Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars

Abstract

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.

Acknowledgements

This research was funded by the National Natural Science Foundation of China (31971648), the China Scholarship Council (202108320301), and the Czech Science Foundation (19-18545S).

Author Contributions

Y.H. and Q.G. designed the experiments; Y.H., Z.Y., X.G., Y.Z. and G.L. performed experiments; Y.H., Z.Y.,X.G. and P.L. analyzed data; Y.H. and Q.G. wrote the manuscript; P. Š. reviewed the manuscript.

Data availability

The high-throughput sequencing data in this study are all open access and have been uploaded to the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn/) with the accession number CRA006613.

Conflict of interest

The authors declare no competing interests.

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