GWAS in tetraploid potato: Identification and validation of SNP markers associated with glycoalkaloid content

Abstract

Abstract Genome wide association studies (GWAS) are a useful tool to unravel the genetic architecture of complex traits, but the results can be difficult to interpret. Population structure, genetic heterogeneity and rare alleles easily result in false positive or false negative associations. This paper describes the analysis of a GWAS panel combined with three bi-parental mapping populations to validate GWAS results, using phenotypic data for steroidal glycoalkaloid (SGA) accumulation and the ratio (SGR) between the two major glycoalkaloids α-solanine and α-chaconine in tubers. SGAs are secondary metabolites in the Solanaceae family, functional as a defence against various pests and pathogens and in high quantities toxic for humans. With GWAS we identified five quantitative trait loci (QTL) of which Sga1.1, Sgr8.1 and Sga11.1 were validated, but not Sga3.1 and Sgr7.1. In the bi-parental populations Sga5.1 and Sga7.1 were mapped, but these were not identified with GWAS. The QTLs Sga1.1, Sga7.1, Sgr7.1, Sgr8.1 co-localize with genes GAME9, GAME 6 / GAME 11, SGT1 and SGT2, respectively. For other genes involved in SGA synthesis no QTLs were identified. The results of this study illustrate a number of pitfalls in GWAS of which population structure seems the most important. We also show that introgression breeding for disease resistance has introduced new haplotypes to the gene pool involved in higher SGA levels in certain pedigrees. Finally we show that high SGA levels remain unpredictable in potato but that α-solanine / α-chaconine ratio has a predictable outcome with specific SGT1 and SGT2 haplotypes.