Genetic diversity, population structure and enhancing selection efficiency in wheat pre-breeding using the CGIAR mid-density DArTag panel

Abstract Bread wheat ( Triticum aestivum L.) is a vital crop with production demand increasing due to population growth. However, bread wheat is facing challenges, including the emergence of pests and diseases, reduced genetic diversity and climate change. To meet food security, pre-breeding can help to develop varieties by incorporating desirable traits from wild relatives and landraces. Although pre-breeding is crucial, it does not often take full advantage of recent genotyping technologies. The DArTag mid-density wheat panel, developed by CIMMYT as part of the CGIAR initiative, offers a low-cost genotyping solution, but its applicability in pre-breeding programs has not been widely evaluated. This study aims to assess population structure, genetic diversity and genomic selection in a set of 484 pre-breeding bread wheat lines derived from crosses with wild relatives, using the DArTag mid-density wheat panel to investigate the ability of this genotyping approach to validate pedigrees, identify specific trait subsets and detect potential introgressions for targeted selection. Our results demonstrate that the panel captured genetic diversity in the pre-breeding population, identifying seven subpopulations with different genetic compositions; analysis confirmed the existence of private alleles associated with important agronomic traits, highlighting the role of wild relatives, especially Aegilops bicornis and Aegilops ovata , in genetic variation. In addition, the genotyping also facilitates pedigree validation and generates trait-specific sub-populations for phenotyping. The sub-populations and markers found in this work are useful resources that can be effectively used to accelerate wheat improvement, offering new insights into the contribution of wild relatives and landraces to wheat diversity.