Genetic diversity and structure of the 4th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook)

Yonglian Jing; Liming Bian; Xuefeng Zhang; Benwen Zhao; Renhua Zheng; Shunde Su; Daiquan Ye; Xueyan Zheng; Yousry A El-Kassaby; Jisen Shi

doi:10.3389/fpls.2023.1106615

Genetic diversity and structure of the 4^th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook)

Front Plant Sci. 2023 Jan 27:14:1106615. doi: 10.3389/fpls.2023.1106615. eCollection 2023.

Authors

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.
² Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China.
³ Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China.
⁴ Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada.

Abstract

Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4^th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4^th cycle breeding population was high with nucleotide diversity (P_i ) of 0.003, and H_o and H_e of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (F_st < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.

Keywords: Chinese fir; RAD-seq; breeding population; genetic diversity; genetic structure.

Grants and funding

This work was supported by the National Key Research and Development Program of China (2022YFD2200201), National Natural Science Foundation of China (32171818), Fujian Province Science and Technology Research Funding on the fourth Tree Breeding Programme of Chinese fir (Min Lin Ke 2016-35, ZMGG-0701, 2022FKJ05), and Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).