scholarly journals AlphaPart - R implementation of the method for partitioning genetic trends

2020 ◽  
Author(s):  
Jana Obšteter ◽  
Justin Holl ◽  
John M. Hickey ◽  
Gregor Gorjanc
Keyword(s):  
Gene Flow ◽  
Open Source ◽  
Open Source Software ◽  
Genetic Gain ◽  
R Package ◽  
Genetic Trend ◽  
Breeding Values ◽  
Breeding Programmes ◽  
Estimated Breeding Values ◽  
Genetic Trends

AbstractBackgroundIn this paper we present the AlphaPart R package, an open-source software that implements a method for partitioning breeding values and genetic trends to identify sources of genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from averaged year of birth estimated breeding values of selection candidates. While sources of the overall genetic gain are generally known, their realised contributions are hard to quantify in complex breeding programmes. The aim of this paper is to present the AlphaPart R package and demonstrate it with a simulated pig breeding example.ResultsThe package includes the main partitioning function AlphaPart, that partitions the breeding values and genetic trends by analyst defined paths, and a set of functions for handling data and results. The package is freely available from CRAN repository at http://CRAN.R-project.org/package=AlphaPart. We demonstrate the use of the package by examining the genetic gain in a pig breeding example, in which the multiplier achieved higher breeding values than the nucleus for traits measured and selected in the multiplier. The partitioning analysis revealed that these higher values depended on the accuracy and intensity of selection in the multiplier and the extent of gene flow from the nucleus. For traits measured only in the nucleus, the multiplier achieved comparable or smaller genetic gain than the nucleus depending on the amount of gene flow.ConclusionsAlphaPart implements a method for partitioning breeding values and genetic trends and provides a useful tool for quantifying the sources of genetic gain in breeding programmes. The use of AlphaPart will help breeders to better understand or improve their breeding programmes.

scholarly journals AlphaPart—R implementation of the method for partitioning genetic trends

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Jana Obšteter ◽  
Justin Holl ◽  
John M. Hickey ◽  
Gregor Gorjanc
Keyword(s):  
Genetic Gain ◽  
R Package ◽  
Breeding Programme ◽  
Genetic Trend ◽  
Breeding Values ◽  
Poultry Breeding ◽  
Breeding Programmes ◽  
Estimated Breeding Values ◽  
The Relationship ◽  
Genetic Trends

Abstract Background In this paper, we present the AlphaPart R package, an open-source implementation of a method for partitioning breeding values and genetic trends to identify the contribution of selection pathways to genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from estimated breeding values averaged by year of birth. While sources of the overall genetic gain are generally known, their realised contributions are hard to quantify in complex breeding programmes. The aim of this paper is to present the AlphaPart R package and demonstrate it with a simulated stylized multi-tier breeding programme mimicking a pig or poultry breeding programme. Results The package includes the main partitioning function AlphaPart, that partitions the breeding values and genetic trends by pre-defined selection paths, and a set of functions for handling data and results. The package is freely available from the CRAN repository at http://CRAN.R-project.org/package=AlphaPart. We demonstrate the use of the package by partitioning the nucleus and multiplier genetic gain of the stylized breeding programme by tier-gender paths. For traits measured and selected in the multiplier, the multiplier selection generated additional genetic gain. By using AlphaPart, we show that the additional genetic gain depends on accuracy and intensity of selection in the multiplier and the extent of gene flow from the nucleus. We have proven that AlphaPart is a valuable tool for understanding the sources of genetic gain in the nucleus and especially the multiplier, and the relationship between the sources and parameters that affect them. Conclusions AlphaPart implements the method for partitioning breeding values and genetic trends and provides a useful tool for quantifying the sources of genetic gain in breeding programmes. The use of AlphaPart will help breeders to improve genetic gain through a better understanding of the key selection points that are driving gains in each trait.

scholarly journals Prevalence and breeding values of elbow dysplasia in the Estrela mountain dog

2013 ◽  
Vol 58 (No. 9) ◽  
pp. 484-490 ◽  
Author(s):  
S. Alves-Pimenta ◽  
B. Colaco ◽  
AM Silvestre ◽  
MM Ginja
Keyword(s):  
Hip Dysplasia ◽  
Mass Selection ◽  
Genetic Trend ◽  
Genetic Progress ◽  
Breeding Values ◽  
Elbow Dysplasia ◽  
Low Mass ◽  
The Mean ◽  
Dog Breed ◽  
Genetic Trends

The aims of this study were to determine the prevalence and heritability of elbow dysplasia in the Estrela mountain dog breed, to investigate genetic trends over the last 20 years (1990–2009) and to evaluate the association of individual records with breeding values. The elbows of 351 Estrela mountain dogs were examined using the flexed mediolateral radiographic view and evaluated using the International Elbow Working Group scoring system. Heritability and breeding values were estimated using a linear model. Elbow Dysplasia was found in 16.5% (59/351) of the dogs; males (27%, 34/127) were more affected than females (11%, 24/224) (P < 0.05). The heritability was very low (0.065) and the genetic trend showed a slight positive slope with an improvement in 2004 and 2005. The mean breeding values in elbow dysplasia grades were different but the overlap among grades was very pronounced. The prevalence and heritability of elbow dysplasia in the breed are thus low. Mass selection using individual phenotypes may not be effective. Elbow dysplasia genetic trends are similar to trends for hip dysplasia and passive hip laxity, so the use of selection against hip dysplasia may also result in genetic progress for elbow dysplasia.  

