Identification of QTL for steviol glycoside biosynthesis using a SNP-based genetic linkage map for Stevia rebaudiana

Stevia rebaudiana (stevia) is an herbaceous perennial grown to produce sweet-tasting non-caloric steviol glycosides produced in the leaves and used as a sugar substitute. While stevia produces more than 60 known steviol glycosides, those with the greatest consumer-desired taste profiles, such as rebaudioside (Reb) D and Reb M, are produced at low concentrations. Efforts to breed stevia with increased concentrations of these minor glycosides have been hampered by limited genetic resources to improve breeding efficiency. We developed the first single-nucleotide polymorphism (SNP)-based genetic linkage map for stevia for a highly heterozygous F1 population. The linkage map consists of 1322 SNPs across the 11 stevia chromosomes. The map covered 2991.8 cM, although this was inflated by large gaps on linkage group 8. Excluding linkage group 8, the remaining 10 linkage groups covered 1947.7 cM, with an average density of 1.48 cM per marker. The mapping population was grown in multiple locations in 2020 and 2021 to evaluate steviol glycoside production (stevioside and Reb A, B, C, D, E, M, N, and O). The population exhibited transgressive segregation for the production of all evaluated glycosides. QTL were identified for all measured glycosides except Reb M and Reb O. A region of chromosome 1 harbored colocalizing quantitative trait loci (QTL) for stevioside, Reb A, Reb B, Reb D, Reb E, and Reb N. This region contained large-effect QTL explaining up to 38.8% of the observed variation (%VE) for Reb D, and 71.9 and 46.8%VE, respectively, for the minor glycosides Reb E and Reb N. The linkage map and population described herein will be useful for identifying QTL for other stevia growth and yield traits exhibiting quantitative inheritance and will aid in the selection of candidate genes underlying these traits for further evaluation.