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This study examined the genomic region surrounding\n                    <jats:italic>sd1<\/jats:italic>\n                    using genome\u2010wide association and haplotype analyses in a multiparent population (MP6\/8) evaluated across environments and in a biparental population (MP\u2010D) for validation. Genomic and phenotypic evidence indicated that an indica\u2010derived haplotype upstream of\n                    <jats:italic>sd1<\/jats:italic>\n                    persists in US tropical\n                    <jats:italic>japonica<\/jats:italic>\n                    and global\n                    <jats:italic>indica<\/jats:italic>\n                    semi\u2010dwarf germplasm and is associated with reduced grain yield. Genome\u2010wide association analysis confirmed\n                    <jats:italic>sd1<\/jats:italic>\n                    as the primary determinant of reduced plant height and identified a quantitative trait locus at 36.69 Mb upstream of\n                    <jats:italic>sd1<\/jats:italic>\n                    that was consistently associated with reduced grain yield (0.6\u20130.9 t ha\n                    <jats:sup>\u22121<\/jats:sup>\n                    ) across populations and environments. Haplotype analysis identified an\n                    <jats:italic>indica<\/jats:italic>\n                    \u2010derived Presidio haplotype spanning this upstream region was associated with significant yield reductions in both populations. Pedigree analysis traced this unfavorable haplotype to the Taichung Native 1 donor lineage, representing one historically deployed\n                    <jats:italic>sd1<\/jats:italic>\n                    \u2010linked introgression class. Although its frequency has declined in modern cultivars, its persistence highlights the long\u2010term impact of linkage drag following major trait introgression. These findings emphasize the value of marker\u2010assisted selection and targeted recombination to separate favorable dwarfing alleles from linked yield penalties and sustain yield gains in US rice improvement programs.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70295","type":"journal-article","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T09:13:46Z","timestamp":1787649226000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A yield\u2010reducing introgression linked to\n                    <i>sd1<\/i>\n                    in rice"],"prefix":"10.1002","volume":"19","author":[{"given":"Flavia","family":"Furlan","sequence":"first","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State University Agricultural Center  Rayne Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7366-3169","authenticated-orcid":false,"given":"Brijesh","family":"Angira","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State University Agricultural Center  Rayne Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8615-6070","authenticated-orcid":false,"given":"Maria","family":"Montiel","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State University Agricultural Center  Rayne Louisiana USA"},{"name":"Horizon Ag LLC  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Richards","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology and Crop Physiology Louisiana State University Agricultural Center  Baton Rouge Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tommaso","family":"Cerioli","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State University Agricultural Center  Rayne Louisiana USA"},{"name":"Corteva Agriscience  Gadesco\u2010Pieve Delmona Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Hernandez","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Nutrition, and Food Systems University System of New Hampshire  Durham New Hampshire USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Fritsche\u2010Neto","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State University Agricultural Center  Rayne Louisiana USA"},{"name":"Department of Horticulture Sciences North Carolina State University  Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6137-5955","authenticated-orcid":false,"given":"John","family":"Platten","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Ba\u00f1os Philippines"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jomar","family":"Punzalan","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State University Agricultural Center  Rayne Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"McCouch","sequence":"additional","affiliation":[{"name":"Cornell Institute for Digital Agriculture Cornell University  Ithaca New York USA"},{"name":"Section of Plant Breeding and Genetics School of Integrative Plant Sciences Cornell University  Ithaca New York USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9522-9585","authenticated-orcid":false,"given":"Kelly","family":"Robbins","sequence":"additional","affiliation":[{"name":"Section of Plant Breeding and Genetics School of Integrative Plant Sciences Cornell University  Ithaca New York USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueyan","family":"Sha","sequence":"additional","affiliation":[{"name":"Rice Research &amp; Extension Center University of Arkansas Division of Agriculture  Stuttgart Arkansas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6461-6504","authenticated-orcid":false,"given":"Adam","family":"Famoso","sequence":"additional","affiliation":[{"name":"H. 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