{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T04:55:14Z","timestamp":1790571314181,"version":"4.1.0"},"reference-count":67,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,9,6]],"date-time":"2026-09-06T00:00:00Z","timestamp":1788652800000},"content-version":"vor","delay-in-days":5,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Seed coat color and patterning are key quality traits in common bean (\n                    <jats:italic>Phaseolus vulgaris<\/jats:italic>\n                    L.) that define market classes and strongly influence consumer preference and market value. These traits are controlled by a complex network of major genes (sometimes with epistatic interactions), which complicates the recovery of desired market class phenotypes following inter\u2010market class hybridization. Although many of the underlying loci have been genetically mapped, diagnostic, high\u2010throughput molecular markers for efficient allele tracking across the Middle American and Andean gene pools remain limited. In this study, we developed and validated 24 gene\u2010specific PCR Allele Competitive Extension (PACE) markers targeting seven major seed coat color genes (\n                    <jats:italic>G<\/jats:italic>\n                    ,\n                    <jats:italic>B<\/jats:italic>\n                    ,\n                    <jats:italic>V<\/jats:italic>\n                    ,\n                    <jats:italic>J<\/jats:italic>\n                    ,\n                    <jats:italic>Rk<\/jats:italic>\n                    ,\n                    <jats:italic>T<\/jats:italic>\n                    , and\n                    <jats:italic>Z<\/jats:italic>\n                    ) and two patterning genes (\n                    <jats:italic>\n                      C\n                      <jats:sup>Pi<\/jats:sup>\n                    <\/jats:italic>\n                    and\n                    <jats:italic>\n                      C\n                      <jats:sup>St<\/jats:sup>\n                    <\/jats:italic>\n                    ), together with a previously reported marker associated with the postharvest seed coat darkening locus (\n                    <jats:italic>\n                      P\n                      <jats:sup>sd<\/jats:sup>\n                    <\/jats:italic>\n                    ). An additional PACE marker targeting the Phaseolin (\n                    <jats:italic>Phs<\/jats:italic>\n                    ) locus was developed to distinguish Middle American (\n                    <jats:italic>S<\/jats:italic>\n                    \u2010type) and Andean (\n                    <jats:italic>T<\/jats:italic>\n                    \u2010type) gene pools, providing a complementary tool for assessing genetic background alongside seed coat\u2010specific loci. Marker performance was evaluated across three diverse panels, revealing high diagnostic accuracy for most loci (90%\u2013100%). However, for loci such as\n                    <jats:italic>J<\/jats:italic>\n                    ,\n                    <jats:italic>V<\/jats:italic>\n                    ,\n                    <jats:italic>Rk<\/jats:italic>\n                    ,\n                    <jats:italic>T<\/jats:italic>\n                    , and\n                    <jats:italic>Z<\/jats:italic>\n                    , allele\u2010specific markers or marker combinations were required to capture full allelic diversity. Haplotype analysis further revealed substantial allelic diversity across market classes and identified background\u2010specific interactions. Collectively, these results provide a comprehensive set of high\u2010resolution, gene\u2010anchored PACE markers for seed coat color, patterning, and gene pool classification in common bean. These markers enable rapid and precise allele tracking in breeding populations and germplasm collections, facilitating marker\u2010assisted selection for market class\u2010specific seed coat traits and accelerating genetic improvement.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70296","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T04:20:35Z","timestamp":1788754835000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic resources to advance seed coat color and patterning genetics and breeding in common bean (\n                    <i>Phaseolus vulgaris<\/i>\n                    L.)"],"prefix":"10.1002","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3390-958X","authenticated-orcid":false,"given":"Jayanta","family":"Roy","sequence":"first","affiliation":[{"name":"Department of Plant Sciences North Dakota State University  Fargo North Dakota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rian","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences North Dakota State University  Fargo North Dakota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Osborne","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences North Dakota State University  Fargo North Dakota USA"},{"name":"Genomics, Phenomics, and Bioinformatics Program North Dakota State University  Fargo North Dakota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6636-454X","authenticated-orcid":false,"given":"Phillip N.","family":"Miklas","sequence":"additional","affiliation":[{"name":"USDA\u2010ARS Grain Legume Genetics and Physiology Research Unit  Prosser Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0905-3523","authenticated-orcid":false,"given":"Juan M.","family":"Osorno","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences North Dakota State University  Fargo North Dakota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillip E.","family":"McClean","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences North Dakota State University  Fargo North Dakota USA"},{"name":"Genomics, Phenomics, and Bioinformatics Program North Dakota State University  Fargo North Dakota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,6]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10681\u2010019\u20102461\u2010y"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.670284"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.21273\/JASHS.120.3.520"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.21273\/JASHS.121.6.1032"},{"key":"e_1_2_10_6_1","first-page":"171","article-title":"Inheritance of the Fib gene from 5\u2013593 for fibula arcs pattern of partly colored seed coat in the background genotype t P [C r] Z J G B V Rk","volume":"44","author":"Bassett M. J.","year":"2001","journal-title":"Annual Report of the Bean Improvement"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/9780470168028.ch8"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.21273\/JASHS.128.4.552"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10681-009-9911-x"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1021\/jf0304324"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2013.00275"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci1998.0011183X003800040031x"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1024146710611"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2025.12.010"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci2014.09.0653"},{"key":"e_1_2_10_16_1","volume-title":"Vegetables