Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.Subject terms: Plant genetics, Plant breeding, Agricultural genetics, Quantitative trait

Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a platform for research and development. In this review, we examine three themes covering new developments in crop MPP research: (1) we survey the rapidly expanding variety of crop MPPs, explaining how differences in their design and construction affect their power and precision in mapping quantitative trait loci (QTL), on which we provide a brief primer. (2) We review the use of genomic technologies in MPPs, which have proven particularly suitable for gathering dense genomic information across large populations. We make general recommendations for collecting genotypic resources in MPPs. (3) We discuss successful applications of MPPs, particularly where they have been used for breeding and pre-breeding. This includes the identification of QTL, the application of genomic prediction to MPPs, and the direct use of MPP lines as germplasm for varietal release or pre-breeding. These recent developments have shown the potential of MPPs for crop improvement.