Revealing Genetic Variations Associated with Chip-Processing Properties in Potato (Solanum tuberosum L.)

Abstract

Although the potato chip industry is booming, and distinct chip-processing clones have been released over the past 60 years, the genetic architecture of their chip-processing characteristics remains largely unknown. Case-control genome-wide association studies (GWAS) with SolCAP SNP array data for chip-processing clones versus all other market classes in the 393-line potato diversity panel were performed using the GWASpoly R package, enabling detection of significant signals on chromosome 10. Our results were replicated using internal replication of a strata-corrected 190-line panel. Furthermore, the genomic scans employing selective sweep approaches such as the cross-population composite likelihood ratio method (XP-CLR) and PCAdapt redetected the same signals as those in our GWAS. Through applications of four selective sweep approaches, various genetic variants were found across the genome that had been differentially selected. These genomic regions under selection along with transcriptomic data analysis are involved in carbohydrate metabolism-related genes or loci and transcription factors, indicating to be associated with the improvement of chip-processing performance of potato cultivars. Kompetitive allele-specific PCR (KASP) assays were designed for the causal SNPs to use in validating the chip-processing clones. The results could have implications for genomics-assisted breeding of the promising chip-processing cultivars in potato.