Development and validation of Kompetitive allele‐specific PCR (KASP) markers for bacterial blight resistant locus BB‐13 in Upland cotton (Gossypium hirsutum L.)

Abstract Cotton bacterial blight (CBB), caused by the pathogen Xanthomonas citri subsp. malvacearum ( Xcm ), can inflict significant damage to cotton ( Gossypium hirsutum L.) production. Previously, we identified and mapped the broad‐spectrum CBB‐resistant locus BB‐13 on the long arm of chromosome D02 using array‐based single nucleotide polymorphisms (SNPs). In the current study, linked SNPs were converted into easily assayable Kompetitive Allele‐Specific PCR (KASP) markers to enable efficient detection and marker‐assisted selection of alleles at the BB‐13 locus. The KASP marker's efficiency in detecting the BB‐13 resistant gene was validated using an Upland cotton diversity panel of 72 accessions phenotyped with Xcm race 18. The KASP marker NCBB‐KASP4, derived from the CottonSNP63K array‐based marker i25755Gh that is closely associated with BB‐13 , predicted the CBB response phenotypes with an error rate of 4.17% in the diversity panel. Additionally, two independent biparental recombinant inbred line populations segregating for resistance to Xcm race 18 were used for KASP marker validation and to test their utility in detecting the presence of the BB‐13 locus in the resistant accession CABD3CABCH‐1‐89. NCBB‐KASP4, validated across breeding populations and broad germplasm, is a reliable KASP marker for detection and testing of BB‐13 locus in cotton. Further, diagnostic array‐based SNP marker i25755Gh's allele pattern and the potential CBB response is described for 875 Gossypium accessions. These SNP‐based phenotypic predictions for 875 accessions along with disease response phenotypes to Xcm race 18 for 253 accessions provide a reference for CBB resistance in diverse cotton germplasm in the United States.