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SNPscan breeder – a computer program to test genomic tools in breeding programs

Open Access
|Jul 2023

References

  1. Bellmann K, Ahrens HJ (1966) Modellpopulationen in der Selektionstheorie und einige Ergebnisse aus Simulationsstudien. Der Züchter 36(4):172-185 https://doi.org/10.1007/bf02394156
  2. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss V, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633-2635. https://dx.doi.org/10.1093/bioinformatics/btm308
  3. Chamberland V, Robichaud F, Perron M, Gelinas N, Bousquet J, Beaulieu J (2020) Conventional versus genomic selection for white spruce improvement: a comparison of costs and benefits of plantations on Quebec public lands. Tree Genetics & Genomes 16(1):16. https://dx.doi.org/10.1007/s11295-019-1409-7
  4. Chen CJ, Garrick D, Fernando R, Karaman E, Stricker C, Keehan M, Cheng H (2022) XSim version 2: simulation of modern breeding programs. G3-Genes Genomes Genetics 12(4):9. https://dx.doi.org/10.1093/g3journal/jkac032
  5. Durel CE, Bertin P, Kremer A (1996) Relationship between inbreeding depression and inbreeding coefficient in maritime pine (Pinus pinaster). Theoretical and Applied Genetics 92(3-4):347-356. https://doi.org/10.1007/bf00223678
  6. Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4(3):250-255. https://dx.doi.org/10.3835/plantgenome2011.08.0024
  7. Eriksson G, Ekberg I, Clapham D (2013) Genetics applied to forestry: an introduction. Uppsala, Sweden: Department of Plant Biology and Forest Genetics, SLU, ISBN 9157691878
  8. Falconer DS, Mackay TF (1996) Introduction to quantitative genetics. London: Longman London, UK, 464 p, ISBN 0582446791
  9. Gaynor RC, Gorjanc G, Hickey JM (2021) AlphaSimR: an R package for breeding program simulations. G3-Genes Genomes Genetics 11(2):5. https://dx.doi.org/10.1093/g3journal/jkaa017
  10. Huang M, Liu XL, Zhou Y, Summers RM, Zhang ZW (2019) BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions. Gigascience 8(2):12. https://dx.doi.org/10.1093/gigascience/giy154
  11. Liu HM, Tessema BB, Jensen J, Cericola F, Andersen JR, Sorensen AC (2019) ADAM-Plant: A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs. Frontiers in Plant Science 9:15. https://dx.doi.org/10.3389/fpls.2018.01926
  12. Pfenninger M, Reuss F, Kiebler A, Schonnenbeck P, Caliendo C, Gerber S, Cocchiararo B, Reuter S, Bluthgen N, Mody K, Mishra B, Balint M, Thines M, Feld-meyer B (2021) Genomic basis for drought resistance in European beech forests threatened by climate change. Elife 10:17. https://dx.doi.org/10.7554/eLife.65532
  13. Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Berges H, Bodenes C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leple JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A (2016) Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Molecular Ecology Resources 16(1):254-265. https://dx.doi.org/10.1111/1755-0998.12425
  14. R-Core-Team (2022) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. [online]. Available from https://www.R-project.org
  15. Sollars ESA, Harper AL, Kelly LJ, Sambles CM, Ramirez-Gonzalez RH, Swarbreck D, Kaithakottil G, Cooper ED, Uauy C, Havlickova L, Worswick G, Studholme DJ, Zohren J, Salmon DL, Clavijo BJ, Li Y, He ZS, Fellgett A, McKinney LV, Nielsen LR, Douglas GC, Kjaer ED, Downie JA, Boshier D, Lee S, Clark J, Grant M, Bancroft I, Caccamo M, Buggs RJA (2017) Genome sequence and genetic diversity of European ash trees. Nature 541(7636):212-+. https://dx.doi.org/10.1038/nature20786
  16. Sun X, Peng T, Mumm RH (2011) The role and basics of computer simulation in support of critical decisions in plant breeding. Molecular Breeding 28(4):421-436. https://dx.doi.org/10.1007/s11032-011-9630-6
  17. Tahmasbi R, Keller MC (2017) GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data. Bioinformatics 33(2):294-296. https://dx.doi.org/10.1093/bioinformatics/btw606
  18. Wang JB, Zhang ZW (2021) GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction. Genomics Proteomics & Bioinformatics 19(4):629-640. https://dx.doi.org/10.1016/j.gpb.2021.08.005
DOI: https://doi.org/10.2478/sg-2023-0013 | Journal eISSN: 2509-8934 | Journal ISSN: 0037-5349
Language: English
Page range: 126 - 131
Published on: Jul 16, 2023
Published by: Johann Heinrich von Thünen Institute
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2023 Bernd Degen, Niels A. Müller, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.