Identification of QTL associated with total dissolved solids in a GWAS of a Beta vulgaris diversity panel

Abstract

The table beet (Beta vulgaris subsp. vulgaris) is often characterized by its distinguishingly sweet, yet earthy flavor profile which can be attributed to its main flavor components: geosmin, oxalic acid, and sucrose. These flavor traits extend through the Beta vulgaris L. crop complex, including sugar beet, Swiss chard, fodder beet, table beet, and wild relatives. The crop types included in this complex have been adapted for specific end uses and thus exhibit pronounced phenotypic differences. Sucrose, commonly quantified by total dissolved solids (TDS), which serves as a proxy for sucrose, is a key determinant of the table beet’s success in the fresh eating market, where its popularity has been growing in recent years. Previous research has suggested TDS is influenced by both genotype and growing environment. Knowing the genetic architecture of TDS is valuable for breeding programs focused on increasing sweetness. Numerous quantitative trait loci (QTL) have been identified for sugar content and related sugar traits in the sugar beet. To date, no QTL associated with TDS or sweetness in table beet have been reported prior to this study. This study investigated regions of the genome associated with TDS through a genome wide association study (GWAS) of a Beta vulgaris diversity panel, with an emphasis on understanding if different crop types possess unique QTL for this trait. The Wisconsin Beta Diversity Panel (WBDP), consisting of 238 accessions from the Beta vulgaris crop complex and wild relatives, was assembled and genotyped using genotyping-by-sequencing technology. The panel was grown in two Wisconsin field locations over two years and phenotyped on a refractometer for TDS. TDS levels varied amongst crop types and a broad sense heritability of 0.90 indicated that phenotypic differences can be attributed in large measure to genetic variation.

GWAS uncovered four QTL identified across multiple models to significantly associate with TDS. A QTL on chromosome two was consistently identified amongst multiple GWAS models, explaining 12.1-62.6% of the phenotypic variation in the full panel. A candidate gene directly involved in the sucrose biosynthesis pathway was located downstream from this significant marker. A second QTL identified on chromosome seven revealed QTL alleles that may differentiate between table beet accessions, explaining nearly half the phenotypic variation (45.28%), and is the first QTL reported in association with TDS that is unique to table beet. Markers linked to this QTL may be useful in breeding for elevated TDS levels within Beta vulgaris, especially to efficiently select for high TDS and negate wide inter-crop type crosses and genetic drag. This study highlights the influence of genotype on Beta vulgaris TDS levels and provides insights into the genetic architecture of the TDS flavor trait across multiple crop type groups.