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Publications

This page contains publications that are related to the development of MateSel. There is a long history, starting with a desire to integrate different issues in animal breeding into a single decision framework.

Kinghorn, B.P. and Van Eenennaam, A.L. 2019. Fine control of bull allocation to help avoid dystocia. Proc. Assoc. Advmt. Anim. Breed. Genet. 23: 226-229. http://www.aaabg.org/aaabghome/AAABG23papers/55Kinghorn23226.pdf
Kinghorn, B.P., 2018. Accommodating recent contributions under optimal contribution selection. Proceedings of the World Congress on Genetics Applied to Livestock Production, 11: 217 http://www.wcgalp.org/system/files/proceedings/2018/accommodating-recent-contributions-under-optimalcontribution-selection.pdf
Kinghorn, B.P., 2017. Committed matings under mate selection. Proc. Assoc. Advmt. Anim. Breed. Genet. 22: 277-280. http://agbu.une.edu.au/AAABG%202017/63Kinghorn22277.pdf
Kinghorn, B.P., Van Eenennaam, A.L., MacNeil, M.D. 2015. Targeting Multiple End-Uses in Beef Cattle Breeding Programs. Proceedings of the 2015 Applied Reproductive Strategies in Beef Cattle conference, August 17-18, 2015, Davis, CA. https://beefrepro.org/wp-content/uploads/2020/09/17Kinghorn-VanEeen-pg250-257.pdf
Kinghorn, B.P. 2011. An algorithm for efficient constrained mate selection. Genetics Selection Evolution. 43:4. http://www.gsejournal.org/content/43/1/4
Kinghorn, B.P. and Shepherd, R.K. 1999. Mate selection for the tactical implementation of breeding programs. Assoc. Advmt. Anim. Breed. Genet. 13:130-133. http://www.aaabg.org/livestocklibrary/1999/AB99025.pdf
Upperman, L.R., Brian P. Kinghorn, Michael D. MacNeil, Alison L. Van Eenennaam, 2019 Management of lethal recessive alleles in beef cattle through the use of mate selection software. Genetics Selection Evolution, 51(1):36. https://gsejournal.biomedcentral.com/articles/10.1186/s12711-019-0477-3
Li, Y.; Van der Werf, J.H.J.; Kinghorn, B.P. 2001. Optimization of selection for two identified quantitative trait loci. Assoc. Advmt. Anim. Breed. Genet. 14: 265-268. http://www.aaabg.org/livestocklibrary/2001/ab01061.pdf

Tests of performance and key implementations

Section titled “Tests of performance and key implementations”
Cowling,W.A.; Castro-Urrea, F.A.; Stefanova, K.T.; Li, L.; Banks, R.G.; Saradadevi, R.; Sass, O.; Kinghorn, B.P.; Siddique, K.H.M. Optimal contribution selection improves the rate of genetic gain in grain yield and yield stability in spring canola in Australia and Canada. Plants 2023, 12, 383. https://doi.org/10.3390/plants12020383
Saradadevi, R., Mukankusi, C., Li, L., Amongi, W., Mbiu, J. P., Raatz, B., Ariza, D., Beebe, S., Varshney, R. K, Huttner, E., Kinghorn, B., Banks, R., Rubyogo, J. C., Siddique, K. H. M., & Cowling, W. A., 2021. Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa. Plant Genome. 2021;e20156. https://doi.org/10.1002/tpg2.20156
Kinghorn, B.P. Kinghorn A.J. 2021. Management of inbreeding and coancestry to target short-term and long-term genetic gains. Proc. Assoc. Advmt. Anim. Breed. Genet. 24: 191-194. https://www.youtube.com/watch?v=NcfFpQ1c3L8
Clare Mukankusi, Wallace A. Cowling, Kadambot K.M. Siddique, Li Li, Brian Kinghorn, Jean Claude Rubyogo (2020) Diversity Breeding Program on Common Bean (Phaseolus vulgaris L.) Targeting Rapid Cooking and Iron and Zinc Biofortification. (Multidisciplinary Digital Publishing Institute) Proceedings 2019, 36, 194; doi:10.3390/proceedings2019036194. https://www.mdpi.com/2504-3900/36/1/194
Cowling, W.A., Li Li, Kadambot H. M. Siddique, Robert G. Banks, Brian P. Kinghorn, 2018. Modeling crop breeding for global food security during climate change. Food Energy Secur. https://onlinelibrary.wiley.com/doi/full/10.1002/fes3.157
Suontama, M., B.P. Kinghorn, W.A. Cowling and H.S. Dungey, 2018. Tactical desired gains for control of red needle cast in radiata pine under optimal contributions selection. Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. 11: 375 http://www.wcgalp.org/system/files/proceedings/2018/tactical-desired-gains-control-red-needle-castradiata-pine-under-optimal-contributions-selection.pdf
Cowling, W.A., L. Li, K.H.M. Siddique, M. Henryon, P. Berg, R.G. Banks and B.P. Kinghorn, 2017. Evolving gene banks: improving diverse populations of crop and exotic germplasm with optimal contribution selection. Journal of Experimental Botany 68, 1927–1939. https://academic.oup.com/jxb/article/68/8/1927/2457456

