Genome-wide scans for selection signatures in indigenous chickens reveal candidate genes associated with local adaptation

作者：Xiaofeng Xie, Zucheng Wang, Ziqi Zhong, Dawei Pan, Guanyu Hou, Qian Xiao · 发表于：animal · 年份：2024 · DOI：10.1016/j.animal.2024.101151 · 被引用次数：13 · 研究领域：Livestock and Poultry Management、Animal Nutrition and Physiology、Genetic and phenotypic traits in livestock

Population growth and climate change pose challenges to the sustainability of poultry farming. The emphasis on high-yield traits in commercialized breeds has led to a decline in their adaptability. Chicken varieties adapted to the local environment, possessing traits that facilitate adaptation to climate change, such as disease resistance and tolerance to extreme weather conditions, can improve hybridization outcomes. In this study, we conducted an analysis of the population structure and genetic diversity of 110 chickens representing indigenous breeds from southern China and two different commercial breeds. Further, we performed comparative population genomics, utilizing nucleotide diversity and fixation statistics, to characterize genomic features of natural selection and to identify unique genetic traits and potential selection markers developed by indigenous breeds after adapting to the local environment. Results based on genetic diversity and population structure analyses showed that indigenous varieties exhibited high levels of genetic diversity. Commercial breeds that have been indigenously bred demonstrated higher levels of genetic diversity than those that have not, and breeds with different selection practices displayed significant differences in genetic structure. Additionally, we further searched for potential genomic regions in native chicken ecotypes, uncovering several candidate genes related to ecological adaptations affecting local breeds, such as IKBKB, S1PR...