Development and applications of KASP markers distinguishing A- and B/K-genomes of Arachis

Peanut is an important global food crop with a narrow genetic base due to its domestication bottleneck and the ploidy barrier between it and almost all of its wild diploid relatives. Increasingly, peanut breeders have been introgressing beneficial alleles from its diploid relatives into the cultigen to improve agronomic traits along with its pathogen and pest resistances. To overcome the ploidy barrier, the process of introgression can be initiated by making hybrids between A- and B/K-genome Arachis diploid species and then doubling their chromosomes to induce tetraploidy. These allotetraploids are generally cross-compatible with peanut. Previously, true allotetraploids were distinguished from selfed progeny by infertile pollen grain counts; however, markers that can distinguish allele dosage between A- and B/K-genomes allow allotetraploids to be confirmed before flowering or even planting and can be more reliable than infertile pollen grain counts. These markers also can be used to confirm and track the inheritance of previously discovered homoeologous recombination events, which commonly occur in synthetic allotetraploid-derived materials. In this study, 105 KASP markers distinguishing A- and B/K-genomes were designed to span the entire peanut genome. These markers can be used as a time and cost-efficient alternative to using the Axiom_Arachis SNP arrays where high-resolution is not required.