PCR primers for detection and identification of plant pathogenic species, subspecies, and strains of acidovorax

An oligonucleotide primer comprising the sequence 5′-AGAACAATTCGTCATTAC TGAAC-3′ (SEQ ID NO:12) or a portion of SEQ ID NO:

• 12, wherein the primer is eighteen to twenty-four nucleotides in length, comprises at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

A primer set comprising oligonucleotides comprising the sequence 5′-GTCATCCTC CACCAACCAAG-3′ (SEQ ID NO:10) and the sequence 5′-AGAACAATTCGTCATTACT GAAC-3′ (SEQ ID NO:12) or portions of SEQ ID NO:

• 10 and SEQ ID NO:12, wherein the primer set comprises primers eighteen to twenty-four nucleotides in length and at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

An oligonucleotide primer comprising the sequence 5′-AGATGCCCTGCGGTAGG GCG-3′ (SEQ ID NO:11) or a portion of SEQ ID NO:

• 11, wherein the primer is eighteen to twenty-four nucleotides in length, comprises at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

A primer set comprising oligonucleotides comprising the sequence 5′-AGATGCCC TGCGGTAGGGCG-3′ (SEQ ID NO:11) and the sequence 5′-AGAACAATTCGTCATTA CTGAAC-3′ (SEQ ID NO:12) or portions of SEQ ID NO:

• 11 and SEQ ID NO:12, wherein the primer set comprises primers eighteen to twenty-four nucleotides in length and at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

An oligonucleotide primer comprising the sequence 5′-AATTTTTGTTGCCGACGG CACG-3′ (SEQ ID NO:16) or a portion of SEQ ID NO:16, wherein the primer is eighteen to twenty-four nucleotides in length, comprises at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

An intergenic spacer region (ISR) sequence selected from the group consisting of:

• ISR1 of rice strains of Acidovorax avenae subsp. avenae comprising the nucleotides of SEQ ID NO:13, ISR2 of corn strains of A. avenae subsp. avenae comprising the nucleotides of SEQ ID NO:14, ISR3 of rescue grass strains of A. avenae subsp. avenae comprising the nucleotides of SEQ ID NO:15, and ISR4 of wheat grass strains of A. avenae subsp. avenae comprising the nucleotides of SEQ ID NO:15.

An oligonucleotide primer comprising a portion of SEQ ID NO:

• 13 or its complement, wherein said primer is eighteen to twenty-four nucleotides in length, comprises at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice (SEQ ID NO:13) and those of corn (SEQ ID NO:14) or rescue or wheat grasses (SEQ ID NO:15), specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

A kit for identifying rice strains of Acidovorax avenae subsp. avenae, comprising at least one primer comprising the sequence 5′-GTCATCCTCCACCAACCAAG-3′ (SEQ ID NO:10) or a portion of SEQ ID NO:10, wherein the primer is eighteen to twenty-four nucleotides in length, comprises at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

A kit for identifying rice strains of Acidovorax avenae subsp. avenae, comprising at least one primer comprising the sequence 5′-AGATGCCCTGCGGTAGGGCG-3′ (SEQ ID NO:11) or a portion of SEQ ID NO:11, wherein the primer is eighteen to twenty-four nucleotides in length, comprises at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.

A kit for identifying rice strains of Acidovorax avenae subsp. avenae, comprising at least one primer comprising the sequence 5′-AGAACAATTCGTCATTACTGAAC-3′ (SEQ ID NO:12) or a portion of SEQ ID NO:

• 12, wherein the primer is eighteen to twenty-four nucleotides in length, comprises at least one unique nucleotide as identified in FIG. 4 as a mismatch between strains of Acidovorax avenae subsp. avenae from rice and those of corn, rescue grass, or wheat grass, specifically hybridizes to a region of SEQ ID NO:13 or its complement, and distinguishes rice strains of Acidovorax avenae subsp. avenae (1) from other strains of Acidovorax avenae subsp. avenae isolated from plants other than rice and (2) from other subspecies of A. avenae.