Plant noncoding RNAS and comparative analysis of insect tolerance loci

Official URL: https://risc01.sabanciuniv.edu/record=b2711494_(Table of contents)

As the growing world population tremendously increases the demand for food every year, challenging environmental conditions continue to threaten agricultural productivity. While plants try to cope with many abiotic stresses such as drought, salinity, heat, and cold, they also have to cope with many biotic stress factors such as insect pests of plants. Obtaining higher-yielding and more resilient crops thus is a necessity to achieve global food security and sustainability. Advances in genome sequencing techniques over the past 15 years revolutionized the way we perceive genomes and comparative genomics studies enabled the analysis of many conserved and diverged inter/intra-specific genomic features of a wide range of organisms. Within the scope of this thesis, we constructed pangenome miRNomics of Brachypodium using de novo genome assemblies of 54 lineages and presented the conservation levels of microRNA families among lineages and their putative targets to uncover the molecular basis of agronomic traits in different lineages. In the second chapter, we carried out a comparative and evolutionary analysis of coding and non-coding features of 4 insect tolerance loci within wheat among other cereals, barley, rye, rice, and oat, and showed different levels of synteny in homologous insect tolerance loci across Poaceae species. In the third chapter, we have carried out miRNA and lncRNA identification in 3 barley cultivars, aiming to unravel the interaction network of barley mRNA-miRNA-lncRNAs. The results of this thesis will shed a light on future gene cloning and editing studies of monocots for food safety and security.