Utility of BSC-seq and Triti-Map for locating agronomically important genes and regulatory elements in Triticeae species

Triticeae species, including wheat, barley, and rye, are critical for global food security. Triticeae also includes many wild relatives with desirable agronomic traits, and distant hybridizations and introgressions occurred frequently during Triticeae evolution, domestication, and modern breeding. Mapping agronomically important genes in Triticeae is crucial for elucidating their molecular mechanisms and improving crops. However, Triticeae crop genomes are generally large and complex, making the localization of genes or functional elements controlling agronomic traits challenging. Here, we introduce the Bulked Segregant ChIP-seq (BSC-seq) method, which uses ChIP-seq data of pooled samples from segregating populations exhibiting a useful phenotype. This method was designed specifically for Triticeae species. It may detect candidate genes or regulatory elements absent in the reference genomes and decrease the time and labor required for gene mapping in species with large genomes. Furthermore, we developed Triti-Map, which contains a suite of user-friendly computational packages and a web interface integrating multi-omics data from Triticeae species, for the efficient mining of genes or functional elements controlling particular traits. We used BSC-seq and Triti-Map to localize and clarify the evolution of a wheat disease resistance gene that was lacking in the reference genome. Both BSC-seq and Triti-Map may facilitate gene isolations and accelerate Triticeae crop breeding.