Research Projects

The tomato (Solanum lycopersicum) is one of the important vegetable crops in India. It is next to potato in production and consumption in our country. Moreover, it is an excellent source of several vitamins and nutrients, which are available at an affordable cost to the common man. The commercial and nutritional importance of the tomato necessitates improvement of the cultivated varieties by a combination of traditional breeding with recent innovations in biotechnology. As the tomato genome sequencing is now completed, efforts are currently being made for functional annotation of the genome. The major challenge in front of crop scientists today is to use the sequence information to develop improved varieties of plants that can withstand the changing climate as well as meet the demands of the ever-increasing population. This also requires the development of tools that can use the available genome sequence information to understand gene function. From an agronomical perspective, the tomato fruit nutritional composition and its shelf life are important traits. Tomato fruits are enriched in lycopene and -carotene, which are considered nutraceuticals and believed to play a vital role in preventing diseases like prostate cancer and blindness, respectively. In addition, the %Brix content, indicative of soluble solid content (SSC) of tomato fruits, is also a highly desirable trait due to demand from the processing industry for making paste, ketchup, juice, etc. In this context, we have been working on two tomato mutants, ahprov7 (Hoffmann`s anthocyanin-less, in Money Maker background; Dhanya AJ PhD thesis, University of Hyderabad, 2025) and Ip (Intense pigment, in VF145 background; Kilambi et al., 2013), for several years, as both the mutants have high carotenoid content in their ripe fruits. In addition, Ip fruits have high %Brix content. The Ip mutant is photomorphogenic at the seedling stage and is shown to be dominant in amplifying phytochrome signalling. However, the candidate genes responsible for these traits are unknown. The ahprov7 has an anthocyanin-less phenotype throughout its life cycle and has been linked to a mutation in bHLH150, which is not linked to carotenoid content (Dhanya AJ, 2025). Whole genome sequencing of ahprov7 and Ip revealed several candidate genes; however, narrowing down to a single candidate gene in the F2 population of both mutants did not yield any lines mutated in a single gene in either homozygous or heterozygous conditions due to the small population size used (Dhanya AJ 2025; unpublished data). In this proposal, we aim to identify the candidate genes responsible for the high carotenoid content in both ahprov7 and Ip, as well as for the high %Brix content in Ip fruits by using a Mutmap/mapping by sequencing approach (Garcia et al., 2016). Here, we intend to grow a large BC1F2 population and collect the ripe fruits from both crosses, and perform carotenoid profiling and %Brix analysis. We then group the DNA from the F2 segregating lines showing similar carotenoid content and %Brix (high/low bulks) and subject it to sequencing and data analysis using the Mutmap pipeline. Once we identify the candidate genes, we shall validate them using CRISPR/Cas9-based gene editing. The functional characterization of the candidate genes will be carried out by combining genetic, molecular, and biochemical approaches in the knock-out lines generated in this project. The tools for developing and characterizing these lines are already available in the PI`s laboratory at the Repository of Tomato Genomics Resources (RTGR), University of Hyderabad.