Opportunities for the use of identity-by-descent information in fruit crops

Identity-by-descent (IBD) information offers opportunities for breeding. The precise tracing of common chromosome segments among individuals enables in-depth insight into the available and exploited genetic diversity, the de novo dissection of trait genetics governed by a few to several polymorphic genes, the validation of historic QTLs, and the unraveling of genetic processes underlying breeding. Clonally propagated crops, including many fruit crops, especially have unique opportunities for IBD-based studies, as many pedigree connections exist across breeding material, and because recent and historically important cultivars and breeding parents are often still available for both genotyping and phenotyping. Pedigree based analyses (PBA) approaches exploit IBD information among multiple full-sib families of in and outbreeding species that are connected by genotyped pedigrees. Their use started 20 years ago and four international projects (HiDRAS, FruitBreedomics, RosBREED 1 & 2) facilitated the development of software tools and proof-of-concept analyses. These projects boosted worldwide collaborative efforts on genetic diversity, pedigree reconstruction, unraveling traits genetics, evaluation of the performance and transferability of predictive genetic markers, and the creation of SNP genotyping arrays. This resulted in the integration of PBA by several ongoing breeding programs and research groups as well as over 14 PhDs, 55 scientific publications, and various software tools. Despite the progress made, a few bottlenecks hamper the future use of IBD information and its spread to a wider public. These involve the need for new and improved bioinformatic tools for integration of IBD and Identity-By-State information in the validation of QTLs within breeding programs, germplasm analysis, data curation, imputation and phasing, accepting data from various genotyping platforms including whole-genome resequencing, and publicly available databases. With this manuscript, we wish to create a common starting point for discussions, collaborations, and funding. Hereto, we provide an overview of current opportunities as well as some of the urgent needs