Identification of Differentially Expressed Genes in Wheat NILs in Response to Leaf 1 Rust Infection using In Silico Analysis

Abstract

In this study, the molecular basis of leaf rust resistance was investigated by examining the differential gene expression of wheat cultivar Thatcher, both with and without a leaf rust resistance gene, in response to rust infection. unigenes/ESTs databases were utilized belonging to three near-isogenic lines (NILs) of Thatcher, including Thatcher, Thatcher + Lr10, and Thatcher + Lr1, to identify differentially expressed unigenes (DEUs) in response to leaf rust. Sixty-eight DEUs were identified using a data mining tool called Digital Differential Display (DDD). Among these DEUs were specific unigenes associated with Lr1 and/or Lr10-mediated resistance, as well as unigenes expressed exclusively in compatible interactions. Our results suggest that photosynthesis, lignin, and antifungal proteins play a role in the leaf rust resistance mechanism, as indicated by the overexpression of Ribulose-1,5-bisphosphate carboxylase/oxygenase, caffeic acid O-methyltransferase, and Glutathione S-transferase unigenes, respectively. Our findings demonstrate both common and distinctive genetic pathways involved in rust resistance in the Lr1 and Lr10 NILs. The expression of most DEUs was found to be high in leaves, moderate in sheath, stem, and inflorescence, and low in seed, root, flower, crown, callus, and cell culture, indicating their role in leaf rust. Using high-throughput microarray gene expression data, a subset of DEUs was validated, and as a result, eleven unigenes were mapped to deletion bins on individual wheat chromosomes. These key genes may be used as molecular markers for genome editing, which could facilitate the development of leaf rust-resistant wheat cultivars.