{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T06:27:56Z","timestamp":1786343276872,"version":"build-2736575974"},"reference-count":58,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T00:00:00Z","timestamp":1786320000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      Faba bean (\n                      <jats:italic>Vicia faba<\/jats:italic>\n                      L.) is a high-yielding, protein-rich grain legume with considerable potential for sustainable cropping systems. However, its genetic improvement has been constrained by a large, complex genome and historically limited genomic resources. We aimed to identify agronomically relevant QTLs in a diverse faba bean panel using genome-wide associations studies (GWAS) with rigorous control of false positives due to model violations.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>The NORFAB faba bean diversity panel was evaluated for agronomic traits over four years (2018\u20132021) at two locations in Denmark. GWAS were conducted using three complementary methods, incorporating a standard predictor-permutation test, novel in a GWAS context, for the top associations post-hoc to rigorously control false positives due to model violations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      This approach identified 13 QTLs associated with nine agronomic traits. Several QTLs colocalized with genes previously associated with similar traits, such as the flowering time regulator\n                      <jats:italic>FLOWERING LOCUS T<\/jats:italic>\n                      . Incorporating a permutation step consistently discovered more internally consistent QTLs compared to using only parametric\n                      <jats:italic>p<\/jats:italic>\n                      -values, with each QTL detected by more GWAS methods and associated with a greater number of SNPs, traits and trials.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Our results add interesting QTLs and biologically plausible candidate genes for multiple agronomic traits for incorporation into the faba bean molecular breeding toolkit and suggest that SNP-level post-hoc permutation testing can improve GWAS reliability.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpls.2026.1895808","type":"journal-article","created":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T05:30:40Z","timestamp":1786339840000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Post-hoc permutation GWAS refinement reveals robust marker-trait associations in faba bean"],"prefix":"10.3389","volume":"17","author":[{"given":"Troels W.","family":"Mouritzen","sequence":"first","affiliation":[{"name":"Plant Molecular Biology, Institute for Molecular Biology and Genetics, Aarhus University","place":["Aarhus, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elesandro","family":"Bornhofen","sequence":"additional","affiliation":[{"name":"Center for Quantitative Genetics and Genomics, Aarhus University","place":["Aarhus, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thilani","family":"Jayakody","sequence":"additional","affiliation":[{"name":"Plant Molecular Biology, Institute for Molecular Biology and Genetics, Aarhus University","place":["Aarhus, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cathrine Kiel","family":"Skovbjerg","sequence":"additional","affiliation":[{"name":"Center for Quantitative Genetics and Genomics, Aarhus University","place":["Aarhus, Denmark"]},{"name":"Nordic Seed","place":["Odder, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"K\u00e6rgaard Nielsen","sequence":"additional","affiliation":[{"name":"Sejet Plant Breeding","place":["Horsens, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Schiemann","sequence":"additional","affiliation":[{"name":"Nordic Seed","place":["Odder, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens Christen N\u00f8rgaard","family":"Knudsen","sequence":"additional","affiliation":[{"name":"Nordic Seed","place":["Odder, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Winnie S.","family":"F\u00fcchtbauer","sequence":"additional","affiliation":[{"name":"Sejet Plant Breeding","place":["Horsens, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jihad","family":"Orabi","sequence":"additional","affiliation":[{"name":"Nordic Seed","place":["Odder, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luc","family":"Janss","sequence":"additional","affiliation":[{"name":"Center for Quantitative Genetics and Genomics, Aarhus University","place":["Aarhus, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stig U.","family":"Andersen","sequence":"additional","affiliation":[{"name":"Plant Molecular Biology, Institute for Molecular Biology and Genetics, Aarhus University","place":["Aarhus, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,10]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.70076","article-title":"Genomic prediction for heat and herbicide tolerance in faba bean","volume":"18","author":"Abou Khater","year":"2025","journal-title":"Plant Genome"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"317","DOI":"10.4310\/sii.2011.v4.n3.a6","article-title":"Controlling population structure in human genetic association studies with samples of unrelated individuals","volume":"4","author":"Allison","year":"2011","journal-title":"Stat Its Interface"},{"key":"B4","doi-asserted-by":"publisher","first-page":"2048","DOI":"10.1038\/s41380-020-0670-3","article-title":"GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size","volume":"26","author":"Asif","year":"2021","journal-title":"Mol. 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