{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T15:28:37Z","timestamp":1789658917952,"version":"4.0.1"},"update-to":[{"DOI":"10.1371\/journal.pgen.1012289","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000}}],"reference-count":96,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2305693"],"award-info":[{"award-number":["2305693"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2239530"],"award-info":[{"award-number":["2239530"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"USDA Agricultural Research Service Plant Genetic Resources Unit","id":[{"id":"https:\/\/ror.org\/02d2m2044","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Charles University Grant Agency","award":["408126"],"award-info":[{"award-number":["408126"]}],"id":[{"id":"https:\/\/ror.org\/024d6js02","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    In the past decade, plant biologists have made several major discoveries pertaining to the genetic basis of apomixis (clonal propagation by seed) that have shown promise in preserving high-value hybrid rice and sorghum genotypes. This progress was made possible by foundational gene discovery efforts in model species and natural apomicts, but pleiotropic obstacles still limit its broad agricultural adoption, especially in eudicots. Thus, it follows that investigations of novel apomicts should lead to the development of new molecular tools for plant breeding. The two most common ways to identify clonal seed production are flow-cytometry seed screens and genome sequencing to compare the DNA sequences of the maternal parent and progeny, traditionally using low-throughput markers. While flow-cytometry has been the dominant method for more than two decades, it provides indirect information on the genetics of a resulting embryo and can be ineffective in certain species. Here we developed a method using short-read whole-genome sequencing at moderately low coverage (averaging 3X and 6X) to screen diverse\n                    <jats:italic>Malus<\/jats:italic>\n                    genotypes maintained in a USDA germplasm collection for clonal seed production. In total, we sequenced 55 genotypes, 1,216 of their embryos, and identified 17 previously undescribed apomictic genotypes. Several more were detected with the flow cytometry seed screen, which helped resolve certain types of reproduction and sources of noise in low-coverage datasets. This low-pass screening-by-sequencing method is a relatively low-cost, rapid method for detecting apomictic genotypes in diverse plant germplasm and when used thoughtfully in conjunction with flow cytometry, provides a new way to visualize the genetic outcomes of sexual and asexual reproduction in plants.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1012289","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T17:52:09Z","timestamp":1788889929000},"page":"e1012289","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of Malus germplasm"],"prefix":"10.1371","volume":"22","author":[{"given":"Charity Z.","family":"Goeckeritz","sequence":"first","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology","place":["Huntsville, Alabama, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3902-8109","authenticated-orcid":true,"given":"V\u00e1clav","family":"Polcar","sequence":"additional","affiliation":[{"name":"Charles University","place":["Praguea, Czech Republic"],"department":["Department of Botany, Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Gutierrez","sequence":"additional","affiliation":[{"name":"United States Department of Agriculture","place":["Geneva, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6878-6503","authenticated-orcid":true,"given":"Tom\u00e1\u0161","family":"Urfus","sequence":"additional","affiliation":[{"name":"Charles University","place":["Praguea, Czech Republic"],"department":["Department of Botany, Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6613-1878","authenticated-orcid":true,"given":"Alex","family":"Harkess","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology","place":["Huntsville, Alabama, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"issue":"5","key":"pgen.1012289.ref001","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1080\/07352689.2014.898488","article-title":"Taxonomy and biogeography of apomixis in angiosperms and associated biodiversity characteristics","volume":"33","author":"D Hojsgaard","year":"2014","journal-title":"CRC Crit Rev Plant Sci"},{"key":"pgen.1012289.ref002","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1146\/annurev.genet.40.110405.090511","article-title":"Mendelian genetics of apomixis in plants","volume":"41","author":"P Ozias-Akins","year":"2007","journal-title":"Annu Rev Genet"},{"issue":"3625","key":"pgen.1012289.ref003","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1038\/143684a0","article-title":"Segregation in asexual (Apomictic) offspring in Rubus","volume":"143","author":"MB Crane","year":"1939","journal-title":"Nature"},{"issue":"3","key":"pgen.1012289.ref004","first-page":"289","article-title":"The cytogenetics of facultative apomixis in Malus species","volume":"40","author":"K Sax","year":"1959","journal-title":"J Arnold Arbor"},{"key":"pgen.1012289.ref005","first-page":"35","article-title":"Autonomous apomictic propagation of Cucumis ficifolius A. 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