Tomato (Solanum lycopersicum) variety discrimination and hybridization analysis based on the 5S rRNA region

Abstract

The tomato (Solanum lycopersicum) is a major vegetable crop worldwide. To satisfy popular demand, more than 500 tomato varieties have been bred. However, a clear variety identification has not been found. Thorough understanding of the phylogenetic relationship and hybridization information of tomato varieties is very important for further variety breeding. Thus, in this study, we collected 26 tomato varieties and attempted to distinguish them based on the 5S rRNA region, which is widely used in the determination of phylogenetic relations. Sequence analysis of the 5S rRNA region suggested that a large number of nucleotide variations exist among tomato varieties. These variable nucleotide sites were also informative regarding hybridization. Chromas sequencing of Yellow Mountain View and Seuwiteuking varieties indicated three and one variable nucleotide sites in the non-transcribed spacer (NTS) of the 5S rRNA region showing hybridization, respectively. Based on a phylogenetic tree constructed using the 5S rRNA sequences, we observed that 16 tomato varieties were divided into three groups at 95% similarity. Rubiking and Sseommeoking, Lang Selection Procedure and Seuwiteuking, and Acorn Gold and Yellow Mountain View exhibited very high identity with their partners. This work will aid variety authentication and provides a basis for further tomato variety breeding.

Keywords: 5S rRNA region; genetic diversity; phylogenetic relationship; tomato variety; variety discrimination.

Figure 1.

DNA alignment of the 5S rRNA gene sequences of 16 tomato varieties including the partial coding region and the non-transcribed spacer (NTS) region. The nucleotide arrays marked with red frames are the end sites of coding regions. The NTS region begins directly following the end site. Dots mark the deletion of a nucleotide, and short lines indicate that a nucleotide is identical to that of the reference sequence.

Figure 1.

DNA alignment of the 5S rRNA gene sequences of 16 tomato varieties including the partial coding region and the non-transcribed spacer (NTS) region. The nucleotide arrays marked with red frames are the end sites of coding regions. The NTS region begins directly following the end site. Dots mark the deletion of a nucleotide, and short lines indicate that a nucleotide is identical to that of the reference sequence.

Figure 2.

Phylogenetic tree constructed based on the 5S rRNA gene sequences of 16 tomato varieties.

Figure 3.

Hybridization analysis of tomato varieties based on the Chromas sequencing result. Yellow Mountain View (No. 8) and Seuwiteuking (No. 13) were used as examples. Hybridized nucleotide sites are marked with arrows under the Chromas sequencing result, and the nucleotides present and the hybridization ratio are shown below. Hybridized nucleotide sites in Yellow Mountain View sequences (A, B and C); a hybridized nucleotide site in a Seuwiteuking sequence (D).