Uncovering genes essential in domestication and breeding of sugar beet

The genus Beta encompasses economically important root crops such as sugar and table beet. A Beta diversity set including the wild relative B. vulgaris ssp. maritima was grown in the field, and a large phenotypic diversity was observed. The genomes of 290 accessions were sequenced, and more than 10 million high-quality SNPs were employed to study genetic diversity. A genome-wide association study was performed, and marker-trait associations were found for nine phenotypic traits. The candidate gene within the M locus controlling monogermity on chromosome 4 was previously unknown. The most significant association for monogermity was identified at the end of chromosome 4. Within this region, a non-synonymous mutation within the zinc-finger domain of the WIP2 gene co-segregated with monogermity. This gene plays a regulatory role in AGL8/FUL in Arabidopsis. Intriguingly, commercial hybrids are in a heterozygous state at this position. Thus, the long-sought gene for monogermity was identified in this study. Red and yellow pigmentation due to betalain accumulation in shoots and roots is an important characteristic of table and leaf beets. The strongest associations were found upstream or downstream of two genes encoding Cytochrome P450 and anthocyanin MYB-like transcription factor proteins involved in betalain biosynthesis. Significant associations for Cercospora leaf spot resistance were identified on chromosomes 1, 2, 7, and 9. The associated regions harbor genes encoding proteins with leucine-rich repeats and nucleotide binding sites whose homologs are major constituents of plant-pathogen defense.