A method for determining the zygosity and/or presence /absence of an bm3 deletion allele using corn plant tissue, the method comprising: obtaining a sample of isolated genomic DNA from the corn plant tissue; contacting the isolated genomic DNA with two nucleic acid molecules each consisting of a polynucleotide that is between 10 and 35 nucleotides in length that is capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions, and two nucleic acid molecules capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions; amplifying the nucleotide sequence of the isolated genomic DNA between nucleotide sequences of the isolated genomic DNA that hybridize to the two nucleic acid molecules each consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions; amplifying the nucleotide sequence of the isolated genomic DNA between nucleotide sequences of the isolated genomic DNA that hybridize to the two nucleic acid molecules each consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions; including in the amplifying reaction at least one nucleic acid molecule consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions that is labeled with a first reporter, and at least one nucleic acid molecule capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions that is labeled with a second reporter; and detecting the levels of the first and second reporter, wherein the nucleotide sequences hybridizing to SEQ ID NO:10 or its complementary sequence are selected from SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6 and the nucleotide sequences hybridizing to SEQ ID NO:11 or its complementary sequence are selected from SEQ ID NO:7, SEQ ID NO:8 and SEQ ID NO:9. obtaining a sample of isolated genomic DNA from the corn plant tissue; contacting the isolated genomic DNA with two nucleic acid molecules each consisting of a polynucleotide that is between 10 and 35 nucleotides in length that is capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions, and two nucleic acid molecules capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions; amplifying the nucleotide sequence of the isolated genomic DNA between nucleotide sequences of the isolated genomic DNA that hybridize to the two nucleic acid molecules each consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions; amplifying the nucleotide sequence of the isolated genomic DNA between nucleotide sequences of the isolated genomic DNA that hybridize to the two nucleic acid molecules each consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions; including in the amplifying reaction at least one nucleic acid molecule consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions that is labeled with a first reporter, and at least one nucleic acid molecule capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions that is labeled with a second reporter; and detecting the levels of the first and second reporter, wherein the nucleotide sequences hybridizing to SEQ ID NO:10 or its complementary sequence are selected from SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6 and the nucleotide sequences hybridizing to SEQ ID NO:11 or its complementary sequence are selected from SEQ ID NO:7, SEQ ID NO:8 and SEQ ID NO:9. amplifying the nucleotide sequence of the isolated genomic DNA between nucleotide sequences of the isolated genomic DNA that hybridize to the two nucleic acid molecules each consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions; amplifying the nucleotide sequence of the isolated genomic DNA between nucleotide sequences of the isolated genomic DNA that hybridize to the two nucleic acid molecules each consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions; including in the amplifying reaction at least one nucleic acid molecule consisting of a nucleotide sequence capable of hybridizing to SEQ ID NO:10 or its complementary sequence under high stringency conditions that is labeled with a first reporter, and at least one nucleic acid molecule capable of hybridizing to SEQ ID NO:11 or its complementary sequence under high stringency conditions that is labeled with a second reporter; and detecting the levels of the first and second reporter, wherein the nucleotide sequences hybridizing to SEQ ID NO:10 or its complementary sequence are selected from SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6 and the nucleotide sequences hybridizing to SEQ ID NO:11 or its complementary sequence are selected from SEQ ID NO:7, SEQ ID NO:8 and SEQ ID NO:9.