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

Peter G Vos; M João Paulo; Peter M Bourke; Chris A Maliepaard; Fred A van Eeuwijk; Richard G F Visser; Herman J van Eck

doi:10.1007/s11032-022-01344-2

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

Mol Breed. 2022 Dec 13;42(12):76. doi: 10.1007/s11032-022-01344-2. eCollection 2022 Dec.

Authors

Peter G Vos^{1

2

3

4}, M João Paulo^{5

2}, Peter M Bourke¹, Chris A Maliepaard¹, Fred A van Eeuwijk⁵, Richard G F Visser^{1

2}, Herman J van Eck^{1

2}

Affiliations

¹ Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.
² Present Address: Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands.
³ Current Address: HZPC, Edisonweg 5, 8501 XG Joure, The Netherlands.
⁴ Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands.
⁵ Biometris, Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands.

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 potato 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, and 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.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-022-01344-2.

Keywords: Haplotypes; Marker-assisted selection; QTL-mapping; Solanum tuberosum; Steroidal glycoalkaloids.

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