News
New software for evaluating genetic management in (small) populations
Populations can suffer from high inbreeding rates and associated inbreeding depression, loss of diversity and expression of genetic defects. Centre for Genetic Resources, the Netherlands (CGN) has developed user friendly software to help population managers and researchers.
Retriever and Pointer
Two questions are important for any population: (1) What is the status of my population regarding inbreeding? and (2) what is the effect of measures to decrease inbreeding rates? Retriever extracts data on population structure and inbreeding from studbooks and pedigrees while Pointer simulates populations to indicate what inbreeding levels can be in the future and what the effect is of different forms of genetic management. Input and output is via a graphical user interface (GUI). In Pointer different options for genetic management are available such as sire restrictions, restrictions on inbreeding levels, mean kinships and breeding circles, while genomic data may be generated and analysed as well. Both Retriever and Pointer can analyze populations with subpopulations and different rates of exchange between them.
For all animal species
Although originally devised for dogs, the software can be, and has been, used for any captive population including livestock and zoo populations. The software has been thoroughly tested in student projects on dog, cattle, horse, donkey, sheep and zoo populations. The programs can be run on the average lap‐top of a student. Retriever runs for pedigrees with up to 25,000 individuals within a quarter of an hour. The largest pedigree analyzed with Retriever up to now contained 766,356 individuals spanning 140 years, which took 13 h. Simulations in Pointer of a population with 100 years of breeding repeated 50 times and 500 offspring born per year also finished within a quarter of an hour. The software is now internationally available and can be downloaded for free from:
Literature
1. Windig, J.J.; Hulsegge, I. Retriever and Pointer: software to evaluate inbreeding and genetic management in captive populations. Animals 2021, 11, 1332. https://doi.org/10.3390/ani11051332
2. Windig, J.J.; Verweij, M.J.W.; Oldenbroek, J.K. Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap. J. Anim. Breed. Genet. 2019, 136, 51–62, doi:10.1111/jbg.12371.
3. Kappelhof, J.; Windig, J.J. Controlling inbreeding rate in the European zoo population of Hamadryas baboons Papio hamadryas with a breeding circle. J. Zoo Aquar. Res. 2021, 9, 26–34, doi:10.19227/jzar.v9i1.585.
4. Windig, J.J.; Doekes, H.P. Limits to genetic rescue by outcross in pedigree dogs. J. Anim. Breed. Genet. 2018, 135, 238–248, doi:10.1111/jbg.12330.
5. Windig, J.J.; Oldenbroek, J.K. Genetic management of Dutch golden retriever dogs with a simulation tool J. Anim. Breed. Genet. 2015, 132, 428–440, doi:10.1111/jbg.12149.
6. Windig, J.J.; Eding, H.; Moll, L.; Kaal, L. Effects on inbreeding of different strategies aimed at eliminating scrapie sensitivity alleles in rare sheep breeds in The Netherlands. Anim. Sci. 2004, 79, 11–20.