scholarly journals Analysing global economic costs of invasive alien species with the invacost R package

2020 ◽  
Author(s):  
Boris Leroy ◽  
Andrew M Kramer ◽  
Anne-Charlotte Vaissière ◽  
Franck Courchamp ◽  
Christophe Diagne
Keyword(s):  
Invasive Species ◽  
Alien Species ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Invasive Alien Species ◽  
Standard Procedure ◽  
R Package ◽  
Economic Costs ◽  
Global Database

Aim: Large-scale datasets are becoming increasingly available for macroecological research from different disciplines. However, learning their specific extraction and analytical requirements can become prohibitively time-consuming for researchers. We argue that this issue can be tackled with the provision of methodological frameworks published in open-source software. We illustrate this solution with the invacost R package, an open-source software designed to query and analyse the global database on reported economic costs of invasive alien species, InvaCost. Innovations: First, the invacost package provides updates of this dynamic database directly in the analytical environment R. Second, it helps understand the nature of economic cost data for invasive species, their harmonisation process, and the inherent biases associated with such data. Third, it readily provides complementary methods to query and analyse the costs of invasive species at the global scale, all the while accounting for econometric statistical issues. Main conclusions: This tool will be useful for scientists working on invasive alien species, by (i) facilitating access and use to this multi-disciplinary data resource and (ii) providing a standard procedure which will facilitate reproducibility and comparability of studies, one of the major critics of this topic until now. We discuss how the development of this R package was designed as an enforcement of general recommendations for transparency, reproducibility and comparability of science in the era of big data in ecology.

scholarly journals Short communication: Estimation of genetic trends for body weight traits in Markhoz goat at different ages

2019 ◽  
Vol 17 (1) ◽  
pp. e04SC01 ◽  
Author(s):  
Meysam Latifi ◽  
Mohammad Razmkabir
Keyword(s):  
Body Weight ◽  
Fixed Effects ◽  
Growth Traits ◽  
Genetic Selection ◽  
Information Criteria ◽  
Pedigree Information ◽  
Genetic Trend ◽  
Breeding Values ◽  
Different Ages ◽  
Genetic Trends

The objective of the present study was to estimate genetic trends for body weight at different ages in Markhoz goat, including birth weight (BW, n = 4758), weaning weight (WW, n= 3685), 6-month weight (6MW, n = 3420), 9-month weight (9MW, n = 3032) and 12-month weight (12MW, n = 2697). Data and pedigree information were collected from 1992 until 2014 at the Breeding Center of Markhoz goat, Sanandaj, Iran. The GLM procedure of SAS was used for selecting the variables and identifying significant fixed effects in the equation of model. Various animal models were applied for genetic analysis and the best model was determined based on Akaike information criteria (AIC). Breeding values of animals were predicted using Wombat program. Genetic trends were obtained by regressing the average predicted breeding values on birth year for each trait. Based on the best model, direct estimated genetic trends were positive and significance for WW, 6MW, 9MW and 12 MW were 15.51, 26.28, 58.36 and 76.70 g/year, respectively (p<0.001). Maternal genetic trend for BW and WW were 0.61 and 5.47 g/year, respectively (p<0.01). The low and moderate generic trends obtained in the present study, indicated the possibility of growth traits improvements through genetic selection at all ages in Markhoz goat.

scholarly journals Genetic parameters and trends for reproductive traits in Blanco Orejinegro cattle from Colombia

2021 ◽  
Vol 42 (4) ◽  
pp. 2523-2538
Author(s):  
Sindy Liliana Caivio-Nasner ◽  
◽  
Albeiro López-Herrera ◽  
Luis Gabriel González-Herrera ◽  
Juan Carlos Rincón Flórez ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Genetic Parameters ◽  
Environmental Influence ◽  
Cattle Breed ◽  
Heritability Estimate ◽  
Reproductive Traits ◽  
Genetic Trend ◽  
Genetic Progress ◽  
Estimated Breeding Values ◽  
Genetic Trends

