Genomic analyses of agronomic traits in tea plants and related Camellia species

Shengchang Duan; Liang Yan; Zongfang Shen; Xuzhen Li; Baozheng Chen; Dawei Li; Hantao Qin; Muditha K Meegahakumbura; Moses C Wambulwa; Lianming Gao; Wei Chen; Yang Dong; Jun Sheng

doi:10.3389/fpls.2024.1449006

Genomic analyses of agronomic traits in tea plants and related Camellia species

Front Plant Sci. 2024 Aug 26:15:1449006. doi: 10.3389/fpls.2024.1449006. eCollection 2024.

Authors

Shengchang Duan^#^{1

2

3}, Liang Yan^#^{4

5}, Zongfang Shen^#^{6

7

8}, Xuzhen Li¹, Baozheng Chen⁹, Dawei Li¹, Hantao Qin^{6

8}, Muditha K Meegahakumbura^{6

10}, Moses C Wambulwa^{6

7

11}, Lianming Gao^{6

12}, Wei Chen^{2

3}, Yang Dong^{2

3}, Jun Sheng^{2

3}

Affiliations

¹ College of Plant Protection, Yunnan Agricultural University, Kunming, China.
² State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
³ Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China.
⁴ College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, China.
⁵ Pu'er Institute of Pu-erh Tea, Pu'er, China.
⁶ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China.
⁷ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China.
⁸ University of Chinese Academy of Science, Beijing, China.
⁹ College of Food Science and Technology, Yunnan Agricultural University, Kunming, China.
¹⁰ Department of Export Agriculture, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla, Sri Lanka.
¹¹ Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya.
¹² Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China.

^# Contributed equally.

Abstract

The genus Camellia contains three types of domesticates that meet various needs of ancient humans: the ornamental C. japonica, the edible oil-producing C. oleifera, and the beverage-purposed tea plant C. sinensis. The genomic drivers of the functional diversification of Camellia domesticates remain unknown. Here, we present the genomic variations of 625 Camellia accessions based on a new genome assembly of C. sinensis var. assamica ('YK10'), which consists of 15 pseudo-chromosomes with a total length of 3.35 Gb and a contig N50 of 816,948 bp. These accessions were mainly distributed in East Asia, South Asia, Southeast Asia, and Africa. We profiled the population and subpopulation structure in tea tree Camellia to find new evidence for the parallel domestication of C. sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS). We also identified candidate genes associated with traits differentiating CSA, CSS, oilseed Camellia, and ornamental Camellia cultivars. Our results provide a unique global view of the genetic diversification of Camellia domesticates and provide valuable resources for ongoing functional and molecular breeding research.

Keywords: Camellia; Camellia sinensis var. assamica cv. ‘Yunkang10’; assembly; pangenome; resequencing.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by Yunnan Provincial Key Programs (2019ZG00908), The NSFC grant (31970363), and The Key Basic Research Program of Yunnan Province (202101BC070003).