基于RAD高通量测序的蓝花楹群体遗传分析

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

摘要:

为了解蓝花楹(Jacaranda mimosifolia)种质资源的遗传多样性和群体遗传结构，对168份种质材料进行RAD-seq测序，构建了系统进化树并进行主成分、群体结构和遗传多样性分析。结果表明，比对参考基因组平均比对率为81.02%，平均测序深度23.18×，最终获得45 552个高质量的SNPs。群体遗传结构分析表明，供试蓝花楹可划分为2个大的类群，来自川、渝地区的种质材料基本归为一类；其余地区归为另一类。19个地区的蓝花楹在SNP水平上的遗传多样性较高，云南昆明(YNKM)居群的核苷酸多样性(π)和期望杂合度(He)最大，表现出最高的遗传多样性。因此，来自川、渝地区的蓝花楹具有相对较近的亲缘关系，推断来自同一祖先，而其余地区的种质可能是随机引种栽培。

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.