Hu Yaping, Yu Zhaoyan, Gao Xiaoge, Liu Ganping, Zhang Yun, Šmarda Petr, Guo Qirong
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Coconut Research Institute of Chinese Academy of Tropical Agricultural Science, Wenchang, Hainan 571339, China.
Hortic Res. 2023 Jul 11;10(8):uhad136. doi: 10.1093/hr/uhad136. eCollection 2023 Aug.
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.
银杏是一种在全球具有经济价值的树种。该物种在第四纪期间几乎灭绝，这可能导致其遗传变异性降低。目前，银杏的遗传变异性在中国的少数自然种群以及一些栽培品种中得以保存，这些栽培品种源自少数古树，从而帮助该物种在中国中世纪时期得以存活。然而，尽管近期人们对银杏颇感兴趣，但对于其在栽培树木和品种中保存的遗传多样性的详细了解仍然匮乏。这限制了对其多样性的有效保护以及对现有种质资源的有效利用。在此，我们对收集到的102份银杏栽培种质进行了简化基因组测序（GBS），以探究它们的遗传结构、亲缘关系和近亲繁殖预测。在银杏研究中首次使用全基因组关联分析研究（GWAS）来尝试对种子性状进行基因定位。结果表明，大多数种质之间未显示出任何明显的遗传关系。银杏种质群体规模在公元1500年左右的隋唐时期显著扩大。基于系统发育视角对种子品种进行分类并不支持当前基于表型的分类标准。在对种子性状进行GWAS分析后定位到了24个候选基因。总体而言，本研究揭示了银杏种子性状的遗传基础，并为其栽培历史提供了见解。这些发现将有助于这种活化石植物驯化种质的保护与利用。
