{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T15:56:03Z","timestamp":1787068563447,"version":"build-2736575974"},"reference-count":102,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,11,24]],"date-time":"2025-11-24T00:00:00Z","timestamp":1763942400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"New Zealand"},{"DOI":"10.13039\/501100004629","name":"Ministry of Business, Innovation and Employment","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004629","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Strategic Science Investment Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Breeding elite apple cultivars with scab resistance is a key global goal, as reliance on fungicides is unsustainable. The causal fungus, Venturia inaequalis, evolves rapidly, threatening cultivars with single-gene resistance. Since the 1980s, breeding programmes have introduced novel resistance sources via backcrossing. Here, we generated a haplotype-phased genome assembly of Russian apple R12740-7A and an Oxford Nanopore assembly of the Rvi2-resistance accession TSR34T15, enabling detailed dissection of the Rvi2 resistance locus. Fine-mapping using a \u2018Royal Gala\u2019 \u00d7 TSR34T15 segregating family delimited Rvi2 to a narrow genomic interval, within which we identified a 10 041\u2005bp long terminal repeat retrotransposon (LTR-RT) insertion\u2014an insert-based structural variant (SV) strongly linked with Rvi2. Notably, this LTR-RT harbours an FPPS gene, a member of the farnesyl pyrophosphate\/geranylgeranyl pyrophosphate (FPP\/GGPP) synthase family, located 2 kb from a key candidate defence gene. Although the FPPS gene exhibits stable expression, its integration within the retrotransposon suggests a cis-regulatory role, potentially priming adjacent defence genes for robust up-regulation upon pathogen attack. We validated the marker derived from this SV in diverse germplasms and successfully implemented it in marker-assisted selection across extensive seedling cohorts. This marker will streamline the development of scab-resistant apple varieties.<\/jats:p>","DOI":"10.1093\/jxb\/eraf504","type":"journal-article","created":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T13:05:54Z","timestamp":1763039154000},"page":"1647-1662","source":"Crossref","is-referenced-by-count":1,"title":["Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene\n                    <i>Rvi2<\/i>"],"prefix":"10.1093","volume":"77","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0376-6135","authenticated-orcid":false,"given":"Elena","family":"L\u00f3pez-Girona","sequence":"first","affiliation":[{"name":"New Zealand Institute for Bioeconomy Science Limited (Bioeconomy Science Institute), Food Innovation Research Centre , Palmerston North 4442 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4351-6181","authenticated-orcid":false,"given":"Chris","family":"Kirk","sequence":"additional","affiliation":[{"name":"New Zealand Institute for Bioeconomy Science Limited (Bioeconomy Science Institute), Food Innovation Research Centre , Palmerston North 4442 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2954-762X","authenticated-orcid":false,"given":"Cecilia H","family":"Deng","sequence":"additional","affiliation":[{"name":"Bioeconomy Science Institute, Mount Albert Research Centre , Auckland 1142 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9025-7253","authenticated-orcid":false,"given":"An\u017ee","family":"\u0160vara","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Science, Cornell University , Geneva, NY 14456 ,","place":["USA"]},{"name":"Department of Plant Sciences, University of Saskatchewan, Saskatoon ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0424-7727","authenticated-orcid":false,"given":"Awais","family":"Khan","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Science, Cornell University , Geneva, NY 14456 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4071-4457","authenticated-orcid":false,"given":"Vincent G M","family":"Bus","sequence":"additional","affiliation":[{"name":"Bioeconomy Science Institute, Hawkes Bay Research Centre , Havelock North 4157 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4018-0694","authenticated-orcid":false,"given":"David","family":"Chagn\u00e9","sequence":"additional","affiliation":[{"name":"New Zealand Institute for Bioeconomy Science Limited (Bioeconomy Science Institute), Food Innovation Research Centre , Palmerston North 4442 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7478-7035","authenticated-orcid":false,"given":"Richard K","family":"Volz","sequence":"additional","affiliation":[{"name":"Bioeconomy Science Institute, Hawkes Bay Research Centre , Havelock North 4157 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,11,24]]},"reference":[{"key":"2026031701063872900_eraf504-B1","first-page":"267","article-title":"Awk \u2014 a pattern scanning and processing language","volume":"9","author":"Aho","year":"1979","journal-title":"Software: Practice and Experience"},{"key":"2026031701063872900_eraf504-B2","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1186\/s13059-022-02823-7","article-title":"Automated 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thaliana","volume":"15","author":"Barragan","year":"2019","journal-title":"PLoS Genetics"},{"key":"2026031701063872900_eraf504-B6","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1111\/mpp.12269","article-title":"Scab resistance in \u2018Geneva\u2019 apple is conditioned by a resistance gene cluster with complex genetic control","volume":"17","author":"Bastiaanse","year":"2016","journal-title":"Molecular Plant Pathology"},{"key":"2026031701063872900_eraf504-B7","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1073\/pnas.0304808101","article-title":"The HcrVf2 gene from a wild apple confers scab resistance to a transgenic cultivated variety","volume":"101","author":"Belfanti","year":"2004","journal-title":"Proceedings of the National Academy of Sciences, USA"},{"key":"2026031701063872900_eraf504-B8","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1186\/s12864-015-2096-x","article-title":"The distribution and impact of common copy-number variation in the 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