Identification of SNPs in Pectin Esterase 1 (PE1) and Polygalacturonase (PG) Genes of Tomato

Tomato (Solanum lycopersicum L.) is one of the most important crops belonging to the Solanaceae family. The fruit fleshiness is one of the important traits affecting the quality of tomato fruit which quantitatively inherited. Pectin esterase 1 (PE1) and polygalacturonase (PG) are two important genes involved in fruit fleshiness of tomato. Given the important role of these genes in tomato fruit quality, the identification of single nucleotide polymorphisms (SNPs) in the coding regions of these genes may be necessary to produce functional markers associated with fruit firmness.

In this study, 96 genotypes from 12 populations collected from different regions of West Azerbaijan Province (Iran) and Turkey were grown in the research greenhouse of the Faculty of Agriculture, Urmia University. To identify SNPs in PE1 and PG genes, specific primers were designed using FastPCR software to amplify fragments of coding regions of these genes in 96 tomato genotypes. Pst1 and TruI enzymes were used to digest the amplified fragments of the two genes. Due to the lack of polymorphisms in the digested patterns of the enzymes used, four individuals from different populations were selected and their amplified fragments were purified and sequenced. After the retrieval of the sequenced fragments, SNPs were identified using multiple alignments of the sequences of the each gene using Clustal Omega.

Four SNPs were identified in PE1, of which 75% was transition with a frequency of 50% A/G, 25% T/C, and 25% of the mutations were transversion (C/A). In PG gene, six SNPs were identified, 66.7% of which was transition with a frequency of 33.3% A/G and 33.3% T/C, while 32.3% of mutations was transversion with a frequency of 16.16 16% T/A and 16.16% G/C.

In general, the results of the present study showed that the mean number of SNPs per 100 bp of exons of PE1 and PG is 1.22 and 0.41, respectively. Also, the frequency of SNPs in PG gene was less than that of PE1. The low number of SNPs observed in the exons of both genes indicates the conserved status of the coding regions of these genes during tomato evolution. Also, identified SNPs in the current investigation could be used in tomato breeding programs for production of functional markers associated with fruit firmness.