Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.).

Carole F S Koning-Boucoiran,Virginia W Gitonga,Marinus J M Smulders,G Danny Esselink,Mirjana Vukosavljev,Dietmar Schulz,Thomas Debener,Chris Maliepaard,Wendy P C Van 'T Westende,Roeland E Voorrips,W Eric Van De Weg,Paul Arens,Frans A Krens

doi:10.3389/fpls.2015.00249

Carole F S Koning-Boucoiran, Virginia W Gitonga + Show 11 more

Open Access

https://doi.org/10.3389/fpls.2015.00249

Copy DOI

Abstract

In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.

Highlights

Whereas, cut rose is economically the most important ornamental crop worldwide (761 million euros in The Netherlands in 2011), the rose genome sequence has not been completed yet
We present the results of (i) three transcriptome de novo assemblies based on tetraploid cut and garden rose genotypes and a diploid rose, (ii) the development of a 68K genotyping single nucleotide polymorphisms (SNPs) marker array on the Axiom platform, and the (iii) construction and (iv) annotation of a non-redundant rose transcriptome for tetraploid roses using the genome sequence of diploid strawberry
For SNP calling it is better to avoid these. On one hand they could represent paralogous genes, which would lead to nucleotide differences between paralogs rather than between alleles of the same locus. If they are from splice variants they may map in multiple contigs, which could mean that all of these would unnecessarily be excluded from the SNP calling

Summary

Introduction

Cut rose is economically the most important ornamental crop worldwide (761 million euros in The Netherlands in 2011), the rose genome sequence has not been completed yet. A long history of interspecific hybridization and selection (Debener and Linde, 2009; Smulders et al, 2011; Vukosavljev et al, 2013; Zhang et al, 2013) has led to a complicated taxonomy that is not fully resolved (Koopman et al, 2008; Fougère-Danezan et al, 2015). Inheritance patterns of quantitative traits may be complex Phenotypic traits such as flower stem production, flower shape, flower color or disease resistance are of economic importance for breeders. Rose Axiom SNP array development and growers (Debener and Linde, 2009; Smulders et al, 2011), and need to be better understood genetically in order to be able to apply marker-assisted selection in breeding programs. There is a consensus genetic map for rose (Spiller et al, 2011)

Methods

Results

Discussion

Conclusion