Adding a list of refs related to genetic trends, part method, and use cases

[gregorgorjanc]

Adding a list of refs related to genetic trends, part method, and use cases

[david20011999]

Here you have ;)

Genetic trends development:

• Henderson et al., 1959 https://doi.org/10.2307/2527669 It describes a way of handling biases due to culling, which was a challenging issue in animal breeding research, thus improving the reliability of genetic trend estimates over time.
• Blair and Pollark, 1984. https://doi.org/10.2527/jas1984.584878x A selection experiment with a control population was performed and the breeding values of the selected population were used to obtain the genetic trend. Fixed effects of both populations were compared to avoid bias.
• Sorensen and Kennedy, 1984 https://doi.org/10.2527/jas1984.5851097x It proposes a Bayesian method of the mixed model that allows calculating genetic trends (and estimates in general) avoiding possible biases by incorporating fixed and random effects

Partitioning method

• Woolliams, Bijma and Villanueva 1999 https://doi.org/10.1093/genetics/153.2.1009 It describes the flow of the genes through the pedigree by decomposing pedigree relationship matrix
• García-Cortés, Marínez-Ávila and Toro 2008 https://doi.org/10.1017/S175173110800205X A partition of the genetic trend in multiple grups of individuals using Woolliams, Bijma and Villanueva 1999 propieties.

Partitioning method extensions

• Škorput et al. 2015 https://doi.org/10.1017/S1751731115001056 They developed a multi-trait and Bayesian approach of the partitioning method.
• Obšteter et al. 2021 https://doi.org/10.1186/s12711-021-00600-x Development of a software (AlphaPartR) to apply the partitioning method.
• Oliveira et al. 2023 https://doi.org/10.1186/s12711-023-00804-3 Decomposition of the genetic trend in genetic mean and variance.
• López-Carbonell et al. 2024 https://doi.org/10.1111/jbg.12918 Development of a software to apply the method from a Bayesian approach.

Aplication of the partitioning method

• Špehar et al. 2011. Agriculturae Conspectus Scientificus, Vol 76, No 4 Application in Simmental Cattle.
• Škorput and Lokovic 2018 https://doi.org/10.5513/JCEA01/19.3.2130 Application in pigs daily gain.
• Nagy et al. 2012 Acta Agriculturae Slovenica, Volume 100, Issue SUPPL.3, Pages 175 - 179 Application in pigs.
• Antonios et al. 2023 https://doi.org/10.1111/jbg.12918 Aplication (AlphaPartR) in dairy sheep.
• Abdollahi-Arpanahi et al. 2023 https://doi.org/10.1186/s12711-021-00683-6 Application (AlphaPartR) in pigs and comparison of results when genomic information is included.
• Obšteter et al. 2021 https://doi.org/10.3168/jds.2022-23132 Application (AlphaPartR) in multiple scenarios of realistic cattle breeding program simulations.
• Škorput et al. 2015 https://doi.org/10.1017/S1751731115001056 Application in pigs.
• Pardo et al. 2023 https://doi.org/10.1111/jbg.12766 Application (AlphaPartR) in Holstein population.
• López-Carbonell et al. 2024 https://doi.org/10.1111/jbg.12918 Application in beef cattle.

[gregorgorjanc]

@david20011999 thanks! Have used some of your suggestions;)

[alegarra]

The notion that one could get trends from BLUOP analysis was not that obvious. See http://www.jstor.org/stable/2529955 who says `Recentlythe BLUP method has been taken to its logical conclusion and Hintz, Everett andVanVleck(1978)have given estimatesof genetic trend using BLUP predictors of bulls and cows. Van Vleck (1977) presents these results, plotting genetic merit for cows against year of first calving.I find it difficult to interpret such graphs because the changes in genetic merit over time are partly due to changes in selection pressure over time.One possibility, by analogy with selection experiments is to plot genetic merit against selection differential. This might make it easier to interpret changes in genetic merit over time."

A good example of partition of genetic trend with Bayesian accounting of incertitude and UPGs: https://www.sciencedirect.com/science/article/pii/S0022030296766043