SNP Markers Associated with Some Root, Stolon, and Tuber Traits in Tetraploid Potatoes (Solanum tuberosum L.) Grown Under Diverse Growing Systems

Numerous loci, environmental factors, and their interactions have an impact on the phenotypic diversity of several significant traits in plants. One approach put forth in recent years for genetic research and finding quantitative trait loci (QTLs) responsible for the specific trait is association mapping. The purpose of the current study was to pinpoint the genetic underpins of significant underground traits in potato. A panel of 192 diverse tetraploid potato genotypes from different countries were grown under different growing conditions (i.e., aeroponics and pot) to study root, stolon and tuber traits. Significant differences (P ≤ 0.01) were found between the genotypes for all examined traits, and the heritability (H2) of the traits ranged from 0.74 to 0.94. Genotyping was carried out using the SolCAP 25K array. 21,226 polymorphic SNPs were used for association mapping of underground traits. A GWASpoly R package was implemented for the marker-trait associations, and 78 genomic regions were found associated with the traits under investigation.. The history of potato breeding was reflected in LD patterns. The identified SNPs have their putative gene functions related to the root and stolon architecture and tuber growth (i.e., WRKY transcription factor, MAPK, the GTP cyclohydrolase 1 (i.e., GTPCHI), Glutathionyl-hydroquinone reductase, and pyrophosphate—fructose 6-phosphate 1-phosphotransferase subunit alpha (PFPase). The results of the present study provides a framework that could be helpful for future potato breeding programs to increase tuber production and reduce the challenges of feeding the world's population in the years to come.