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Sugar beet (\n                      <jats:italic>Beta vulgaris ssp. vulgaris<\/jats:italic>\n                      ) breeding relies exclusively on it and combines cytoplasmic male sterility (CMS) and monogermity to exploit heterosis by combining male and female parental pools. The genomic consequences of this breeding scheme remain poorly characterized. We assembled a unique dataset comprising 1285 accessions spanning 21\u00a0years of selection within a breeding program, genotyped for 10,033\u00a0SNPs, to investigate genetic structuring and selection dynamics. Principal component and admixture analyses revealed a clear differentiation between parental pools. Over 21\u00a0years, males displayed a significant decline in within-pool diversity, accompanied by a rise in inter-pool differentiation. Linkage disequilibrium decreased in recent male lines, reflecting breeding practices that increase allele shuffling. Selection scans identified 174 outlier SNPs differentiating pools. Outliers clustered into seven haploblocks, including a region encompassing rhizomania-resistance gene (\n                      <jats:italic>Rz1<\/jats:italic>\n                      ) and, more surprisingly, a region encompassing the domestication bolting locus B (\n                      <jats:italic>BvBTC1<\/jats:italic>\n                      ). These results demonstrate that over the last 21\u00a0years, three-way hybrid breeding has increased differentiation between heterotic pools and shaped haplotypic variation at agronomically relevant loci, providing a genomic basis for future evaluation of their effects on agronomic performance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s00122-026-05366-8","type":"journal-article","created":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T03:56:41Z","timestamp":1789790201000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Twenty-one years of three-way hybrid breeding shaped diversity and complementarity of male and female gene pools in sugar beet"],"prefix":"10.1007","volume":"139","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-3698-4987","authenticated-orcid":false,"given":"Augustin","family":"Desprez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Henry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno","family":"Desprez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Devaux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain","family":"Charcosset","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0867-3678","authenticated-orcid":false,"given":"Maud I.","family":"Tenaillon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7195-1327","authenticated-orcid":false,"given":"Laurence","family":"Moreau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,19]]},"reference":[{"key":"5366_CR1","first-page":"493","volume":"53","author":"FA Abegg","year":"1936","unstructured":"Abegg FA (1936) A genetic factor for the annual habit in beets and linkage relationship. 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