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.