Biology subjects

Gaynor, C. R.

Publications and source records attributed to Gaynor, C. R..

3 recordsLinked to original sources

bioRxiv2023

Plant breeding simulations with AlphaSimR

Plant breeding plays a crucial role in the development of high-performing crop varieties that meet the demands of society. Emerging breeding techniques offer the potential to improve the precision and efficiency of plant breeding programs; however, their optimal implementation requires refinement of existing breeding programs or the design of new ones. Stochastic simulations are a cost-effective solution for testing and optimizing new breeding strategies. The aim of this paper is to provide an introduction to stochastic simulation with software AlphaSimR for plant breeding students, researchers, and experienced breeders. We present an overview of how to use the software and provide an introductory AlphaSimR vignette as well as complete AlphaSimR scripts of breeding programs for self-pollinated, clonal, and cross-pollinated plants, including relevant breeding techniques, such as backcrossing, speed breeding, genomic selection, index selection, and others. Our objective is to provide a foundation for understanding and utilizing simulation software, enabling readers to adapt the provided scripts for their own use or even develop completely new plant breeding programs. By incorporating simulation software into plant breeding education and practice, the next generation of plant breeders will have a valuable tool in their quest to provide sustainable and nutritious food sources for a growing population.

genetics↗

bioRxiv2020

Modelling illustrates that genomic selection provides new opportunities for intercrop breeding

Intercrop breeding programs using genomic selection can produce faster genetic gain than intercrop breeding programs using phenotypic selection. Intercropping is an agricultural practice in which two or more component crops are grown together. It can lead to enhanced soil structure and fertility, improved weed suppression, and better control of pests and diseases. Especially in subsistence agriculture, intercropping has great potential to optimise farming and increase profitability. However, breeding for intercrop varieties is complex as it requires simultaneous improvement of two or more component crops that combine well in the field. We hypothesize that genomic selection can significantly simplify and accelerate the process of breeding crops for intercropping. Therefore, we used stochastic simulation to compare four different intercrop breeding programs implementing genomic selection and an intercrop breeding program entirely based on phenotypic selection. We assumed three different levels of genetic correlation between monocrop grain yield and intercrop grain yield to investigate how the different breeding strategies are impacted by this factor. We found that all four simulated breeding programs using genomic selection produced significantly more intercrop genetic gain than the phenotypic selection program regardless of the genetic correlation with monocrop yield. We suggest a genomic selection strategy which combines monocrop and intercrop trait information to predict general intercropping ability to increase selection accuracy in early stages of a breeding program and to minimize the generation interval.

genetics↗

bioRxiv2017

A strategy to exploit surrogate sire technology in livestock breeding programs

In this work, we performed simulations to develop and test a strategy for exploiting surrogate sire technology in animal breeding programs. Surrogate sire technology allows the creation of males that lack their own germline cells, but have transplanted spermatogonial stem cells from donor males. With this technology, a single elite male donor could give rise to huge numbers of progeny, potentially as much as all the production animals in a particular time period.\n\nOne hundred replicates of various scenarios were performed. Scenarios followed a common overall structure but differed in the strategy used to identify elite donors and how these donors were used in the product development part.\n\nThe results of this study showed that using surrogate sire technology would significantly increase the genetic merit of commercial sires, by as much as 6.5 to 9.2 years worth of genetic gain compared to a conventional breeding program. The simulations suggested that a strategy involving three stages (an initial genomic test followed by two subsequent progeny tests) was the most effective of all the strategies tested.\n\nThe use of one or a handful of elite donors to generate the production animals would be very different to current practice. While the results demonstrate the great potential of surrogate sire technology there are considerable risks but also other opportunities. Practical implementation of surrogate sire technology would need to account for these.

genetics↗