Root shape is a defining feature of marketability and breeding strategies in the Beta vulgaris crop complex encompassing sugar beet, fodder beet, table beet, and Swiss chard. This study leverages the Wisconsin Beta Diversity Panel of 234 accessions to understand the genetic architecture underlying root shape traits, utilizing field trials, genome-wide association, and population structure analyses. High heritability estimates for many root shape traits (H2 > 0.9) suggest genetic control as the primary determinant of root shape with minimal genotype-by-environment interactions across locations and years. Digital biomass was not correlated with length-width ratio, a key shape descriptor. Key quantitative trait loci (QTL) on Chromosomes 4, 7, and 8 associated with traits such as length, width, and length-to-width ratio, collectively explained up to 55% of phenotypic variance. Several loci co-localize with predicted gene families known to influence organ shape in other plant species. Candidate genes near shape QTL were significantly enriched for microtubule organization and auxin response. Genomic estimated breeding values for shape traits showed high predictive accuracy, particularly for length-to-width ratio. Admixture analyses revealed eight genetic populations, suggesting distinct domestication and breeding histories of crop types in the complex. Swiss chard and wild germplasm showed unique ancestry, while sugar and fodder beet shared genetic proximity. Our analysis identifies candidate loci and molecular markers for root shape, providing resources for molecular breeding strategies in B. vulgaris. The findings add to and clarify the current knowledge on root shape inheritance, advancing the genetic improvement of these crops of economic, nutritional, and cultural significance.

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