From MateSel users (Research and/or making design and breeding decisions)

Section titled “From MateSel users (Research and/or making design and breeding decisions)”
Trevor D. Walker, Cooperative Tree Improvement Program. 2021 Coastal 5th‐Cycle Candidate Selection Analysis. January 15, 2021. https://matesel.com/content/documentation/ ncsu_tree_improvement_program_2021_candidate_selection_a nalysis.pdf
Varshney, R.K., Roorkiwal, M., Sun, S. et al. A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature (2021). https://www.nature.com/articles/s41586-021-04066-1
Walkom, S.F., K.A. Donoghue, P.F. Arthur, S.A. Clark and B.J. Walmsley. 2021. Using Matesel to aid sire allocation in genomic reference populations – southern multi-breed an example. Proc. Assoc. Advmt. Anim. Breed. Genet. 24: 419-422
Martin, S.J. and T. Granleese, 2021. MerinoLink/UNE DNA Stimulation Project: Doubling the rate of genetic gain – Where are we after 4 years? Proc. Assoc. Advmt. Anim. Breed. Genet. 24: 476-479

These publications aimed to integrate different issues (initially selection, crossing and costs) into a single decision framework.

Kinghorn, B.P. 1980. A model for the optimisation of genetic improvement by the introduction of novel breeds into a native population. J. Anim. Breed. Genet. 97, 95-100. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1439-0388.1980.tb00915.x
Kinghorn, B.P. 1982. Genetic effects in crossbreeding. II Multibreed selection indices. J. Anim. Breed. Genet. 99, 315-320. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1439-0388.1982.tb00390.x
Kinghorn, B.P. 1983. Genetic effects in crossbreeding. IV A simulation study on global selection of sires for an open population. J. Anim. Breed. Genet. 100, 223-237. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1439-0388.1983.tb00728.x
Kinghorn, B.P. 1984. A single approach to genetic improvement which exploits both selection and crossbreeding effects. Proc. 2nd World Congress on Sheep and Beef Cattle Breeding. pp 473-482.
Kinghorn, B.P. 1986. Mating plans for selection across breeds. Proc. 3rd World Congress on Genetics Applied to Livestock Production. Nebraska, July 1986. Vol XII, 233-244. https://www.cabidigitallibrary.org/doi/full/10.5555/19860199119 [GENUP module MATE is based on this method.]
Kinghorn, B.P. 1987. On computing strategies for mate allocation. J. Anim. Breed. Genet. 104, 12-22. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1439-0388.1987.tb00104.x
Kinghorn, B.P. 1982. Multibreed selection indices for dairy cattle. European Association of Animal Production. (Leningrad) 33, 8pp https://rdcu.be/cmgFM
Kinghorn, B.P. 1989. Exploiting the total genetic resource in beef cattle. Proceedings of Beef Breeding Workshop, South Australian Department of Agriculture, 23-26 October 1989. Paper 11. [This led to the name Total Genetic Resource Management in 1998, with thanks to Robert Banks for “Management” rather than “Exploitation”.].
Klieve, H.M., Kinghorn, B.P. and Barwick, S.A. 1994. The joint regulation of genetic gain and inbreeding under mate selection. J. Anim. Breed. Genet. 111:81-88.
Kinghorn, B.P. 1998. Mate selection by groups. J. Dairy Science. 81:55-63.
Piyasatian, N. and Kinghorn, B.P. 2003. Balancing genetic diversity, genetic merit and population viability in conservation programs. Journal of Animal Breeding and Genetics. 120: 137-149. https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1439-0388.2003.00383.xx
Li, Yongjun, Van der Werf, J.H.J. and Kinghorn, B.P. 2006 Optimisation of a crossing system using mate selection. Genetics, Selection, Evolution. 38:147-165.
Carvalheiro, R., S.A. Queiroz and B.P. Kinghorn, 2010. Optimum contribution selection using differential evolution. Revista Brasileira de Zootecnia. 39:1429-1436. http://www.scielo.br/scielo.php?pid=S1516- 35982010000700005&script=sci_arttext
