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(Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by\n                    <jats:italic>Ceratobasidium theobromae<\/jats:italic>\n                    , is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTLs). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome\u2010level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the\n                    <jats:italic>nucleotide\u2010binding site leucine\u2010rich repeat<\/jats:italic>\n                    class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates in proximity to informative QTLs. We identified structural variants within NLRs inherited from parentals. We present the first diploid, fully scaffolded, and parentally phased genome resource for\n                    <jats:italic>T. cacao<\/jats:italic>\n                    L. and provide insights into the genetics underlying resistance and susceptibility to VSD.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.20524","type":"journal-article","created":{"date-parts":[[2024,10,15]],"date-time":"2024-10-15T22:28:45Z","timestamp":1729031325000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback"],"prefix":"10.1002","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5645-0161","authenticated-orcid":false,"given":"Peri A.","family":"Tobias","sequence":"first","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Camperdown New South Wales Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob","family":"Downs","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Camperdown New South Wales Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Epaina","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Camperdown New South Wales Australia"},{"name":"Cocoa Board of Papua New Guinea  Kokopo Papua New Guinea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gurpreet","family":"Singh","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Camperdown New South Wales Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert F.","family":"Park","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Camperdown New South Wales Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard J.","family":"Edwards","sequence":"additional","affiliation":[{"name":"Minderoo OceanOmics Centre at UWA, Oceans Institute The University of Western Australia  Perth Western Australia Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eirene","family":"Brugman","sequence":"additional","affiliation":[{"name":"Cocoa Research Center Faculty of Agriculture Universitas Hasanuddin  Makassar Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andi","family":"Zulkifli","sequence":"additional","affiliation":[{"name":"Megarezky University  Makassar Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junaid","family":"Muhammad","sequence":"additional","affiliation":[{"name":"Cocoa Research Center Faculty of Agriculture Universitas Hasanuddin  Makassar Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agus","family":"Purwantara","sequence":"additional","affiliation":[{"name":"Mars Cocoa Research Station  Pangkep Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David I.","family":"Guest","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Camperdown New South Wales Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2024,10,15]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40694\u2010019\u20100077\u20106"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022\u20102836(05)80360\u20102"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010021\u201004556\u2010z"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010017\u20104120\u20109"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.736"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0107987"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010024\u201003198\u20107"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24789-2"},{"key":"e_1_2_9_10_1","article-title":"Plant NLR diversity: The known unknowns of Pan\u2010NLRomes A brief history of plant NLRs","author":"Barragan A. 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