and pulses outlook: July 2026","author":"Davis W. V.","year":"2026"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/os\u20105.1.368"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122\u2010020\u201003571\u20107"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122\u2010021\u201003922\u2010y"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF02859660"},{"key":"e_1_2_10_21_1","first-page":"xxiv","article-title":"Linkage mapping in common bean","volume":"36","author":"Gepts P.","year":"1993","journal-title":"Annual Report of the Bean Improvement"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1002\/ppp3.10132"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01975768"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci1997.0011183X003700020049x"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci2007.04.0227"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.92.4.1101"},{"key":"e_1_2_10_27_1","unstructured":"Kelly J. D.(2010).The story of bean breeding: White paper prepared for BeanCAP & PBG works on the topic of dry bean production and breeding research in the U.S.Michigan State University.https:\/\/www.canr.msu.edu\/beanbreeding\/_pdf\/Story_of_Bean_Breeding_in_the_US.pdf"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci1998.0011183X003800010056x"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1601\u20105223.1932.tb02567.x"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1601\u20105223.1936.tb03196.x"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1303.3997"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodchem.2007.08.038"},{"key":"e_1_2_10_34_1","first-page":"115","article-title":"Iakttagelser r\u00f6rande fr\u00f6f\u00e4rgen hos avkommen av en spontan korsning mellan tvenne former av Phaseolus vulgaris","volume":"27","author":"Lundberg J. F.","year":"1917","journal-title":"Uts\u00e4desf\u00f6renings Tidskr"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1071\/FP11124"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/93.2.148"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.15259"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.869582"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci1993.0011183X003300010034x"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkae184"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.3198\/jpr2010.03.0124crg"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci2006.04.0246"},{"key":"e_1_2_10_43_1","doi-asserted-by":"publisher","DOI":"10.3835\/plantgenome2016.02.0012"},{"key":"e_1_2_10_44_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1233285"},{"key":"e_1_2_10_45_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122\u2010026\u201005256\u2010z"},{"key":"e_1_2_10_46_1","doi-asserted-by":"publisher","DOI":"10.3198\/jpr2012.07.0014crc"},{"key":"e_1_2_10_47_1","doi-asserted-by":"publisher","DOI":"10.3198\/jpr2016.02.0008crc"},{"key":"e_1_2_10_48_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.16947"},{"key":"e_1_2_10_49_1","first-page":"1","article-title":"Inheritance of colour in Phaseolus vulgaris L. II. A critical review","volume":"70","author":"Prakken R.","year":"1970","journal-title":"Meded Landbouwhogeschool Wageningen"},{"key":"e_1_2_10_50_1","first-page":"1","article-title":"Inheritance of colour in Phaseolus vulgaris L. IV. Recombination within the \u2018complex locus C.\u2019","volume":"74","author":"Prakken R.","year":"1974","journal-title":"Meded Landbouwhogeschool Wageningen"},{"key":"e_1_2_10_51_1","first-page":"35","article-title":"Crosses with some Phaseolus varieties that are \u2033constantly patterned with a dark pattern colour","volume":"20","author":"Prakken R.","year":"1977","journal-title":"Annual Report of the Bean Improvement"},{"key":"e_1_2_10_52_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"e_1_2_10_53_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodres.2020.109713"},{"key":"e_1_2_10_54_1","first-page":"116","article-title":"Diagnostic molecular markers associated with the dominant cranberry (S) and pinto (Pi) seedcoat patterning phenotypes","volume":"68","author":"Roy J.","year":"2025","journal-title":"Annual Report of the Bean Improvement"},{"key":"e_1_2_10_55_1","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20380"},{"key":"e_1_2_10_56_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870\u2010025\u201006282\u20107"},{"key":"e_1_2_10_57_1","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20173"},{"key":"e_1_2_10_58_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3008"},{"key":"e_1_2_10_59_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-015-9211-6_1"},{"key":"e_1_2_10_60_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci2001.411275x"},{"key":"e_1_2_10_61_1","doi-asserted-by":"publisher","DOI":"10.3733\/hilg.v12n09p551"},{"key":"e_1_2_10_62_1","first-page":"141","article-title":"The complex C locus: Genomic organization in the Andean genepool","volume":"69","author":"Soler\u2010Garzon A.","year":"2026","journal-title":"Annual Report of the Bean Improvement"},{"key":"e_1_2_10_63_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2024.1469381"},{"key":"e_1_2_10_64_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01508281"},{"key":"e_1_2_10_65_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01910333"},{"key":"e_1_2_10_66_1","doi-asserted-by":"publisher","DOI":"10.1002\/leg3.155"},{"key":"e_1_2_10_67_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jff.2021.104444"},{"key":"e_1_2_10_68_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10722\u2010019\u201000823\u20104"}],"container-title":["The Plant Genome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/acsess.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/tpg2.70296","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/acsess.onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/tpg2.70296","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/acsess.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/tpg2.70296","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T04:01:17Z","timestamp":1790568077000},"score":1,"resource":{"primary":{"URL":"https:\/\/acsess.onlinelibrary.wiley.com\/doi\/10.1002\/tpg2.70296"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":67,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["10.1002\/tpg2.70296"],"URL":"https:\/\/doi.org\/10.1002\/tpg2.70296","archive":["Portico"],"relation":{},"ISSN":["1940-3372","1940-3372"],"issn-type":[{"value":"1940-3372","type":"print"},{"value":"1940-3372","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"2026-04-27","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-26","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-06","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70296"}}