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Article|11 Jul 2023|OPEN
Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars
Yaping Hu1 , Zhaoyan Yu2 , Xiaoge Gao1 , Ganping Liu1 , Yun Zhang3 , Petr Smarda4 and Qirong Guo,1 ,
1Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2Coconut Research Institute of Chinese Academy of Tropical Agricultural Science, Wenchang, Hainan 571339, China
3Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
4Department of Botany and Zoology, Faculty of Science, Masaryk University, Koltlárská 2, Brno 61137, Czech Republic
*Corresponding author. E-mail:

Horticulture Research 10,
Article number: uhad136 (2023)
Views: 111

Received: 21 Nov 2022
Accepted: 02 Jul 2023
Published online: 11 Jul 2023


Ginkgo biloba is an economically valuable tree worldwide. The species has nearly become extinct during the Quaternary, which has likely resulted in reduction of its genetic variability. The genetic variability is now conserved in few natural populations in China and a number of cultivars that are, however, derived from a few ancient trees, helping the species survive in China through medieval times. Despite the recent interest in ginkgo, however, detailed knowledge of its genetic diversity, conserved in cultivated trees and cultivars, has remained poor. This limits efficient conservation of its diversity as well as efficient use of the existing germplasm resources. Here we performed genotyping-by-sequencing (GBS) on 102 cultivated germplasms of ginkgo collected to explore their genetic structure, kinship, and inbreeding prediction. For the first time in ginkgo, a genome-wide association analysis study (GWAS) was used to attempt gene mapping of seed traits. The results showed that most of the germplasms did not show any obvious genetic relationship. The size of the ginkgo germplasm population expanded significantly around 1500 years ago during the Sui and Tang dynasties. Classification of seed cultivars based on a phylogenetic perspective does not support the current classification criteria based on phenotype. Twenty-four candidate genes were localized after performing GWAS on the seed traits. Overall, this study reveals the genetic basis of ginkgo seed traits and provides insights into its cultivation history. These findings will facilitate the conservation and utilization of the domesticated germplasms of this living fossil plant.