Kinghorn, B.P. 2012 The use of genomics in the management of livestock. Animal Production Science. 52:78-91. http://www.publish.csiro.au/?paper=AN11092 [This gives the best description of Total Resource Management – sort of Matesel for the production system.]
Clark, S.A., B .P. Kinghorn, J.M. Hickey, J.H.J.van der Werf. 2013. The effect of genomic information on optimal selection in livestock breeding programs. Genet. Sel. Evol. 45:44
Kinghorn, B.P. 1993. Mate selection for the design of breeding programs. In: Design of Livestock Breeding Programs. H-U. Graser editor. AGBU, University of New England. ISBN 0 86389 066 1. Pages 165-170.
Kinghorn, B.P. 1999. Total Resource Management: Tactical optimisation of vertically integrated animal production systems. In: The application of artificial intelligence, optimisation and Bayesian methods in agriculture. Eds. Abbass, H. A. and Towsey, M. Queensland University of Technology. ISBN 1 86435 463 1. Pages 95 - 100.
Vagg, R.D., Meszaros, S.A. and Kinghorn, B.P. 1999. Delivering the power of artificial intelligence to the practitioner: a client/server solution to a complex optimisation problem. In: The application of artificial intelligence, optimisation and Bayesian methods in agriculture. Eds. Abbass, H. A. and Towsey, M. Queensland University of Technology. ISBN 1 86435 463 1. Pages 153 - 162.
Kinghorn, B.P. 2000. The tactical approach to implementing breeding programs. Chapter 22 in “Animal Breeding – Use of New Technologies”, Kinghorn, B.P., Van der Werf, J.H.J. and Ryan, M. (eds.). The Post Graduate Foundation in Veterinarian Science of the University of Sydney. ISBN 0 646 38713 8. Pages 291- 308.
Kinghorn. B.P. 2005. Mating Systems. In Encyclopedia of Animal Science. Edited by W. G. Pond and A.W. Bell. CRC Press 2005. Pages 615-621.
Kinghorn B. P., R. Banks, C. Gondro, V. D. Kremer, S. A. Meszaros, S. Newman, R. K. Shepherd, R. D. Vagg and J. H. J. van der Werf (2008). Strategies to exploit genetic variation while maintaining diversity. In: Adaptation and fitness in animal populations. J. H. J. van der Werf, R. Frankham, H. -U. Graser and C. Gondro. Berlin, Springer. Pages 191-200.
Kinghorn. B.P. 2010. Mating Systems. In Encyclopedia of Animal Science.2nd Edition. Edited by W. G. Pond and A.W. Bell. Taylor and Francis. Pages 744-747. http://www.informaworld.com/10.1081/E-EAS2- 120045691
Kinghorn, B.P. and Shepherd, R.K. 1994. A tactical approach to breeding for information-rich designs. 5th World Congress on Genetics Applied to Livestock Production. Guelph, 7 - 12 August 1994. 18: 255-261.
Kinghorn, B.P. 1998. Managing genetic change under operational and cost constraints. 36th National Congress of the South African Association of Animal Science. University of Stellenbosch 5-8 April. pp 9- 16.
Kinghorn, B.P. 1999. The tactical approach to design and implementation of beef breeding programs. World Gelbvieh Conference, 26-30 March 1999, Sydney. Pages 35-41.
Kinghorn, B.P. 2000. Tactical implementation of beef cattle breeding programs. 3rd National Symposium on Animal Breeding. Belo Horizonte, Brazil. 5-8 June 2000. 8 pages.
Kinghorn, B.P.; Meszaros S.A.; Vagg, R.D. 2002: Dynamic tactical decision systems for animal breeding. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production. 33: 179-186. [CDROM communication n° 23-07. ISBN 2-7380-1052-0]
Newman, S., V. D. Kremer and B.P. Kinghorn 2009 Mate Selection Strategies - Balancing Genetic Gain and Diversity in Livestock Improvement Programs. 58th Annual National Breeders Roundtable. St Louis Missouri, 7-8 May 2009.
Shepherd, R.K. and Kinghorn, B.P. 1998. A tactical approach to the design of crossbreeding programs. 6th World Congress on Genetics Applied to Livestock Production. Armidale, 11-16 January, 1998. 25: 431-438
Kinghorn, B.P. 2011. Automated mate selection analyses. Assoc. Advmt. Anim. Breed. Genet. 19:15-22.
