Breeding Beyond the Model: Genomics and Computation for Non-Traditional Genetic Systems in Crops and Wild Relatives

Computational tools for genetic analysis were developed primarily for diploid model genetic systems, where meiosis follows relatively predictable patterns and can be safely embedded as assumptions within statistical genetic models. This framework enabled rapid advances in major crops through approaches such as haplotyping, quantitative trait locus (QTL) mapping, and genomic selection (GS). However, these assumptions do not hold universally across the diversity of biological and genetic systems.With the increasing accessibility of high-quality reference genome assemblies and affordable genotyping technologies, specialty crops now have unprecedented opportunities to adopt marker-assisted and genomics-informed breeding strategies. Yet, many of these species exhibit genetic architectures and meiotic behaviors that deviate substantially from classical model assumptions. As a result, existing computational tools may perform poorly, yield biased results, or fail entirely when applied to such systems.In some breeding contexts, these exceptional mechanisms may be rare and reasonably ignored without major consequences. In others, however, they represent the primary source of phenotypic variation or the most promising targets for breeding strategies. Distinguishing between these scenarios is critical, yet often computationally and conceptually challenging.This Research Topic aims to highlight non-traditional genetic systems in crops and their wild relatives, evaluate the computational tools currently available to support breeding in these contexts, and identify key methodological gaps. We are particularly interested in manuscripts that address which biological questions can and which cannot be answered with current methods; how non-traditional mechanisms are detected and quantified; their frequency and impact within breeding populations; and how computational approaches can be innovated to better support breeding in genetically complex or non-canonical systems.Submissions should be grounded in clearly defined biological questions and plant breeding relevant outcomes, such as trait mapping accuracy, recombination rate estimation, genotype to phenotype inference, or genomic prediction performance, in crops and their wild relatives. We will also consider studies in non-plant systems when they provide clear and transferable insights for plant genomic inference or plant relevant outcomes, such as pollination related traits that influence crop performance. Contributions may take the form of case studies, methodological assessments, tool development reports, or forward-looking conceptual perspectives.We particularly encourage manuscripts that critically assess the applicability of existing analytical frameworks in practical breeding settings, describe challenges encountered during implementation, and provide balanced evaluations of their strengths and limitations. For manuscripts introducing computational methods or tools, rigorous validation and benchmarking are strongly encouraged. This may include comparisons with established approaches, analyses across multiple datasets or populations, and empirical support where appropriate, such as controlled crosses, replicated field trials, cytogenetic evidence, or high-quality reference assemblies.Examples of non-traditional or underexplored genetic mechanisms include, but are not limited to:- Genome instability: The occurrence, maintenance, and inheritance of whole-chromosome or segmental copy-number variation, and their impact on phenotypic variation, fitness, and breeding outcomes.- Segmental allopolyploidy: Genetic systems in which different chromosomal regions follow distinct inheritance modes.- Meiotic drive: Non-Mendelian transmission resulting from preferential segregation of specific alleles or chromosomes, leading to distorted segregation ratios and biased genetic inference.- Novel translocations and inversions in modern crop breeding: Structural rearrangements arising from hybridization, polyploidization, or selection that alter recombination patterns and challenge single reference-based analyses.- Sex chromosomes and sex determination: Diverse and lineage specific mechanisms of sex determination, including evolving sex chromosomes and environmental influences. Studies in this area are particularly welcome when they directly inform crop performance, fertility, breeding system design, or breeding outcomes.- Chromosome substitution lines: Breeding materials in which entire chromosomes are introgressed into a recipient background, enabling trait dissection but violating assumptions of independent segregation.- Chromosome inheritance in partially fertile intergeneric crosses: Hybrid systems with incomplete or biased chromosome transmission.- Apomixis and parthenogenesis: Clonal reproduction through seeds that bypasses meiosis and fertilization, fundamentally altering expectations for segregation (and pedigree), recombination, and genetic gain. Topic editors: Cristiane Hayumi Taniguti, Moira Jane Sheehan, João Ricardo Bachega Feijó Rosa, Michelle L. Gaynor Source: https://www.frontiersin.org/research-topics/81994/breeding-beyond-the-model-genomics-and-computation-for-non-traditional-genetic-systems-in-crops-and-wild-relatives