{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T18:34:15Z","timestamp":1786732455532,"version":"build-2736575974"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Sichuan Provincial Special Project for Central Guidance of Local Science and Technology Development","award":["2024ZYD0040"],"award-info":[{"award-number":["2024ZYD0040"]}]},{"name":"Sichuan Major Vegetable Innovation Team Project of the National Modern Agricultural Industry Technology System","award":["SCCXTD-2024-5"],"award-info":[{"award-number":["SCCXTD-2024-5"]}]},{"name":"2026 Annual Project of Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources","award":["TSYY202602"],"award-info":[{"award-number":["TSYY202602"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Cowpea (\n                    <jats:italic>Vigna unguiculata<\/jats:italic>\n                    (L.) Walp.) is a globally important legume crop. However, the scarcity of efficient molecular markers has hindered molecular breeding efforts and the protection of plant breeders\u2019 rights. In this study, we employed double-digest restriction-site associated DNA sequencing (ddRAD-seq) to characterize the genetic diversity of 19 cowpea accessions. A total of 791,621 SNPs were identified, of which 13,469 high-quality SNPs were retained after filtering. Population structure and phylogenetic analyses revealed that these accessions clustered into three distinct groups. To facilitate cost-effective and rapid genotyping, we developed a panel of KASP (Kompetitive Allele-Specific PCR) markers. Through rigorous screening for polymorphism and stability, we identified six core KASP markers located in exonic regions. These six markers alone were sufficient to discriminate all 19 accessions. Based on these core markers, we constructed a unique DNA fingerprinting profile and assigned specific QR codes for each accession. This study demonstrates that selecting core KASP markers from ddRAD-seq data is a powerful strategy for germplasm identification. The developed fingerprinting system provides a robust, low-cost tool for seed purity testing, variety authentication, and marker-assisted selection in cowpea breeding programs.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0343756","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T17:56:39Z","timestamp":1786730199000},"page":"e0343756","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development of KASP molecular markers and construction of fingerprinting for cowpea (Vigna unguiculata (L.) Walp.) based on ddRAD-Seq"],"prefix":"10.1371","volume":"21","author":[{"given":"Juan","family":"Xiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuoling","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengming","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lanping","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3910-8836","authenticated-orcid":true,"given":"Shilin","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Zou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kehao","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huimin","family":"Qiu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bengang","family":"Xian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaohong","family":"Fu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4298-6720","authenticated-orcid":true,"given":"Xiaowei","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,14]]},"reference":[{"issue":"13","key":"pone.0343756.ref001","doi-asserted-by":"crossref","first-page":"4793","DOI":"10.1002\/jsfa.9074","article-title":"Cowpea: an overview on its nutritional facts and health benefits","volume":"98","author":"C Jayathilake","year":"2018","journal-title":"J Sci Food Agric"},{"issue":"5","key":"pone.0343756.ref002","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1038\/s41588-024-01722-w","article-title":"Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement","volume":"56","author":"X Wu","year":"2024","journal-title":"Nat Genet"},{"issue":"4","key":"pone.0343756.ref003","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1111\/pbr.12589","article-title":"Cowpea (Vigna unguiculata): genetics, genomics and breeding","volume":"138","author":"O Boukar","year":"2018","journal-title":"Plant Breeding"},{"issue":"7","key":"pone.0343756.ref004","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1111\/pbi.14047","article-title":"Comprehensive genomic analyses of Vigna unguiculata provide insights into population differentiation and the genetic basis of key agricultural traits","volume":"21","author":"L Pan","year":"2023","journal-title":"Plant Biotechnol J"},{"key":"pone.0343756.ref005","article-title":"Studies on genetic divergence in vegetable cowpea [vigna unguiculata (L.) Walp.]","author":"R Chandrakar","year":"2016","journal-title":"Int J Agricul Sci"},{"issue":"3","key":"pone.0343756.ref006","article-title":"Development of a core set of single nucleotide polymorphism markers for genetic diversity analysis and cultivar fingerprinting in cowpea","volume":"3","author":"X Wu","year":"2021","journal-title":"Legume Science"},{"key":"pone.0343756.ref007","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.3389\/fpls.2015.01271","article-title":"Validating DNA polymorphisms using KASP assay in prairie cordgrass (Spartina pectinata Link) populations in the U.S","volume":"6","author":"H Graves","year":"2016","journal-title":"Front Plant Sci"},{"issue":"7","key":"pone.0343756.ref008","doi-asserted-by":"crossref","first-page":"8945","DOI":"10.1007\/s10722-025-02462-4","article-title":"Analysis of genetic diversity and development of Kompetitive allele specific PCR (KASP) markers for Lithocarpus litseifolius (Hance) Chun resources based on dd-RAD-Seq","volume":"72","author":"Y Tian","year":"2025","journal-title":"Genet Resour Crop Evol"},{"key":"pone.0343756.ref009","doi-asserted-by":"crossref","DOI":"10.3390\/horticulturae10121325","article-title":"Kasp markers for identifying roselle (Hibiscus sabdariffa L.) key varieties based on genetic polymorphisms revealed by ddRAD-seq","volume":"10","author":"SJ Huang","year":"2024","journal-title":"Horticulturae"},{"issue":"1","key":"pone.0343756.ref010","doi-asserted-by":"crossref","first-page":"90","DOI":"10.5147\/pggb.v2i1.155","article-title":"Introduction of high throughput and cost effective SNP genotyping platforms in Soybean","volume":"2","author":"J Yuan","year":"2017","journal-title":"PGGB"},{"issue":"4","key":"pone.0343756.ref011","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1007\/s11032-018-0777-2","article-title":"Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice","volume":"38","author":"KA Steele","year":"2018","journal-title":"Mol Breed"},{"key":"pone.0343756.ref012","doi-asserted-by":"crossref","first-page":"6572969","DOI":"10.1155\/2017\/6572969","article-title":"Development of SNP genotyping assays for seed composition traits in Soybean","volume":"2017","author":"G Patil","year":"2017","journal-title":"Int J Plant Genomics"},{"issue":"11","key":"pone.0343756.ref013","doi-asserted-by":"crossref","first-page":"5312","DOI":"10.3390\/ijms26115312","article-title":"Construction of SNP fingerprinting and genetic diversity analysis of eggplant based on KASP technology","volume":"26","author":"W Wang","year":"2025","journal-title":"Int J Mol Sci"},{"issue":"1","key":"pone.0343756.ref014","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2041-2223-5-1","article-title":"DNA fingerprinting in botany: past, present, future","volume":"5","author":"H Nybom","year":"2014","journal-title":"Investig Genet"},{"key":"pone.0343756.ref015","doi-asserted-by":"crossref","first-page":"1460603","DOI":"10.3389\/fpls.2024.1460603","article-title":"Development of KASP markers, SNP fingerprinting and population genetic analysis of Cymbidium ensifolium (L.) 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