Comparative transcriptome analysis of vase life and carnation type in Dianthus caryophyllus L.

Abstract

Vase life (VL) and storage are the main breeding objectives in carnations due to their direct influence on consumer satisfaction and the transportability around the world. Molecular markers in carnation are available for different traits but not so far for VL, especially not SNP-based markers (single nucleotide polymorphism). Therefore, bulked segregant analysis (BSA) was introduced in carnation for the first time. 500 genotypes were phenotyped for the trait VL, contrasting bulks were generated and used for transcription sequencing with a combination of RNA-Seq and MACE (massive analysis of cDNA ends). Gene ontology (GO) terms were used for comparative analysis of annoted transcripts by comparing bulks with short and long VL. Differential expression (DE) of transcripts between the bulks with short and long VL was detected only by a higher expression of transcripts in the GO terms in the bulk with short VL. By literature review, many DE transcripts attributable to VL were identified. Little is known about the molecular differences between the carnation types standard and mini. The comparison of carnation types showed more DE transcripts as compared to the analysis of VL. Potential SNP markers were selected, but they are usable only for one carnation type, which indicates that the markers have to be established separately for the carnation types standard or mini.