Genetic dissection of yield and quality-related traits in a Colombian Andigenum potato collection, revealed by genome-wide association and genomic prediction analyses

Genetic diversity in plant breeding is key to dissecting the genetic architecture of complex economical traits. Genome-wide association studies (GWAS) and genomic selection (GS) have emerged as promising tools to accelerate agronomic trait improvement efficiency, defining current breeding strategies. The key objective of this study was to investigate the genetic architecture and perform genomic prediction of yield, specific gravity (SG), and dry matter (DM) traits, using a diversity panel of 568 Solanum tuberosum Andigenum accessions. Analyses were carried out using a total of 4271 Single Nucleotide Polymorphisms (SNPs) obtained using the SolCAP SNP array 8 K version. Yield data were collected from field evaluations during three consecutive years, while tuber quality traits (SG and DM) were evaluated in 1 year. To this end, population structure was first examined and revealed two main subpopulations. GWAS analysis identified candidate loci for yield in chromosomes 1, 3, 4 and 11, with minor effects on phenotypic variation (< 1–10%). Important genomic regions were detected for SG in chromosomes 5, 6, and 8, and in DM in chromosome 7, though they explained only a small fraction of the phenotypic variation (< 1–2% for SG and 3% for DM). Functional annotation of candidate genes showed promising genomic regions related to tuber growth, quality and development that could further be verified by other tools (i.e., gene editing). Furthermore, the predicted capacity of the cross-validation process between subpopulations was low for yield and specific gravity. However, when the prediction process was conducted across the entire population, the predictive power increase, as a greater diversity in the data enables better prediction. Instead, dry matter genomic prediction accuracies were higher in accordance with its higher narrow sense heritability value. These findings enriched GWAS analyses in an Andigenum potato collection and reinforce the potential of applying GS in Colombian breeding programs using diverse populations.