Journal Article

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

Eduardo, Iban, Alexiou, Konstantinos G., Arús, Pere

2025

Overview

Background 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. Results 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. Conclusions 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agricultural economics / Agricultural research / Algorithms / Bioinformatics / Biomedical and Life Sciences / Breeding / Chromosomes / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Crops / Cultivars / Economic importance / Flowers & plants / Fruit trees / Genetic aspects / Genomes / Genotype / Genotype & phenotype / Genotypes / Genotyping / Genotyping Techniques / Heterozygosis / Heterozygosity / Heterozygote / Hybridization, Vegetable / Inbreeding / Life Sciences / Microarrays / Missing data / Offspring / Parallelization / Parental selection / Plant breeding / Plant Breeding - methods / Plant species / Progeny / Python / Python (Programming language) / Resynthesis / Software / Statistical software / Toolkits