Assessing the Contribution of Sli to Self-Compatibility in North American Diploid Potato Germplasm Using KASP™ Markers

Diploid hybrid potato variety development requires the introduction of reliably transmitted self-compatibility (SC) to largely self-incompatible elite diploid germplasm. The diploid Solanum chacoense clone M6 has been widely used to introgress SC into North American potato diploid breeding programs. We determined that M6 is homozygous for six DNA Kompetitive Allele Specific PCR (KASP)(TM) markers spanning a 224 kb region, linked to Sli in Dutch germplasm. Self-compatible Sli alleles were identified in dihaploids of the cultivars 'Atlantic' and 'Superior' and breeding clone NY148. This finding demonstrates the potential of Sli genotyping to select S. tuberosum dihaploids that will contribute to SC. We appraised the transmission of Sli in a diploid recurrent selection population and in a diploid backcross population, each designed to introgress SC while improving agronomic traits. The frequency of the homozygous self-compatible Sli genotype at the six marker loci increased over the course of four cycles of recurrent selection. The homozygous Sli self-compatible genotype at any one of five marker loci within an 80.8 kb region on chromosome 12 (58,960,090-59,040,898 bp) perfectly predicted a SC phenotype in the recurrent selection population. The heterozygous Sli genotype was found in self-compatible and self-incompatible individuals. The discrepancy between phenotype and marker genotype can be attributed in part to the difficulty of accurately phenotyping SC. We also identified self-compatible individuals with the homozygous self-incompatible Sli genotype at all tested loci. The presence of the homozygous self-incompatible Sli haplotype in self-compatible clones 1S1 and DMRH-89 and a self-compatible individual from the S. chacoense PI 133664 further suggests that other genetic components contribute to SC. This work illustrates the ability of Sli markers to predict SC in some germplasm, but it also underscores the need to identify other genomic regions critical to SC and the role of the environment in expression of genes involved in the SC reaction.

Automated summary

The study identified a suitable Solanum chacoense clone for introducing self-compatibility and determined the association of the Sli gene with this trait. The frequency of the self-compatible Sli genotype increased during breeding cycles, and genotypes at five marker loci on chromosome 12 accurately predicted the self-compatibility phenotype. However, accurate phenotyping of self-compatibility remains challenging, and other genetic components may also play a role in determining this trait.