Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

Jun Zeng; Jie Chen; Yixuan Kou; Yujin Wang

doi:10.7717/peerj.5606

Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

PeerJ. 2018 Sep 19:6:e5606. doi: 10.7717/peerj.5606. eCollection 2018.

Authors

Jun Zeng¹, Jie Chen², Yixuan Kou³, Yujin Wang²

Affiliations

¹ Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
² State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China.
³ Laboratory of Subtropical Biodiversity, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, China.

Abstract

Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species' genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag-simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis.

Keywords: EST-SSRs; Population structure; Torreya grandis; Transcriptome.

Associated data

figshare/10.6084/m9.figshare.7006220.v2

Grants and funding

This work was supported by the National Natural Science Foundation of China (Nos. 81274024 and 41461008). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.