{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:44:05Z","timestamp":1785426245185,"version":"3.56.0"},"reference-count":33,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004493","name":"International Atomic Energy Agency","doi-asserted-by":"crossref","award":["25156"],"award-info":[{"award-number":["25156"]}],"id":[{"id":"10.13039\/501100004493","id-type":"DOI","asserted-by":"crossref"}]},{"award":["25156"],"award-info":[{"award-number":["25156"]}],"id":[{"id":"https:\/\/ror.org\/02zt1gg83","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Black soybean is an important functional crop valued for its high anthocyanin content and associated health benefits, attracting increasing interest in plant breeding and mutation-based approaches to enhance its nutritional and agronomic traits. Here, we investigated a DT26 black seed-coat mutant (DT26BS) derived from the Vietnamese cultivar DT26 following gamma irradiation. Genetic analysis of F2 populations indicated that the phenotype is controlled by a single recessive mutation, with additional epistatic interactions observed in other genetic backgrounds. MutMap analysis based on whole-genome sequencing of pooled F2 individuals identified a candidate region on chromosome 8 corresponding to the I locus. A large deletion (~176 kb) was identified in this region, affecting multiple Chalcone Synthase (CHS) gene repeats, and which may disrupt RNAi-mediated silencing of CHS, thereby triggering anthocyanin restoration in the seed coat. PCR-based markers confirmed tight linkage between this deletion and the black seed-coat phenotype. Crosses with elite lines and further selection until F7 generations showed that the mutation has no adverse effects on major agronomic traits and is useful as a donor for developing improved lines with black seed coat, shorter maturity, high yield, and enhanced anthocyanin content for nutritional improvement. These results demonstrate the utility of MutMap for detecting irradiation-induced structural variants and extend its application to a non-reference elite tropical soybean background, providing a useful genetic resource for black soybean breeding.<\/jats:p>","DOI":"10.3390\/genes17070814","type":"journal-article","created":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T05:32:17Z","timestamp":1784266337000},"page":"814","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MutMap Reveals a Structural Deletion at the Chalcone Synthase Locus Controlling Black Seed Coat in a Gamma-Irradiated Vietnamese Soybean Mutant"],"prefix":"10.3390","volume":"17","author":[{"given":"Chung Thi Bao","family":"Pham","sequence":"first","affiliation":[{"name":"Agricultural Genetics Institute, Hanoi 122000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lieu Thi","family":"Le","sequence":"additional","affiliation":[{"name":"Agricultural Genetics Institute, Hanoi 122000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manh Van","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Agricultural Genetics Institute, Hanoi 122000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thao Duc","family":"Le","sequence":"additional","affiliation":[{"name":"Agricultural Genetics Institute, Hanoi 122000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong Thi Anh","family":"Le","sequence":"additional","affiliation":[{"name":"Agricultural Genetics Institute, Hanoi 122000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nhu Thi","family":"Le","sequence":"additional","affiliation":[{"name":"Agricultural Genetics Institute, Hanoi 122000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuyen Thi Minh","family":"Vo","sequence":"additional","affiliation":[{"name":"Agricultural Genetics Institute, Hanoi 122000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1745-248X","authenticated-orcid":false,"given":"Cuong","family":"Nguyen","sequence":"additional","affiliation":[{"name":"The Information Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dat Tien","family":"Nguyen","sequence":"additional","affiliation":[{"name":"LOBI Vietnam Company Limited, Dai Mo, Hanoi 100000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pooja","family":"Bhatnagar-Mathur","sequence":"additional","affiliation":[{"name":"Plant Breeding & Genetics Section, Joint FAO\/IAEA Centre of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, 1400 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minh Hong","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa School of Engineering, Phenikaa University, Duong Noi, Hanoi 12116, Vietnam"},{"name":"Bioresource Research Center, Phenikaa School of Engineering, Phenikaa University, Duong Noi, Hanoi 12116, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Son Lang","family":"Vi","sequence":"additional","affiliation":[{"name":"Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa School of Engineering, Phenikaa University, Duong Noi, Hanoi 12116, Vietnam"},{"name":"Bioresource Research Center, Phenikaa School of Engineering, Phenikaa University, Duong Noi, Hanoi 12116, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"19960","DOI":"10.1038\/s41598-020-76985-4","article-title":"Isoflavones, anthocyanins, phenolic content, and antioxidant activities of black soybeans (Glycine max (L.) 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