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Merr.) is one of the most important tropical fruits worldwide. It is primarily propagated clonally and exhibits high heterozygosity which can mask deleterious mutations, potentially leading to inbreeding depression and hindering breeding efforts. To address this, we conducted a comprehensive genome-wide analysis of 91 pineapple accessions and identified over 7.9\u00a0million high-quality SNPs. We utilized these SNPs to investigate the genetic structure and reproductive patterns of diverse cultivars and related varieties. Population structure analysis revealed a unique genetic makeup of <jats:italic>A. comosus<\/jats:italic> var. <jats:italic>microstachys<\/jats:italic> accessions and unidirectional gene flow from <jats:italic>A. comosus<\/jats:italic> var. <jats:italic>microstachys<\/jats:italic> into <jats:italic>A. comosus<\/jats:italic> var. <jats:italic>comosus<\/jats:italic>,<jats:italic> A. comosus<\/jats:italic> var. <jats:italic>bracteatus<\/jats:italic>, and <jats:italic>A. comosus<\/jats:italic> var. <jats:italic>erectifolius<\/jats:italic>. Among the cultivated pineapples, \u2018Mordilona-related\u2019 and \u2018Smooth Cayenne\u2019 cultivars showed unidirectional gene flow from \u2018Singapore Spanish\u2019, \u2018Queen\u2019, and the wild <jats:italic>A. comosus<\/jats:italic> var. <jats:italic>microstachys<\/jats:italic>. Heterozygosity patterns suggested predominantly asexual reproduction in \u2018Queen\u2019, \u2018Singapore Spanish\u2019, \u2018Smooth Cayenne\u2019, and <jats:italic>A. comosus<\/jats:italic> var. <jats:italic>microstachys<\/jats:italic> populations, while \u2018Mordilona-related\u2019 and <jats:italic>A. comosus<\/jats:italic> var. <jats:italic>bracteatus<\/jats:italic> populations might have experienced increased sexual reproduction or population expansion. We developed two SNP panels: one for germplasm identification and the other one for pedigree analysis. These resources will facilitate pineapple germplasm evaluation, diversity analysis, and informed breeding decisions for cultivar improvement.<\/jats:p>","DOI":"10.1007\/s00438-025-02275-1","type":"journal-article","created":{"date-parts":[[2025,7,19]],"date-time":"2025-07-19T08:40:35Z","timestamp":1752914435000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Unraveling genetic diversity and population structure of pineapple germplasm using genome-wide SNP markers"],"prefix":"10.1007","volume":"300","author":[{"given":"Haomin","family":"Lyu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tracie","family":"Matsumoto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5393-5764","authenticated-orcid":false,"given":"Qingyi","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,7,19]]},"reference":[{"key":"2275_CR1","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander DH, Novembre J, Lange K (2009) Fast model-based Estimation of ancestry in unrelated individuals. 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