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The<jats:italic> Pun4<\/jats:italic> locus, responsible for the reduced pungency of the mutant fruits, was localized to a 208 Mb region on chromosome 6. DEMF06G16460, encoding 3-ketoacyl-CoA synthase, was proposed as a strong candidate gene based on the genetic analyses of bulked segregants, DEG, and expression analyses.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Abstract<\/jats:title>\n                <jats:p>Capsaicinoids are unique alkaloids present in pepper (<jats:italic>Capsicum<\/jats:italic> spp.), synthesized through the condensation of by-products from the phenylpropanoid and branched-chain fatty acid pathways, and accumulating in the placenta. In this study, we characterized two allelic ethyl methanesulfonate-induced mutant lines with extremely low pungency (\u2018221-2-1a\u2019 and \u20181559-1-2h\u2032). These mutants, derived from the pungent Korean landrace 'Yuwolcho,' exhibited lower capsaicinoid content than Yuwolcho but still contained a small amount of capsaicinoid with functional capsaicinoid biosynthetic genes. Genetic crosses between the mutants and Yuwolcho or pungent lines indicated that a single recessive mutation was responsible for the low-pungency phenotype of mutant 221-2-1a; we named the causal locus <jats:italic>Pungency 4<\/jats:italic> (<jats:italic>Pun4<\/jats:italic>). To identify <jats:italic>Pun4<\/jats:italic>, we combined genome-wide polymorphism analysis and transcriptome analysis with bulked-segregant analysis. We narrowed down the location of <jats:italic>Pun4<\/jats:italic> to a 208-Mb region on chromosome 6 containing five candidate genes, of which <jats:italic>DEMF06G16460<\/jats:italic>, encoding a 3-ketoacyl-CoA synthase associated with branched-chain fatty acid biosynthesis, is the most likely candidate for <jats:italic>Pun4<\/jats:italic>. The expression of capsaicinoid biosynthetic genes in placental tissues in Yuwolcho and the mutant was consistent with the branched-chain fatty acid pathway playing a pivotal role in the lower pungency observed in the mutant. We also obtained a list of differentially expressed genes in placental tissues between the mutant and Yuwolcho, from which we selected candidate genes using gene co-expression analysis. In summary, we characterized the capsaicinoid biosynthesis-related locus <jats:italic>Pun4<\/jats:italic> through integrated of genetic, genomic, and transcriptome analyses. These findings will contribute to our understanding of capsaicinoid biosynthesis in pepper.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1007\/s00122-024-04602-3","type":"journal-article","created":{"date-parts":[[2024,4,12]],"date-time":"2024-04-12T11:02:01Z","timestamp":1712919721000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Genetic characterization of a locus responsible for low pungency using EMS-induced mutants in Capsicum annuum L."],"prefix":"10.1007","volume":"137","author":[{"given":"Seungki","family":"Back","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jung-Min","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hayoung","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joung-Ho","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koeun","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doyeon","family":"Hwang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin-Kyung","family":"Kwon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7606-7258","authenticated-orcid":false,"given":"Byoung-Cheorl","family":"Kang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,4,12]]},"reference":[{"issue":"2","key":"4602_CR1","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/nbt.2095","volume":"30","author":"A Abe","year":"2012","unstructured":"Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. 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