GCCVision: An integrated toolkit for calculating and visualizing parental genome contribution in breeding populations.

Enhui Shen, Yifan Yu, Xiaoya Ma, Zhicheng Shen, Yuxuan Ye

Abstract read

In one paragraph

Article in iScience, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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4 · The record

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5 · Who and what money

Authors and funding

5 authors.

Enhui ShenInstitute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.

Yifan YuState Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.

Xiaoya MaState Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.

Zhicheng ShenState Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.

Yuxuan YeState Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Tracking parental genome contributions in segregating populations is crucial for accelerating genetic gain in plant breeding. We introduce GCCVision (Genome Contribution Calculator and Visualizer), an integrated bioinformatics toolkit to simplify this process. GCCVision uses an efficient Python-based backend and a user-friendly web-based frontend to analyze Variant Call Format (VCF) files from biparental crosses. The software identifies informative single-nucleotide polymorphisms (SNPs), calculates parental contribution rates, and generates clear, customizable graphical genotype maps where chromosome segments are color-coded by parental origin. By providing clear visualizations of genomic composition, GCCVision assists breeders in selection decisions for backcrossing, F

Indexed as

biocomputational methodgenomic analysisplant bioinformaticsplant geneticstechniques in genetics

Identifiers

PMID41488786

DOI10.1016/j.isci.2025.114286

PMCPMC12757579

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.