Browsing by Subject "Genome editing"

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The potential of gene editing and genomic selection in improving quantitative traits: A simulation study regarding dual-purpose chicken
(2024) Chuang, Edward; Bennewitz, Jörn
The practice of chick culling is the killing of day-old chicks of the layer line chicken. Because of their inability to lay eggs and inefficiency to grow meat, killing them instead of raising them is more economically efficient. In recent years, this practice has raised ethical concerns and led to the ban of this practice in several countries, including Germany and France. One of the several possible solutions is the use of dual-purpose chicken. Unlike the commercial layers, the dual-purpose chicken has abilities in both egg laying and meat production. Even though dual-purpose chicken has better meat growth performance compared to the commercial layers, the use of dual-purpose chicken is still challenging. One of the major challenges to improve dual-purpose chicken is the negative correlation between egg production and meat production. To cope with this negative correlation, some have proposed that gene editing could be a helpful tool to mitigate the problem. The aim of this simulation study is to explore the potential of gene editing to improve negatively correlated quantitative traits. To be more specific, given the aforementioned reasons, the negative correlation between the meat and egg production traits in chicken was chosen as the topic of this study. That is, chicken breeding programs that develop and improve dual-purpose chicken were simulated to discuss the potential of gene editing in animal breeding programs. Chapter 1 begins this thesis with a general introduction of the background to the problem of chick culling, the challenge of developing dual-purpose chicken, and the use of gene editing. Some previous simulation studies on the use of gene editing to improve quantitative traits in animal breeding programs is also introduced in this chapter. Chapter 2 presents a literature review that discusses how gene editing technologies could change the breeding and production of farm animals. In accordance with this thesis's aim, a specific focus was placed on improving quantitative traits. By reviewing the technical and social limitations of gene editing, this review provides a basis for further discussion of the feasibility of the gene-editing implementation as presented in the next chapters. Chapter 3 introduces the simulation framework to explore the potential of gene editing in chicken breeding programs. This framework first simulates two divergently selected lines that reflect the commercial layers and broilers. Based on these two lines, two alternative breeding programs were simulated. One is to develop a dual-purpose line from a layer line (the L-Pure Scenario), while the other selects and improves a synthetic line obtained from a cross between a layer line and a broiler line (the L-B cross scenario). In both breeding schemes, gene editing was integrated into the genomic selection scheme applying optimal contribution selection. The simulation presented in Chapter 4 considers multiplex genome editing that could edit five to one hundred single nucleotide variants at a time. These variants include the causal variants and other falsely edited variants. The results suggest that multiplex gene editing is beneficial in both the L-Pure and the L-B cross scenarios. It also demonstrated that when the risk of negative off-target effect exists, editing more nucleotides does not guarantee extra genetic gain. The simulation presented in Chapter 5 considers the introduction of major genes that would have larger effects on meat production. Here, only the L-Pure scenario is considered. Different to Chapter 4, in this chapter, editing is only possible with only one gene at a time. This chapter aims to study the effects of the numbers of major genes and the pleiotropy (on egg production and meat production). The results suggest that gene editing would be beneficial in dual-purpose chicken breeding programs when the gene is mildly pleiotropic. Chapter 6 ends the thesis with a general discussion that covers the limitations of this study and the possibilities to further expand the simulation study.