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. 2021 Jul 15;53(8):1250–1259. doi: 10.1038/s41588-021-00895-y

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© The Author(s) 2021

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a, A proposed road map of parallel domestication in CSA and CSS. Early domestication involved genes related to glucoside and glycoside transport and photomorphogenesis and plant height in CSA and herbivore-induced chemicals in CSS. The improvement mainly focused on genes related to alkaloid and aromatic chemicals in CSA and genes related to cold stress and photomorphogenesis and plant height in CSS. The number of artificially selected genes are labeled in each domestication process. b, Genome-wide distribution of selective-sweep signals identified based on cross-population extended haplotype homozygosity (XP-EHH). Genes with important functions that are linked to sweeps are highlighted in Manhattan plots. Genes that were involved in early domestication were identified based on a comparison between CSA and CSS landraces, and ACSA, while genes under improvement were selected based on a comparison between CSA and CSS elite, and CSA and CSS landraces. c, Signals of artificial selection in the XDH gene. Purple and green solid lines indicate Tajima’s D statistics in CSA landraces and CSA elite cultivars, respectively. The blue dashed line indicates the fixation index (F_ST) between CSA landrace and elite populations, while the red dashed line is the threshold of the top 5% F_ST. d, Signals of artificial selection in the CM (chorismate mutase) gene. Purple and green solid lines indicate Tajima’s D statistics in CSA landraces and CSA elite cultivars, respectively. e, Signals of artificial selection in the F3′H gene. Left, F3′H is one of the key genes in catechin biosynthetic pathways. Right, signals of artificial selection in this gene. f, Signals of artificial selection in BAS1 and DWF4 genes, related to plant height. The leftmost panel shows different morphological features in tea accessions. In contrast to ACSA, CCSA and CCSS are featured with decreased plant height, with most CCSA being small trees or semi-shrubs and CCSS being shrubs. Scale bar, 0.5 m. Middle and rightmost panels show signals of artificial selection in BAS1 and DWF4. g, Expression of artificially selected genes in the six tissues examined, including root (RT), stem (ST), flower (FL), bud (BD), young leaf (YL) and old leaf (OL).