Development of SSR and InDel markers with the use of next generation sequencing data in groundnut

Groundnut (Arachis hypogaea L.), a member of the Leguminosae family, has economic importance as a source of protein, minerals, and which is used extensively in the food and feed industry. The crop is produced in more than 100 countries in the world and intensive breeding studies are carried out to obtain high yield and quality and also resistance to biotic/abiotic stress factors which are main targets of these studies. Marker assisted selection, which has been successfully applied in groundnut breeding programs in recent years, has greatly increased the speed of breeding and improved the selection efficiency. However, the number of markers developed for use in groundnut breeding programs for different purposes is not at the desired level compared to industrial plants such as soybean and sunflower. In this thesis project, it is aimed to develop InDel (insertion-deletion) and SSR (simple sequence repeat) markers that can be used in groundnut breeding studies. The 25 groundnut genotypes originating from different continents were sequenced with ddRAD-Seq approach and later 62728 loci differing from the reference genome were identified with bionformatic analysis. Among them, 35140 and 27588 regions were defined as deletion and insertion, respectively. In terms of availability in agarose gel, 1013 insertion-deletion sites of 10 bp and above were identified as potential markers, while 24 sites were used for primer design. The developed 3 SSR and 21 InDel markers were tested on genotypes and bands were obtained in the expected regions. It is expected that the developed SSR and InDel markers will contribute to molecular-based groundnut breeding studies.