Predicting breed by environment interaction using ecological modelling

Abstract

Lozano-Jaramillo, M. (2019). Predicting breed by environment interaction using ecological modelling. PhD thesis, Wageningen University, the Netherlands.Animal production plays an important socio-economic role in developing countries. Livestock largely contribute to the local food production, and they represent a source of income for many smallholder farmers. Smallholder production systems are characterized by low producing indigenous breeds. To enhance food security, several breeding projects have introduced commercial breeds as an alternative to help smallholder farmers to increase the food supply. As a common practice in animal breeding, commercial breeds are introduced from a nucleus to different locations. However, no knowledge on the new environmental conditions in the new tropical environment are taken into account. The aim of this thesis was to understand how the environment plays a role in shaping the variation in breed performance across different agro-ecologies. To achieve this, I used different approaches than what it is commonly used in animal breeding, to understand the environmental variation. I use Geographic Information Systems (GIS) along with different models used in ecology to predict the performance of genotypes in changing environments. Results highlight the importance of acknowledging the environment being composed of many variables that have continuous variation when designing breeding programs or testing schemes. I recommend the application of these models to livestock to make predictions on how productivity traits respond as a function of the environment.

Adaptive phenotypic and genetic variation in chickens: a landscape genomics approach

“…Analytical frameworks (experimental designs and evaluation methods) are not available to compare candidate breeds and identify those with optimal productive performance and adaptability for wider use by smallholder farmers. Previous researches that focused on estimating GxE in smallholder poultry systems de Kinderen et al, 2020;Lozano-Jaramillo et al, 2019a;Lozano-Jaramillo, 2019) did not consider evaluation of yield stability in livestock performance analyses. Yield stability refers to the ability of a breed to be less affected by environmental influences and to provide reasonable yield.…”

“…The realized niche is smaller and refers to those parts of the fundamental niche where the species can survive despite the presence of competitors or negative interactions. In recent years, the conceptual framework for SDMs has been extended by livestock scientists and used to identify environmental predictors associated with habitat suitability and local adaptation in livestock populations (Gheyas et al, 2021;Lozano-Jaramillo, 2019;Vajana et al, 2018;Vallejo-Trujillo et al, 2018). Phenotypic distribution models (PDMs) use associations between phenotypes and environmental variables to map the phenotypes of populations within that species' distribution (Michel et al, 2017).…”

“…We combine Species Distribution Modelling (SDMs), signatures of selection analyses, and association analyses to study adaptive variation in Ethiopian chickens. SDMs are useful to identify environmental predictors associated with habitat suitability and local adaptation in indigenous livestock populations (Gheyas et al, 2021;Lozano-Jaramillo, 2019;Vajana et al, 2018;Vallejo-Trujillo et al, 2018). Signatures of selection analysis identify regions of the genome that have differentiated between populations, possibly in response to selective pressure (Sabeti et al, 2006;Voight et al, 2006).…”

Genomic characterization and conservation of genetic diversity in cattle

“…Consequently, breeding for traits like tick resistance may become important in areas where it is currently not. Emerging tools such as ecological modelling [382] and landscape genomics [383] may help to improve our understanding of the association between environments and genotypes.…”