Discovery and genomic analysis of rust resistance in wheat

Abstract

Deploying resistance (R) genes is vital for protecting wheat against serious diseases such as rust. Along with the availability of widely effective R genes from landraces and wild relatives of bread wheat, identification of molecular markers tightly linked to these genes accelerate wheat breeding for rust resistance. Here I mapped an R gene for each stem, leaf and stripe rust of wheat using RNA sequencing, mutagenesis, resistance gene enrichment, and sequencing and comparative genomics. Sr65, from Indian bread wheat landrace Hango-2 was mapped to chromosome arm 1AS and exhibited resistance against Ug99 and TTRTF, African and European Puccinia graminis f. sp. tritici (causing wheat stem rust) races virulent to most commonly used R genes. RNASeq, MutRenSeq, and pangenome analysis failed to detect any candidate gene but were useful in detecting tightly linked molecular markers. The leaf rust R gene, Lr80, also from Hango-2, displayed resistance to Australian and Indian P. triticina (causing wheat leaf rust) races and was mapped on Chromosome arm 2DS. RNASeq revealed a kinase gene with deletion and SNP changes in the tested loss of function mutants as the candidate and the source for a gene-specific marker for Lr80. The stripe rust R gene, Yr35, introduced into bread wheat from tetraploid wheat species Triticum dicoccoides, conveyed a resistance response against Australian P. striiformis f. sp. tritici (causing wheat stripe rust) races. Comparative analysis of RNASeq and MutRenSeq data from Yr35 carrying wheat lines and the loss of function mutants with Chromosome 6B specific sequences of T. dicoccoides reference predicted a receptor kinase/RGA5-like disease resistance gene as the ideal candidate and the source for a diagnostic marker.KASP_12147, sunCS_265, sunCS_49, and sunCS_Yr35 linked tightly with Sr65, Lr80, and Yr35, respectively, were validated on Australian cereal cultivar panel for rapid breeding of rust resistance wheat lines through marker-assisted selection.