# ResynPy: a software for selecting pairs of complementary inbred lines to resynthesize valuable heterozygous genotypes

## TL;DR

ResynPy is a Python-based software that helps plant breeders identify complementary inbred lines to recreate valuable hybrid genotypes efficiently.

## Contribution

ResynPy introduces an automated, efficient tool for selecting complementary genotypes in plant breeding using parallelization.

## Key findings

- ResynPy efficiently identifies complementary genotype pairs from selfing populations using molecular markers.
- The software is optimized for speed and low memory usage, making it suitable for large datasets.
- ResynPy is freely available and can be integrated into plant breeding programs to accelerate variety development.

## Abstract

Using cultivars based on a single, partly heterozygous, genotype is one of the bases of agriculture, frequently used in seed-propagated species such as vegetables and field crops (F1 hybrid varieties), and in most fruit trees and ornamentals (clonal varieties) that reproduce vegetatively. Producing two inbred lines that fully or partly reconstruct a given high-value heterozygous individual is now possible with the Resynthesis method, which uses molecular markers to select pairs of complementary genotypes in the F2 and subsequent selfing generations. The objective of this paper was to develop a software to facilitate the selection of such complementary pairs from a large number of segregating genotyped individuals.

The ResynPy tool we developed screens the genotyping data of a segregating population, originating from selfing a top-performing partly heterozygous individual, and detects pairs of individuals that could produce progeny containing individuals nearly identical to the initial elite genotype. Our software selects candidate pairs of individuals in a small timeframe window with a low memory footprint. ResynPy tool could be part of a breeding toolkit to accelerate breeding programs in any plant species of economic importance capable of producing self-pollinated progeny.

ResynPy is a software developed in Python language and is freely available on GitHub (HYPERLINK “https://github.com/kostasgalexiou/ResynPy/tree/main”). ResynPy automates the process of individual selection implemented by the Resynthesis method, in a highly efficient manner through parallelization, allowing to plant breeders for detection of pairs of complementary individuals in a selfing population that could be suitable parents to a plant variety with economically important agronomic traits. With ResynPy, breeders are provided with a fast and easy-to-use tool that will aid them to advance their plant breeding programs.

The online version contains supplementary material available at 10.1186/s12859-025-06279-x.