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Impact of erroneous marker data on the accuracy of narrow-sense heritability Open
Genomic relationship matrices computed from single nucleotide polymorphism (SNP) data are now widely used to estimate narrow-sense heritability (h2), yet the impact of genotyping error on these estimates is not well understood. We used sto…
Characterization of a novel heat tolerance trait and subsequent haplotype block-based analysis to identify associated regions in Dutch Holstein cattle Open
Heat stress is a major environmental challenge affecting dairy cattle, leading to behavioral changes, production losses, and welfare concerns. As heat stress events intensify and become more frequent due to climate change, identifying anim…
The heritability accuracy in forest tree breeding programs relying on random mating Open
In forest tree breeding, there is a growing trend towards using pedigree reconstruction after offspring are produced through natural random mating (open-pollination), as an alternative to traditional controlled crosses and full-sib genetic…
Utilizing low-pass sequence data to study the impact of structural variants on polygenic traits Open
Background The impact of single nucleotide polymorphisms (SNPs) on polygenic traits have been well studied because of technological advances making SNP genotyping cost effective. Studying the impact of structural variants (SV) on polygenic…
Alleviating the Concerns About Pollen‐Based Assisted Migration Open
Our recent publication on pollen‐based assisted migration has prompted concerns about its feasibility and effectiveness. In this response article, we address those concerns by presenting large‐scale examples of supplemental and controlled …
Optimization of recurrent rapid cycle breeding in maize for sustained long-term genetic improvement via stochastic simulations Open
In recent years, the turnover of germplasm in plant breeding has substantially increased as the use of genomic information allows for earlier selection and the integration of controlled growing environments reduces the time to reach a part…
Characterization of a novel heat tolerance trait and subsequent haplotype block-based analysis to identify causal regions in Dutch Holstein cattle Open
Heat stress is a major environmental challenge affecting dairy cattle, leading to behavioral changes, production losses, and welfare concerns. As heat stress events intensify and become more frequent due to climate change, identifying heat…
Optimization of wheat breeding programs using an evolutionary algorithm achieves enhanced genetic gain through strategic resource allocation Open
Plant breeding is a complex process that involves trade-offs among competing breeding objectives and limited resources. Despite the necessity for optimization of breeding program design, the inherent complexity can make optimization challe…
Strategies to improve selection compared to selection based on estimated breeding values Open
Background Selection of individuals based on their estimated breeding values aims to maximize response to selection to the next generation in the additive model. However, when the aim is not only about short-term population-wide genetic ga…
A Pollen‐Based Assisted Migration for Rapid Forest Adaptation Open
Climate change poses an unprecedented threat to forest ecosystems, necessitating innovative adaptation strategies. Traditional assisted migration approaches, while promising, face challenges related to environmental constraints, forestry p…
Optimization of breeding program design through stochastic simulation with evolutionary algorithms Open
The effective planning and allocation of resources in modern breeding programs is a complex task. Breeding program design and operational management have a major impact on the success of a breeding program and changing parameters such as t…
Genomic selection strategies for the German Merino sheep breeding programme – A simulation study Open
Genomic selection is widely implemented in livestock breeding programmes across species. Its potential is also evident for sheep breeding; however, it has several limitations, particularly because of the high genetic diversity across and w…
Evaluation of breeding strategies to reduce the inbreeding rate in the Friesian horse population: Looking back and moving forward Open
In the past, small population sizes and unequal ancestor contributions have resulted in high inbreeding rates (Δ F ) in the Friesian horse. Two decades ago, the studbook implemented a mating quota and started publishing individual kinships…
Genomic prediction within and across maize landrace derived populations using haplotypes Open
Genomic prediction (GP) using haplotypes is considered advantageous compared to GP solely reliant on single nucleotide polymorphisms (SNPs), owing to haplotypes’ enhanced ability to capture ancestral information and their higher linkage di…
Optimization Strategies to Adapt Sheep Breeding Programs to Pasture-Based Production Environments: A Simulation Study Open
Strong differences between the selection (indoor fattening) and production environment (pasture fattening) are expected to reduce genetic gain due to possible genotype-by-environment interactions (G × E). To investigate how to adapt a shee…
The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation Open
Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown…
Optimization of breeding program design through stochastic simulation with kernel regression Open
In recent years, breeding programs have increased significantly in size and complexity, with various highly interdependent parameters and many contrasting breeding goals. As a result, resource allocation in these programs has become more c…
View article: Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction
Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction Open
In the last decade, a number of methods have been suggested to deal with large amounts of genetic data in genomic predictions. Yet, steadily growing population sizes and the suboptimal use of computational resources are pushing the practic…
View article: Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction
Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction Open
In the last decade, a number of methods have been suggested to deal with large amounts of genetic data in genomic predictions. Yet, steadily growing population sizes and the suboptimal use of computational resources are pushing the practic…
How economic weights translate into genetic and phenotypic progress, and vice versa Open
Background This paper highlights the relationships between economic weights, genetic progress, and phenotypic progress in genomic breeding programs that aim at generating genetic progress in complex, i.e., multi-trait, breeding objectives …
Beyond Scenarios - Optimization of breeding program design (MoBPSopti) Open
In recent years, breeding programs have become increasingly larger and more structurally complex, with various highly interdependent parameters and contrasting breeding goals. Therefore, resource allocation in a breeding program has become…
Genomic prediction using information across years with epistatic models and dimension reduction via haplotype blocks Open
The importance of accurate genomic prediction of phenotypes in plant breeding is undeniable, as higher prediction accuracy can increase selection responses. In this regard, epistasis models have shown to be capable of increasing the predic…
Imputation of low‐density marker chip data in plant breeding: Evaluation of methods based on sugar beet Open
Low‐density genotyping followed by imputation reduces genotyping costs while still providing high‐density marker information. An increased marker density has the potential to improve the outcome of all applications that are based on genomi…
Development and validation of a horse reference panel for genotype imputation Open
Background Genotype imputation is a cost-effective method to generate sequence-level genotypes for a large number of animals. Its application can improve the power of genomic studies, provided that the accuracy of imputation is sufficientl…
Imputation of Low-density Marker Chip Data in Plant Breeding: Evaluation of Methods Based on Sugar Beet Open
Low-density genotyping followed by imputation reduces genotyping costs while still providing high-density marker information. An increased marker density has the potential to improve the outcome of all applications that are based on genomi…
Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant Open
Multi-parent advanced generation inter-cross (MAGIC) populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC populati…
Simulated Comparison Between Different Scenarios of Modular Chicken Breeding Program using MoBPSweb v.1.6.62 Open
Background: An optimal selective breeding program must balance ethical risks and operational costs without necessarily compromising its effectiveness and aims. For this purpose, a modular breeding simulator was used. Modular simulation act…