Insilico Identification of Markers for Determinacy in Tomato

Abstract

Tomato is a major vegetable crop that has achieved tremendous popularity over the last century. The market value for the tomato is highly fluctuating because of the season bound yield of the crop and the usage of determinate cultivars. The determinate type of tomatoes is preferred by the farmers for outdoor cultivation because of less maintenance, short duration and easy harvest. However indeterminate tomato cultivars are suitable for greenhouse cultivation and preferred by the food processing industries. Identification of markers for the growth habit determination will be useful to improve the tomato cultivars based on the preference of farmers and consumers. Available Single Nucleotide Polymorphism (SNP) data of six tomato cultivars of both determinate and indeterminate types were compared in the present study. The genome wide SNPs were analysed for SNPs differentiating the determinate and indeterminate nature of the crop. From a list of 1,473,798 SNPs, 986 SNPs were found to be differentiated the varieties compared. The locations of the obtained SNPs were identified and 254 SNPs were present within the transcribed region and the rest were found within the intergenic region. These SNPs were considered for further analysis, with respect to growth habit regulation. From the list of SNPs present in transcribed region, SNPs associated with the genes regulating the growth habit were identified. The SNPs within the intergenic region were analysed for their association with the non-coding RNAs. The results showed that 58 SNPs spread over 15 genes were found to be involved in regulation of growth habit. These SNPs could be validated using determinate and indeterminate cultivars and could be utilized for marker assisted breeding programs favouring growth habit determination.