The Colombian creole cattle breed Blanco Orejinegro (BON) is an important zoogenetic resource, but there is little knowledge about the genetic parameters and trends of its reproductive traits. Therefore, the aim of this study was to estimate parameters for the reproductive traits calving interval (CI), age at first calving (AFC), gestation duration (GD) and genetic trends for CI in the BON breed. Genealogy information from 7,799 animals was used, and employing the MTDFREML program, the components of the variance, heritability (h2), repeatability (rep), and estimated breeding values (EBV) for CI (n=3308), AFC (n=729), and GD (n=306) were estimated, in addition to the inbreeding coefficient (F) of the population. Genetic trends were established through linear regression using R software. Finally, the animals were classified as inbred (F > 0) and noninbred (F=0), and the effect of inbreeding on reproductive performance was established through a generalized linear model using the R program. An average F value of 4.41%±0.06 was observed. The h2 for CI was 0.11±0.03 with a rep of 0.15±0.04; for AFC, h2 was 0.00±0.05; and for GD, h2 was 0.00±0.08. The genetic trend for CI was -0.01 days/year. Finally, for CI, inbreeding depression was evident; this trait increased when inbreeding increased. These results indicate an important environmental influence on reproductive traits. The heritability estimate for CI suggests that little genetic progress could be achieved through selection. The evidence of inbreeding depression raises the need to control inbreeding to conserve this genetic resource.

scholarly journals ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun-Hui Gao ◽  
Guangchuang Yu ◽  
Peng Cai
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
R Package ◽  
Venn Diagram ◽  
Free Access ◽  
High Quality ◽  
Venn Diagrams ◽  
Label Edge ◽  
The Cost

Venn diagrams are widely used diagrams to show the set relationships in biomedical studies. In this study, we developed ggVennDiagram, an R package that could automatically generate high-quality Venn diagrams with two to seven sets. The ggVennDiagram is built based on ggplot2, and it integrates the advantages of existing packages, such as venn, RVenn, VennDiagram, and sf. Satisfactory results can be obtained with minimal configurations. Furthermore, we designed comprehensive objects to store the entire data of the Venn diagram, which allowed free access to both intersection values and Venn plot sub-elements, such as set label/edge and region label/filling. Therefore, high customization of every Venn plot sub-element can be fulfilled without increasing the cost of learning when the user is familiar with ggplot2 methods. To date, ggVennDiagram has been cited in more than 10 publications, and its source code repository has been starred by more than 140 GitHub users, suggesting a great potential in applications. The package is an open-source software released under the GPL-3 license, and it is freely available through CRAN (https://cran.r-project.org/package=ggVennDiagram).

Genetic changes generated within the Katanning Merino Resource flocks

2006 ◽  
Vol 46 (7) ◽  
pp. 803 ◽  
Author(s):  
J. C. Greeff ◽  
G. Cox
Keyword(s):  
Body Weight ◽  
Phase 1 ◽  
Fibre Diameter ◽  
Linear Unbiased Prediction ◽  
Genetic Changes ◽  
Breeding Values ◽  
Best Linear Unbiased ◽  
Fleece Weight ◽  
Estimated Breeding Values ◽  
Genetic Trends

Genetic changes for clean fleece weight, fibre diameter and hogget body weight were determined in the Katanning Merino Resource flocks from 1982 to 2004. From 1982 to 1992 genetic trends are presented for individual studs that used mainly subjective classing selection methods (Phase 1) and the genetic trends from 1997 to 2004 demonstrate the genetic changes that can be achieved from using estimated breeding values calculated from best linear unbiased prediction (BLUP) mixed methodology (Phase 2). The results during the first phase show that very few genetic changes occurred in most studs, except for the 4 studs of the Performance Sheep Breeding strain which showed genetic increases in hogget body weight. The genetic trends show that some studs generated change towards their breeding objective, while others show no changes or changes in the opposite direction. In contrast, the use of BLUP estimated breeding values resulted in positive changes in clean fleece weight, fibre diameter and body weight in accordance with the defined breeding objectives.

scholarly journals Mendelian sampling terms as a selective advantage in optimum breeding schemes with restrictions on the rate of inbreeding

2004 ◽  
Vol 83 (1) ◽  
pp. 55-64 ◽  
Author(s):  
S. AVENDAÑO ◽  
J. A. WOOLLIAMS ◽  
B. VILLANUEVA
Keyword(s):  
Genetic Variation ◽  
Genetic Gain ◽  
Selective Advantage ◽  
Breeding Values ◽  
Truncation Selection ◽  
Joint Management ◽  
Breeding Schemes ◽  
Estimated Breeding Values ◽  
Available Information ◽  
Mendelian Sampling

Quadratic indices are a general approach for the joint management of genetic gain and inbreeding in artificial selection programmes. They provide the optimal contributions that selection candidates should have to obtain the maximum gain when the rate of inbreeding is constrained to a predefined value. This study shows that, when using quadratic indices, the selective advantage is a function of the Mendelian sampling terms. That is, at all times, contributions of selected candidates are allocated according to the best available information about their Mendelian sampling terms (i.e. about their superiority over their parental average) and not on their breeding values. By contrast, under standard truncation selection, both estimated breeding values and Mendelian sampling terms play a major role in determining contributions. A measure of the effectiveness of using genetic variation to achieve genetic gain is presented and benchmark values of 0·92 for quadratic optimisation and 0·5 for truncation selection are found for a rate of inbreeding of 0·01 and a heritability of 0·25.

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