{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T05:59:39Z","timestamp":1790747979585,"version":"4.1.0"},"reference-count":71,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE\u2010AC02\u201005CH11231"],"award-info":[{"award-number":["DE\u2010AC02\u201005CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Crimson clover (\n                    <jats:italic>Trifolium incarnatum<\/jats:italic>\n                    L.) is an obligately outcrossing, cool\u2010season annual legume valued for forage and cover cropping, yet genomic resources to support systematic improvement are limited. We performed the first whole\u2010genome re\u2010sequencing of global crimson clover germplasm to (i) develop a public mid\u2010density enrichment capture panel for breeding applications and (ii) characterized genetic diversity among the sampled genotypes to validate the representativeness of the germplasm for panel design. From 45 crimson clover accessions, we sequenced 194 genotypes: 45 at \u223c50X, generating 5.84 million variants and 149 at \u223c2.54X, yielding 17.05 million variants. After filtering, we retained 542,790 high\u2010confidence single\u2010nucleotide polymorphisms (SNPs) from the high\u2010coverage dataset and \u223c2.4 million from the low\u2010pass cohort, respectively. From these resources, we designed a 28,867\u2010SNP Twist hybrid\u2010capture panel enriched for genic regions and evenly distributed across seven chromosomes. This panel is being deployed within Auburn University's crimson clover breeding program to support population improvement and cultivar development. Genetic diversity analyses (principal component analysis, ADMIXTURE) revealed compact clustering of cultivars, broader dispersion of wild and uncertain\u2010status accessions, and low overall differentiation (fixation index [FST]\u00a0=\u00a00.0105) with excess heterozygosity (inbreeding coefficient [FIS]\u00a0=\u00a0\u22120.0592), consistent with a high level of outcrossing. The resulting genomic resources provide a reproducible, mid\u2010density genotyping platform for trait discovery, predictive breeding, and diversity monitoring. Together, these advances bring crimson clover genomic resources on par with other legumes such as soybean (\n                    <jats:italic>Glycine max<\/jats:italic>\n                    L. Merr.) and alfalfa (\n                    <jats:italic>Medicago sativa<\/jats:italic>\n                    L.), establishing a robust foundation for genomics\u2010assisted improvement of this key cover and forage crop in US sustainable agriculture.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70297","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T05:26:52Z","timestamp":1790746012000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development and deployment of a public mid\u2010density genotyping panel for crimson clover (\n                    <i>Trifolium incarnatum<\/i>\n                    L.) based on whole\u2010genome re\u2010sequencing of diverse germplasm"],"prefix":"10.1002","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6686-8211","authenticated-orcid":false,"given":"Mark Philip","family":"Castillo","sequence":"first","affiliation":[{"name":"Department of Crop, Soils and Environmental Sciences Auburn University  Auburn Alabama USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oluwaseye Gideon","family":"Oyebode","sequence":"additional","affiliation":[{"name":"Department of Crop, Soils and Environmental Sciences Auburn University  Auburn Alabama USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayson","family":"Talag","sequence":"additional","affiliation":[{"name":"Arizona Genomics Institute, School of Plant Sciences, College of Agriculture and Life Sciences University of Arizona  Tucson Arizona USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Bunting","sequence":"additional","affiliation":[{"name":"Arizona Genomics Institute, School of Plant Sciences, College of Agriculture and Life Sciences University of Arizona  Tucson Arizona USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Navneet","family":"Kaur","sequence":"additional","affiliation":[{"name":"US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory  Berkeley California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Doran","sequence":"additional","affiliation":[{"name":"Twist Bioscience  South San Francisco California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerrie","family":"Barry","sequence":"additional","affiliation":[{"name":"US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory  Berkeley California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dario","family":"Competti","sequence":"additional","affiliation":[{"name":"Arizona Genomics Institute, School of Plant Sciences, College of Agriculture and Life Sciences University of Arizona  Tucson Arizona USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Schmutz","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandon","family":"Schlautman","sequence":"additional","affiliation":[{"name":"The Land Institute  Salina Kansas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Humphries","sequence":"additional","affiliation":[{"name":"South Australian Research and Development Institute  Adelaide South Australia Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kioumars","family":"Ghamkhar","sequence":"additional","affiliation":[{"name":"New Zealand (NZ) Bioeconomy Science Institute\u2013AgResearch Group Grasslands Research Centre  Palmerston North New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginia","family":"Moore","sequence":"additional","affiliation":[{"name":"Plant Breeding &amp; 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