Grundy, B., Kinghorn, B.P., Villanueva, B., and Woolliams J.A. 1998. A breeding programme for in-situ genetic conservation of livestock. In: The potential role of rare livestock breeds in the UK farming systems. Appleby Castle, Appleby, Cumbria, 1 – 2 December 1997. British Society of Animal Science, Meeting and Workshop Publication No. 41.
Hayes, B.J., Shepherd R.K., Newman S. and Kinghorn B.P. 1998. A tactical approach to improving long term response in across breed mating plans. 6th World Congress on Genetics Applied to Livestock Production. Armidale, 11-16 January, 1998. 25:439-442.
Kinghorn, B.P., Shepherd, R.K. and Woolliams, J.L. 1999. An index of EBV, parental coancestry and progeny inbreeding to help maximise genetic gains. Assoc. Advmt. Anim. Breed. Genet. 13:412-415.
Shepherd, R.K. and Kinghorn, B.P. 1999. Algorithms for mate selection. Assoc. Advmt. Anim. Breed. Genet. 13:126-129.
Chaiwong, N. and Kinghorn, B.P. 1999. Use of genetic markers to aid conservation decisions for groups of rare domestic breeds. Assoc. Advmt. Anim. Breed. Genet. 13:365-368.
Banks, R.G., Ball, A.J. and Kinghorn, B.P. 1999. Total Genetic Resource Management - application in the breeding industries. Assoc. Advmt. Anim. Breed. Genet. 13:134-137.
Shepherd, R.K. and Kinghorn, B.P. 2001. Designing algorithms for mate selection when major genes or QTL are important. Assoc. Advmt. Anim. Breed. Genet. 14: 377-380.
Kinghorn, B.P.; Meszaros, S.A. and Vagg, R.D. 2001. Progeny Explorer - desired gains in progeny based on EBVs of current candidates. Assoc. Advmt. Anim. Breed. Genet. 14: 449-452.
Upton, W.H.; Meszaros, S.A.; Barwick, S.A. and Kinghorn, B.P. 2001. Mate allocation in beef cattle herds. Assoc. Advmt. Anim. Breed. Genet. 14: 457-460. http://www.aaabg.org/livestocklibrary/2001/ab01109.pdf
Y. Li, J. H. J. van der Werf and Kinghorn, B.P. 2002. Mate selection in parental lines to exploit known dominant QTL in crosses. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production. 33:191-194. [CD-ROM communication n° 23-09. ISBN 2-7380-1052-0]
Newman, S., Kremer, V. and Kinghorn, B. 2006. Managing Selection and Diversity in a Breeding Program. Proceedings of the US National Swine Improvement Federation, Nashville, 7-8 Dec. 2006. http://www.nsif.com/Conferences/2006/contents.html
Kremer, V. D., S. Newman, B.P. Kinghorn, P. W. Knap, E. R. Wilson. 2009. Strategic versus tactical management of pig genetics. European Association of Animal Production, Barcelona August 2009. Page 131.
Roberto Carvalheiro, Brian Kinghorn, Sandra Aidar de Queiroz 2009. Seleção de Acasalamentos Considerando Diferentes Funções Objetivo. 46a Reuniao Annual da Sociedade Brasileira de Zootecnia, Maringa, PR-UEM, 14-17 de julho de 2009.
Carvalheiro, R., B.P. Kinghorn and S.A. Queiroz. 2010. Mate Selection accounting for connectedness. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production. Paper 0275.
Kremer, V.D., S. Newman, E.R. Wilson and B.P. Kinghorn. 2010. Mate Selection for sustained genetic improvement in small populations. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production. Paper 0536.
Newman, S., Kinghorn, B.P. and Kremer, V. 2010. Mate Selection in Pigs: A Genetic Match.com. Pig genetics workshop notes. 2010, University of New England, Armidale, NSW. Pages 9-15 http://agbu.une.edu.au/pig_genetics/pdf/2010/P02-Scott-Newman-Mate%20selection.pdf
Van Eenennaam, A. L. and Kinghorn, B.P. 2014. Use of mate selection software to manage lethal recessive conditions in livestock populations. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. Paper 408, https://www.asas.org/docs/default-source/wcgalp-posters/408_paper_9819_manuscript_1027_0.pdf?sfvrsn=4b887dd1_2
Upperman, L, Brian Kinghorn, Michael MacNeil, Alison Van Eenennaam, 2018. Management of lethal recessive alleles while optimizing genetic gain in beef cattle. Proceedings of the World Congress on Genetics Applied to Livestock Production, 11: 701 https://www.asas.org/docs/default-source/western-section/asasws_western_book_060217.pdf?sfvrsn=e72946d1_0%EF%BB%BF#page=133