1 Introduction
Chickens were domesticated from red jungle fowl subspecies Gallus gallus spadiceus ~6,000 - 8,000 years ago in South and Southeast Asia (Larson and Fuller, 2014; Miao et al., 2013; Wang et al., 2020). Subsequently, numerous indigenous local breeds were formed after a long period of natural and artificial selection, and have evolved genetic adaption to a wide range of eco-geographic conditions, especially those in tropical and frigid, and high-attitude regions (Lawal et al., 2018). As we all know, environmental pressure is an important driver shaping the animal genome, so the detection of genomic differences can clarify the genetic basis of adaptation to diverse environments and provide insights into functionally important genetic variants (Andersson and Georges, 2004; Shi et al., 2022). Meanwhile, considering their short reproductive and growth periods and wide distribution, chickens can be used as ideal models to study genetic adaptations to environments (Li et al., 2022).
To our best knowledge, genetic adaptions to naturally extreme environments in chickens have attracted many researchers, but mainly focused on high attitude adaption of Chinese chicken (Wang et al., 2015; Zhang et al., 2018b) and hot and arid environments of African and Asian chickens (Fleming et al., 2017; Tian et al., 2020) by chip analysis or whole genome analysis. There were few studies aiming at tropical and frigid environment adaption of Chinese chickens in spite of diverse Chinese local chicken breeds. In consideration of current and future global effects of climate changes (Tian et al., 2020), the genetic footprints of adaption to tropical and frigid climates in Chinese chickens are critical for modern chicken industry.
In this study, with the aim of better understanding the genetic footprints of extreme environments adaption, we applied an integrated analysis combining liver high-throughput chromosome conformation capture (Hi-C) data (Lieberman-Aiden et al., 2009) with transcriptome sequencing of Lindian chicken (LDC) and Wenchang chicken (WCC) from two extant extreme environments (more frigid to more tropical environments). We generated genome-wide profiles of chromatin contacts using Hi-C technology, which was allowed to character spatial chromatin compartments and evaluate DNA interaction frequencies at a resolution from dozens of kilobases to megabases (Battulin et al., 2015; Veniamin et al., 2018). We identified characteristics of A/B compartments and topologically associating domains (TADs) in two different sources of livers. We also reported changes in gene expression and enriched pathways associated with the variant 3D genome, which implicated the tropical and frigid environments genetic adaption.