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. 2024 Jun 28;15:5470. doi: 10.1038/s41467-024-49721-z

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a–b Genetic basis of subsp. chinensis var. parachinensis selection. (a) and (b) show highly divergent regions between Par and DG, and DG and PC, respectively. The F_ST values are plotted against the position on each chromosome. The horizontal pink lines indicate the genome-wide thresholds (5%) of differentiation signals. The peach bar on Chr. A09 intersecting (a) and (b) indicates the candidate selection sweep (A09: 26,630,001…27,300,000) studied. c A temperature-responsive QTL(HT) co-locates with the region of gQTL^A09-1. An F2 population established from a cross between Par and PC, was used for the analysis. Half of the 4-week-old seedlings continued to grow under normal conditions (NC), while the other half of the seedlings were moved to high temperature (HT) conditions until flowering. Flowering-related quantitative trait loci (ftQTLs) responding to different temperatures were then identified. The green and brown dot lines indicate QTLs responding to NC and HT, respectively. The horizontal red line indicates the 95% confidence interval of Δ(SNP-index). gQTL represents QTLs (quantitative trait locus) associating with Par domestication generated from (a). Black triangle, the genome position of BrJMJ18. d The local π value features for the selection sweep on chromosome A09 (26,630,001…27,300,000) of PC, DG, and Par around gQTL^A09-1. Black triangle, the genome position of BrJMJ18. e, f Sequence polymorphisms and haplotype analysis of BrJMJ18 in PC, DG, and Par. Red lines in (e) indicate different nucleotide alterations and corresponding amino acid substitutions are shown. JmjN: Jumonji N-terminal domain; JmjC: Jumonji C-terminal domain; Zf-C5HC2: C5HC2 zinc finger domain; FYRN: FY-rich domain, N-terminal region; FYRC: FY-rich domain, C-terminal region. The alteration of allelic frequencies of BrJMJ18 in PC, DG, and Par are shown in (f). BrJMJ18^PC and BrJMJ18^Par represent the BrJMJ18 allele coming from PC and Par, respectively; n denotes the number of lines of PC, DG, and Par used for the analysis.