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

Abstract

Ginkgo biloba is worldwide an economically valuable tree. The species has nearly got extinct during the Quaternary which likely result in reduction of its genetic variability. This is now conserved in few natural populations in China and number of cultivars which are, however, derived from a few ancient trees, helping the species survival in China through medieval times. Despite the recent interest on ginkgo, however, the detail knowledge of its genetic diversity, conserved in cultivated trees and cultivars remained poor. This limit efficient conservation of its diversity as well as efficient use of the existing germplasm resources. Here we performed genotyping-by-sequencing (GBS) sequencing on 102 ginkgo cultivated germplasm collected to explore their genetic structure, kinship and inbreeding prediction. And for the first time in ginkgo, genome-wide association analysis study (GWAS) was used to try gene mapping of seed traits. The results showed that the most of the germplasm did not show obvious genetic relationship. The size of ginkgo germplasm population expanded significantly around 1500 years ago during the Sui and Tang dynasties. Classification of seed cultivars based on 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 reveal the genetic basis of ginkgo seed traits and shed insights into its cultivation history, these findings will facilitate the conservation and utilization of the domesticated germplasms of this living fossil plants.

Efficient purging of deleterious mutations contributes to the survival of a rare conifer

“…2E ; Supplementary Data Figs S10 and S11 ), indicating a higher level of inbreeding in C. gigantea . Using a threshold for ROH length of >1 Mb to evaluate recent inbreeding levels [ 15 , 22 ], we found that 0.2198% of the C. gigantea and 0.1171% of the C. duclouxiana genome consisted of such long ROH regions ( Fig. 2E ).…”

Genetic architecture and genomic prediction of plant height-related traits in chrysanthemum

“…Chrysanthemum is a complex species with high heterozygosity (>3%), high repetitiveness (>80%), huge genome size (8.47–9.02 Gb) [ 9 ], rapid decay rate, and a relatively low gene density of approximately one gene per 58.74 kb, which makes it rather challenging to identify causal genes underlying the detected association loci within a relatively narrow genomic region. It has been documented that a wide range of 100 kb region centered on the peak SNPs has been employed to explore candidate genes in species with rapid decay rate, such as ginkgo [ 55 ] and apple [ 56 ]. Therefore, to overcome the challenge of candidate gene identification in chrysanthemum GWAS, a relatively less stringent range of 100 kb upstream and downstream of the significant SNPs was first used to detect the putative candidate genes, and then we combined the RNA-seq data and qRT–PCR analyses to verify the candidate genes responsible for PH traits.…”

Analysis of the Genetic Diversity in Tea Plant Germplasm in Fujian Province Based on Restriction Site-Associated DNA Sequencing

“…The sequencing original data from the Illumina platform were screened through FASTP software (version 0.18.0). Reads with unknown nucleotides (N) ≥ 10%, Phred quality score ≤ 20 with more than 50% base content and those containing connectors were excluded [ 65 ]. Subsequently, the filtered reads were compared to the reference genome using the software BWA (version 0.7.12).…”