{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T06:15:51Z","timestamp":1788156951228,"version":"build-2803163510"},"reference-count":36,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Chromosome 4 introgression in Timor hybrid-derived\n                    <jats:italic>Coffea arabica<\/jats:italic>\n                    is established, but the robustness of accession prioritization and the relative strength of cultivated\u2013introgressed differentiation across the canephora-derived (sgC) and eugenioides-derived (sgE) subgenomes remained unclear under explicit subgenome filtering. We reanalyzed public genomic resources from 44 coffee accessions using strict contig-level subgenome filtering, Arabica-only population-structure analysis, SNP-panel sensitivity testing, genome-wide differentiation scans, permutation testing, and direct sequence alignment. Population structure and accession rankings were stable across marker densities and random seeds, and the same six introgressed references were retained throughout. Chromosome 4 ranked first in both subgenomes, with a strong sgC signal and a markedly weaker sgE signal; independent baseline-panel permutation tests supported both chromosome 4-associated signals. Direct alignment supported correspondence to the expected chromosome 4 pseudomolecules while showing incomplete source coverage and unresolved exact boundaries. Alignment-supported blocks contained 88 sgC and 62 sgE provisional defense-, signaling-, and regulatory-associated annotations. These results provide a genome-wide, quantitatively validated framework for prioritizing introgressed germplasm and candidate chromosome 4 regions for phenotype-linked coffee research without implying equivalent introgression, exact liftover, or causal resistance genes.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1925916","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T05:41:02Z","timestamp":1788154862000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressed Coffea arabica accessions"],"prefix":"10.3389","volume":"17","author":[{"given":"Ezekiel","family":"Ahn","sequence":"first","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture","place":["Beltsville, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunchung","family":"Park","sequence":"additional","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture","place":["Beltsville, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Insuck","family":"Baek","sequence":"additional","affiliation":[{"name":"Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture","place":["Beltsville, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moon S.","family":"Kim","sequence":"additional","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture","place":["Beltsville, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lyndel W.","family":"Meinhardt","sequence":"additional","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture","place":["Beltsville, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"894","DOI":"10.1007\/s00122-001-0798-8","article-title":"The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers","volume":"104","author":"Anthony","year":"2002","journal-title":"Theor. 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