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

Jun Zeng,Jie Chen,Yujin Wang,Yixuan Kou

doi:10.7717/peerj.5606

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.

Highlights

The Chinese nutmeg tree, Torreya grandis Fort. et Lindl. (Taxaceae), is a conifer species restricted to only a few mountainous regions in Zhejiang, Anhui, Jiangxi, Hunan, and Fujian, China (Kang & Tang, 1995; Cheng et al, 2007)
Transcriptome sequencing and assembly A total of 39,526,668 raw reads were generated from the Illumina sequencing of T. grandis
The average HO across six populations of T. grandis (0.540) was higher than that reported for T. grandis “Merrillii” (0.439), while the average HE (0.432) was lower than that reported for the cultivar (0.522) (Yi et al, 2016). These results suggest that the polymorphism level of the 11 expressed sequence tag (EST)-simple sequence repeats (SSRs) markers developed in this study is moderate in comparison with other conifer species and comparable to T. grandis “Merrillii” (Yi et al, 2016)

Summary

Introduction

The Chinese nutmeg tree, Torreya grandis Fort. et Lindl. (Taxaceae), is a conifer species restricted to only a few mountainous regions in Zhejiang, Anhui, Jiangxi, Hunan, and Fujian, China (Kang & Tang, 1995; Cheng et al, 2007). The Chinese nutmeg tree, Torreya grandis Fort. (Taxaceae), is a conifer species restricted to only a few mountainous regions in Zhejiang, Anhui, Jiangxi, Hunan, and Fujian, China (Kang & Tang, 1995; Cheng et al, 2007). Its wood, being highly valued for its durability, along with pest and decay resistance, was widely used to make furniture, How to cite this article Zeng et al (2018), Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree. In combination with habitat destruction, the population of T. grandis has decreased drastically in recent years, and was listed as a threatened species on the International Union for Conservation of Nature Red List (Yang & Luscombe, 2013). The objective evaluation of wild resources is crucial for improving breeding programs and conservation of T. grandis

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Discussion

Conclusion