ChineseFirPedV: a transferable web tool for multi-generational pedigree and kinship visualization and management in forest tree breeding

Abstract

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a major afforestation species in southern China, currently advancing through multi-objective, advanced-generation breeding. As breeding programs progress, maintaining genetic diversity and minimizing inbreeding depression are critical. Traditional pedigree management, which relies primarily on static documentation, is often inefficient, inaccurate, and non-interactive, making it difficult to support data-driven parental selection. To overcome these limitations, we developed ChineseFirPedV, a web-based system for interactive genealogy visualization and kinship management tailored to Chinese fir breeding. Built with Python, the system uses NetworkX for constructing pedigree graphs and Pyvis for dynamic visualization. It integrates both traditional pedigree records and SNP genotyping data from 174 elite Chinese fir individuals to generate both network-based genealogical diagrams and kinship cluster maps. The system offers interactive tools for exploring kinship networks, customizing node attributes, and designing mating strategies. When molecular data are available, the system computes genomic relationship matrices and visualizes them as clustering graphs to highlight relatedness patterns. The integration of pedigree and genomic information enhances accuracy in identifying optimal parental combinations and detecting anomalies or errors in recorded lineage. ChineseFirPedV effectively supports kinship verification, pedigree reconstruction, and breeding value estimation, improving decision-making in advanced-generation breeding. Its modular design allows for scalability and potential adaptation to other long-cycle, complex-genome tree species. This system provides a centralized, digital platform for managing genealogical and molecular data, facilitating more precise and efficient genetic improvement strategies for Chinese fir and other forest trees.

Keywords

Kinship visualization / Chinese fir breeding / Genealogical network diagrams / Information management system / NetworkX and Pyvis

References

[1] Bennett RL, Steinhaus KA, Uhrich SB, O’Sullivan CK, Resta RG, Lochner-Doyle D, Markel DS, Vincent V, Hamanishi J. Recommendations for standardized human pedigree nomenclature. J Genet Couns, 1995, 4(4): 267-279

[2] Berglund RC, Tippets FE (1989) Progress on PRISM, an advanced liquid metal reactor power plant concept for the future. In Proceedings of the 24th Intersociety Energy Conversion Engineering Conference, 5: 2431–2435

[3] Carver T, Cunningham AP, Babb de Villiers C, Lee A, Hartley S, Tischkowitz M, Walter FM, Easton DF, Antoniou AC. Pedigreejs: a web-based graphical pedigree editor. Bioinformatics, 2018, 34(6): 1069-1071

[4] Egan LM, Hofmann RW, Barrett BA, Ghamkhar K, Hoyos-Villegas V. Identification of founding accessions and patterns of relatedness and inbreeding derived from historical pedigree data in a white clover germplasm collection in New Zealand. Crop Sci, 2019, 59(5): 2087-2099

[5] Egan LM, Hofmann RW, Seguin P, Ghamkhar K, Hoyos-Villegas V. Pedigree analysis of pre-breeding efforts in Trifolium spp. germplasm in New Zealand. BMC Genet, 2020, 21(1 104

[6] Hagberg A, Conway D (2020) Networkx: Network analysis with python. URL: https://networkx.github.io

[7] Han YY, Wang KY, Liu ZQ, Pan SH, Zhao XY, Wang SF. Golden seed breeding cloud platform for the management of crop breeding material and genealogical tracking. Comput Electron Agric, 2018, 152: 206-214

[8] Jeong MG, Lee C, Kim JH, Park JS, Choi Y, Kim HJ, Chung YS, Choi HK. SoyPedi: a searchable pedigree-linked web interface for phenotypic data of soybean cultivars. Crop Sci, 2022, 62(6): 2319-2331

[9] Kamada T, Kawai S. An algorithm for drawing general undirected graphs. Inf Process Lett, 1989, 31(1): 7-15

[10] Kinghorn B, Kinghorn S (1994) Pedigree Viewer-a graphical utility for browsing pedigreed data sets. In 5th World Congress on Genetics Applied to Livestock Production, University of Guelph Canada, 22: 85–86

[11] Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.

[12] Mäkinen VP, Parkkonen M, Wessman M, Groop PH, Kanninen T, Kaski K. High-throughput pedigree drawing. Eur J Hum Genet, 2005, 13(8): 987-989

[13] Mulitze DK. AGROBASE/4: a microcomputer database management and analysis system for plant breeding and agronomy. Agron J, 1990, 82(5): 1016-1021

[14] Perrone G, Unpingco J, Lu HM (2020) Network visualizations with Pyvis and VisJS. arXiv preprint arXiv:2006.04951. https://doi.org/10.25080/Majora-342d178e-008

[15] Shaw PD, Graham M, Kennedy J, Milne I, Marshall DF. Helium: visualization of large scale plant pedigrees. BMC Bioinform, 2014, 15(1): 259

[16] Thiele H, Nürnberg P (2005) HaploPainter: a tool for drawing pedigrees with complex haplotypes. Bioinformatics 21(8):1730–1732. https://doi.org/10.1093/bioinformatics/bth488

[17] van Berloo R, Hutten RCB. Peditree: pedigree database analysis and visualization for breeding and science. J Hered, 2005, 96(4): 465-468

[18] VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci, 2008, 91(11): 4414-4423

[19] Velinder M, Lee D, Marth G. Ped_draw: pedigree drawing with ease. BMC Bioinform, 2020, 21(1): 569

[20] Voorrips RE, Bink MCAM, van de Weg WE. Pedimap: software for the visualization of genetic and phenotypic data in pedigrees. J Hered, 2012, 103(6): 903-907

[21] Wu HX, Hallingbäck HR, Sánchez L. Performance of seven tree breeding strategies under conditions of inbreeding depression. G3 (Bethesda), 2016, 6(3): 529-540

[22] Zhao BW, Bian LM, Feng QH, Wu JZ, Zhang XF, Zheng RH, Zheng XY, Yang ZY, Chen ZQ, Wu HX, Shi JS. Development of an advanced-generation multi-objective breeding population for the 4th cycle of Chinese fir (Cunninghamia lanceolata (lamb.) hook.). Forests, 2023, 14(8 1658

[23] Zhao XY, Pan SH, Liu ZQ, Han YY, Zhang Q, Wang KY. Intelligent upgrading of plant breeding: decision support tools in the Golden Seed Breeding Cloud Platform. Comput Electron Agric, 2022, 194 106672

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