Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra

Odile Rogier,Marie-Claude Lesage-Descauses,Véronique Brunaud,José Caius,Sandrine Balzergue,Aurélien Chateigner,Vincent Segura,Souhila Amanzougarene,Véronique Jorge,Ludivine Soubigou-Taconnat

doi:10.1186/s12864-018-5239-z

Abstract

BackgroudPopulus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Polymorphisms (SNPs) typically needed to carry out a genome scan, the present study aimed at evaluating RNA sequencing as a tool to discover and type SNPs in genes within natural populations of P. nigra.ResultsWe have devised a bioinformatics pipeline to call and type SNPs from RNAseq reads and applied it to P. nigra transcriptomic data. The accuracy of the resulting RNAseq-based SNP calling and typing has been evaluated by (i) comparing their position and alleles to those previously reported in candidate genes, (ii) assessing their genotyping accuracy with respect to a previously available SNP chip and (iii) evaluating their inter-annual repeatability. We found that a combination of several callers yields a good compromise between the number of variants type and the accuracy of genotyping. We further used the resulting genotypic data to carry out basic genetic analyses whose results confirm the quality of the RNAseq-based SNP dataset.ConclusionsWe demonstrated the potential and accuracy of RNAseq as an efficient way to genotype SNPs in P. nigra. These results open prospects towards the use of this technology for quantitative and population genomics studies.

Highlights

Populus nigra is a major tree species from Eurasian riparian ecosystems and one of the 3 main parental species used in poplar breeding programs to develop highly productive interspecific cultivated hybrids
Studies in P. nigra have focused on re-sequencing specific candidate genes from the lignin pathway [3,4,5], but more recent work has broadened the scope of analyses through the development of a genotyping chip from Single nucleotide polymorphism (SNP) detected by whole-genome sequencing [1, 2]
The present study aims at evaluating RNA sequencing (RNAseq) as a tool to type a sufficiently large amount of SNPs within natural populations of P. nigra to carry out a genome-wide association study (GWAS)

Summary

Introduction

Populus nigra is a major tree species from Eurasian riparian ecosystems and one of the 3 main parental species used in poplar breeding programs to develop highly productive interspecific cultivated hybrids. Studies in P. nigra have focused on re-sequencing specific candidate genes from the lignin pathway [3,4,5], but more recent work has broadened the scope of analyses through the development of a genotyping chip from SNPs detected by whole-genome sequencing [1, 2]. This genotyping tool was successfully used to study the structure of the genetic diversity of the species [1] and to identify some genomic regions associated with economically important traits [6].

Methods

Results

Conclusion