Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens

Fasil Getachew Kebede; Hans Komen; Tadelle Dessie; Setegn Worku Alemu; Olivier Hanotte; John W M Bastiaansen

doi:10.3389/fgene.2021.723360

Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens

Front Genet. 2021 Sep 8:12:723360. doi: 10.3389/fgene.2021.723360. eCollection 2021.

Authors

Fasil Getachew Kebede^{1

2}, Hans Komen¹, Tadelle Dessie², Setegn Worku Alemu², Olivier Hanotte^{2

3}, John W M Bastiaansen¹

Affiliations

¹ Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands.
² International Livestock Research Institute, Addis Ababa, Ethiopia.
³ Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.

Abstract

Smallholder poultry production dominated by indigenous chickens is an important source of livelihoods for most rural households in Ethiopia. The long history of domestication and the presence of diverse agroecologies in Ethiopia create unique opportunities to study the effect of environmental selective pressures. Species distribution models (SDMs) and Phenotypic distribution models (PDMs) can be applied to investigate the relationship between environmental variation and phenotypic differentiation in wild animals and domestic populations. In the present study we used SDMs and PDMs to detect environmental variables related with habitat suitability and phenotypic differentiation among nondescript Ethiopian indigenous chicken populations. 34 environmental variables (climatic, soil, and vegetation) and 19 quantitative traits were analyzed for 513 adult chickens from 26 populations. To have high variation in the dataset for phenotypic and ecological parameters, animals were sampled from four spatial gradients (each represented by six to seven populations), located in different climatic zones and geographies. Three different ecotypes are proposed based on correlation test between habitat suitability maps and phenotypic clustering of sample populations. These specific ecotypes show phenotypic differentiation, likely in response to environmental selective pressures. Nine environmental variables with the highest contribution to habitat suitability are identified. The relationship between quantitative traits and a few of the environmental variables associated with habitat suitability is non-linear. Our results highlight the benefits of integrating species and phenotypic distribution modeling approaches in characterization of livestock populations, delineation of suitable habitats for specific breeds, and understanding of the relationship between ecological variables and quantitative traits, and underlying evolutionary processes.

Keywords: breeds and ecotypes; chickens; local adaptation; niche and agroecology; phenotypic differentiation; phenotypic distribution models (PDMs); poultry genetics and breeding; species distribution models (SDMs).