Open Access

ARTICLE

Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) K untze) Germplasm in Qiannan, China, Based on SLAFSeq Technology

by Fen Zhang¹, Weili Tian¹, Lu Cen¹, Litang Lv², Xiaofang Zeng¹, Yulu Chen¹, Yichen Zhao^2,*, Yan Li^1,*

1 The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, 550025, China
2 College of Tea Sciences, Guizhou University, Guiyang, 550025, China

* Corresponding Authors: Yichen Zhao. Email: ; Yan Li. Email:

(This article belongs to the Special Issue: Plant Ecophysiology: Recent Trends and Advancements)

Phyton-International Journal of Experimental Botany 2022, 91(4), 791-809. https://doi.org/10.32604/phyton.2022.018104

Received 29 June 2021; Accepted 14 September 2021; Issue published 09 December 2021

Abstract

Duyun Maojian tea is a famous tea in China. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of 2 leaf traits of 123 tea plants in Qiannan, China. A total of 462,019 SLAF tags and 11,362,041 single-nucleotide polymorphism (SNP) loci were obtained. The results of phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 123 tea germplasms were clustered into three groups, and the heterozygosity rates for Groups I, II, and II were 0.206, 0.224, and 0.34, respectively. Generally, tea germplasms in a production area are clustered in a group, indicating that tea germplasms in different production areas have certain genetic diversity. The traditional Duyun Maojian tea core production areas, TS and DC-SJ, are clustered into Group I and Group II respectively, while the ZY production area is relatively independent in Group III. Furthermore, based on GWAS analysis, 11 candidate genes related to leaf apex and 7 candidate genes related to leaf shape were obtained. This study clarified the genetic relationship among eight Duyun Maojian tea production areas and obtained candidate genes related to leaf apex and leaf shape development. The results showed that population structure and candidate genes are an effective basis for the breeding of Duyun Maojian tea germplasm.

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