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.)

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.

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

“…We found a lower percentage of polymorphic loci in the climber (40.9%) and ground cover genotypes (50.2%). This could indicate some degree of ascertainment bias if the genetic background of these groups of roses is partly different from those of the cut and garden roses from which the SNPs derived (Koning-Boucoiran et al, 2015; Smulders et al, 2015). This would require further studies, for instance, a study that searches for homologous regions in the genomes of diploid species that have contributed to the tetraploid groups.…”

“…SNPs were analyzed using the Axiom WagRhSNP array, which contains 89,893 SNPs derived from cut roses and from garden roses (Koning-Boucoiran et al, 2015). The hybridisation intensities were interpreted as tetraploid SNP dosage scores (AAAA, AAAB, AABB, ABBB, and BBBB) using fitTetra (Voorrips et al, 2011) and were used to calculate the statistics required for the association study.…”

“…Recently, an analysis of a large collection of rose ESTs and the development of an Axiom SNP array was described (Koning-Boucoiran et al, 2015). These resources are a significant extension of the genomic resources available for roses because they now permit the highly reproducible genotyping of rose genomes with approximately 68,000 SNP markers each represented by two probes.…”

Development and validation of the Axiom®Apple480K SNP genotyping array

“…A number of medium-density SNP arrays for plants have been published and extensively used for genetic studies, such as linkage mapping, population structure and linkage disequilibrium (LD) (for a review see Ganal et al, 2014). More recently, Axiom â high-density genotyping arrays have been developed to perform genome-wide association (GWA) studies on strawberry, cotton, rose and soybean (Bassil et al, 2015;Hulse-Kemp et al, 2015;Koning-Boucoiran et al, 2015;Lee et al, 2015). Such genotyping tools are now starting to become available also for apple, and we believe this will boost GWA studies in this species.…”

Genetic mapping in polyploids

“…The expressed sequence tags (ESTs) from which the WagRhSNP 68k Axiom SNP array markers were derived were used in a BLASTn search against the woodland strawberry genome assembly (Fragaria vesca v2.0.a1 pseudomolecules (downloaded on 19/09/2016 from http://www.rosaceae.org)) with 'N' used at the SNP position, as provided in Supplementary Table 2 of Koning-Boucoiran et al (2015). An E-value threshold of 1x10 -20 was used to retain only highly-homologous hits, with multiple hits filtered out to avoid targeting multi-gene families.…”