X-cross/over: a web tool for graph-based estimation of meiotic crossover events in plants

Crossovers are essential for genome stability and genetic diversity, yet in plants they occur infrequently, typically restricted to only one to three per chromosome pair. Genotyping approaches such as SNP arrays or genotyping-by-sequencing (GBS) enable high-resolution detection of crossover frequency, a critical step for elucidating the mechanisms that regulate meiotic recombination and for exploiting it in plant breeding. Despite their widespread use and the availability of highly reproducible marker sets, user-friendly tools for reliable recombination analysis remain scarce.

Here we present X-cross/over, a web-based platform that applies a graph-theoretical algorithm to estimate crossover frequencies from SNP datasets in HapMap format. The platform was evaluated using publicly available barley backcross inbred populations and newly developed wheat doubled haploid lines. Across both datasets, X-cross/over detected crossover events with high accuracy and sensitivity, yielding results consistent with published genotyping and cytological analyses. Importantly, the tool produces outcomes comparable to expert analyses while remaining accessible to users without bioinformatics expertise.

X-cross/over provides a consistent and transparent framework for detecting crossover sites and quantifying their frequency. Implemented in a platform-independent environment, the application is freely available at https://insilicolabdesk.atk.kinin.hu , making it a versatile resource for exploring the genetic and epigenetic regulation of meiotic recombination across plant species.