Identification of SNPs in CYC-B and PSY1 genes responsible for fruit color in tomatore

To identify single nucleotide polymorphisms (SNP) in beta-cyclase (B-CYC) and phytoene synthase (PSY1) genes in 93 tomato genotypes and three commercial cultivars, fragments with a length of 409 and 1000 bp were amplified from the coding regions of these two genes. The amplified fragments of both genes were digested using Tru1I and PstI restriction enzymes to visualize polymorphisms among the studied genotypes, but no polymorphism was observed. Therefore, four individuals from different populations (Urmia, Sardasht, Turkey and Boukan for CYC-B; Urmia, Sardasht, Turkey and Piranshahr for PSY1) were selected and the amplified fragment of the genes were sequenced in these genotypes. After retrieval of the sequenced fragments of each gene, multiple alignment was used for the sequences of the genes to identify SNPs using Clustal omega software. Eight SNPs were identified in the CYC-B gene, 75% of which was transition with a frequency of 50% A/G, 25% T/C, and 25% of which was transversion with a frequency of 12.5% ​​C/A and 12.5% G/C. In PSY1 gene, eight SNPs were also identified in the PSY1 gene, with three and five SNPs in the exon and intron regions, respectively. 62.5% of these SNPs was transition with a frequency of 37.5% A/G, 25% T/C, and 37.5% of them was transversion with a frequency of 25% C/G and 12.5% ​​C/A. The average number of SNPs per 100 bp in the amplified fragment of CYC-B was 0.44, while taht was 1.26 and 0.71 for intron and exon of PSY1, respectively. The SNPs identified in this study can be used in the preparation of genetic maps as well as the identification of functional markers associated with fruit color in tomato.