by producing double haploids of plants with epigenetic modifications initiated in a parental line by suppression of MSH1. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided.

Abstract: The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Abstract: Methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plants are provided. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Abstract: The subject invention relates to nematode responsive domains obtained from soybean promoters for phosphoribosylformylglycinamidine ribonucleotide (FGAM) synthase paralogs. The nematode responsive domains can be used in promoters that are linked to heterologous DNA. Such constructs can be expressed in transfected or transformed soybean and used in the control of nematode infection of soybean.

Abstract: Plant MSH1 polynucleotides and polypeptides are described. Also described are methods for the use and modulation of such MSH1 polynucleotides and polypeptides.

Abstract: Plant MSH1 polynucleotides and polypeptides are described. Also described are methods for the use and modulation of such MSH1 polynucleotides and polypeptides.

Abstract: The subject invention relates to nematode responsive domains obtained from soybean promoters for phosphoribosylformylglycinamidine ribonucleotide (FGAM) synthase paralogs. The nematode responsive domains can be used in promoters that are linked to heterologous DNA. Such constructs can be expressed in transfected or transformed soybean and used in the control of nematode infection of soybean.

Abstract: Plant MSH1 polynucleotides and polypeptides are described. Also described are methods for the use and modulation of such MSH1 polynucleotides and polypeptides.