Population Genetic Analysis of Jacaranda mimosifolia by RAD Hight Throughput Sequencing Technique

Abstract:

In order to understand the genetic diversity of Jacaranda mimosifolia germplasm resources, 168 germplasms of Jacaranda mimosifolia were restriction-site associated DNA sequencing (RAD-seq), and then the phylogenetic tree was constructed, principal component (PCA), population structure and genetic diversity were analyzed. The results showed that the mean alignment rates to the reference genomes were 81.02% with an average sequencing depth of 23.18×. After cleaned and filtered, a total of 45 552 SNPs were obtained. All tested germplasms could be clustered into two groups, those from Sichuan-Chongqing region were in one group, and the rest were in another group. Jacaranda mimosifolia has a high genetic diversity at the SNP level. Among them, nucleotide diversity (π) and expected heterozygosity (He) in YNKM population is the largest, showing the highest genetic diversity. Therefore, Jacaranda mimosifolia from Sichuan-Chongqing region showed relatively close genetic relationship, suggesting that they might from the same ancestor, and those from other regions might be randomly introduced and cultivated.

Key words:Jacaranda mimosifolia;RAD-seq;Genetic diversity;Population genetic