Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies

Abstract

BackgroundRosa hybrida is a valuable ornamental, food and medicinal crop worldwide, but with relatively limited molecular marker resources, especially for flower-specific markers. In this study, we performed genomic and floral transcriptomic sequencing of modern rose. We obtained comprehensive nucleotide information, from which numerous potential simple sequence repeat (SSR) markers were identified but were found to have high rates of amplification failure and PCR product redundancy.ResultsWe applied a filtering strategy for BLAST analysis with the assembled genomic sequence and identified 124,591 genomic and 2,292 EST markers with unique annealing sites. These markers had much greater reliability than those obtained before filtering. Additional BLAST analysis against the transcriptomic sequences uncovered 5225 genomic SSRs associated with 4100 transcripts, 2138 of which were associated with functional genes that were annotated against the non-redundant database. More than 90% of these newly developed molecular markers were polymorphic, based on PCR using a subset of SSRs to analyze tetraploid modern rose accessions, diploid Rosa species and one strawberry accession. The relationships among Rosa species determined by cluster analysis (based on these results) were in agreement with modern rose breeding history, whereas strawberry was isolated in a separate cluster, as expected.ConclusionsOur results provide valuable molecular-genetic tools for rose flower trait improvement, breeding and taxonomy. Importantly, we describe a reproducible organ-specific strategy for molecular marker development and selection in plants, which can be applied to other crops.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1322-5) contains supplementary material, which is available to authorized users.

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

“…Potter et al [1] reported that the phylogenetic relationship between Fragaria and Rosa is closer than between Fragaria and Rubus. Qi et al [63] evaluated the SSR primer pairs using in silico PCR and demonstrated that strawberry is the closest to the rose followed by the raspberry. We found an interesting regularity in the size of alleles during cross-species amplification: alleles in Rubus species amplified using Fragaria primers had sizes similar to the expected, while alleles in Fragaria species amplified using Rubus primers were significantly smaller than expected.…”

Development of EST-SSR markers and association mapping with floral traits in Syringa oblata

“…SSR markers, also known as microsatellite markers, are short tandem repeats of one to six nucleotides, which are widely distributed in coding and non-coding regions of the eukaryotic genome [ 18 ]. Over the past years, SSRs were successfully developed in different ornamental plants via data mining, such as Magnolia ashei [ 19 ], Lagerstroemia indica [ 20 ], Paeonia suffruticosa [ 21 ], and Rosa hybrida [ 22 ]. In addition, SSRs have also been widely used in plant genetics and breeding for genetic diversity analysis [ 23 ], cultivar identification [ 24 ], DNA fingerprinting [ 25 ], linkage mapping [ 26 ], and association mapping [ 27 ].…”

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

“…viridulum Baker [27], crataegus Pinnatifida Bunge [28], Acer miaotaiense P. C. Tsoong [29], and Rosa hybrida hort. ex Lavalle [30]. Among the third-generation sequencing platforms, PacBio RS II, which is regarded as the first commercialized third-generation sequencer, is based on single-molecule real-time (SMRT) technology [31].…”