# Positive selection on rare variants of IGF1R and BRD4 underlying the cold adaptation of wild boar

## TL;DR

Wild boars have evolved genetic changes in IGF1R and BRD4 that help them survive in cold climates, which could inform strategies to improve piglet survival in cold environments.

## Contribution

The study identifies two rare genetic variants under positive selection in IGF1R and BRD4 that are nearly fixed in cold-adapted wild boar populations.

## Key findings

- Candidate genes for cold adaptation are enriched in thermogenesis and adipose tissue pathways.
- Two rare variants—IGF1R rs341219502 and BRD4 rs327139795—are under positive selection and nearly fixed in cold-region wild boar populations.
- The IGF1R variant affects enhancer function, while the BRD4 variant may alter amino acid phosphorylation.

## Abstract

Domestic piglets often die of hypothermia, whereas Eurasian wild boar (Sus scrofa) thrives from tropical lowlands to subarctic forests. The thermoregulation of wild boar offers a natural experiment to uncover the genetic basis of cold adaptation.

We conducted whole-genome resequencing on wild populations from cold regions (northern and northeastern Asia, with six samples) and warm regions (southeastern Asia and southern China, with five samples). By integrating publicly available data, we compiled a core dataset of 48 wild boar samples and an extended dataset of 445 wild boar and domestic pig samples to identify candidate genes related to cold adaptation. To investigate the functional effects of two candidate variants under positive selection, we performed CUT&Tag and RNA-seq using the northeastern Asian Min pig breed as a proxy for a cold-adapted population.

Our study identified candidate genes associated with cold adaptation, which are significantly enriched in thermogenesis, fat cell development, and adipose tissue pathways. We discovered two enhancer variants under positive selection: an intronic variant of IGF1R (rs341219502) and an exonic variant of BRD4 (rs327139795). These variants exhibited the highest differentiation between populations of wild boar and domestic pigs in cold and warm region populations. Furthermore, these rare variants were absent in outgroup species and warm-region wild boars but were nearly fixed in cold-region populations. The H3K27ac CUT&Tag profiling revealed that the rs341219502 variant of IGF1R is linked to the gain of novel binding sites for three transcription factors involving regulatory changes in enhancer function. In contrast, the rs327139795 variant of BRD4 may result in the loss of a phosphorylation site due to an alteration in the amino acid sequence.

Our study identified candidate genes for cold adaptation in wild boar. The variant rs341219502 in the IGF1R enhancer and the variant rs327139795 in the BRD4 exon, both of which were under positive selection and nearly fixed in populations from cold regions, suggest they may have originated de novo in these populations. Further analysis indicated that rs341219502 could influence enhancer function, while rs327139795 may affect amino acid alterations. Overall, our study highlights the adaptive evolution of genomic molecules that contribute to the remarkable environmental flexibility of wild boar.

The online version contains supplementary material available at 10.1186/s12711-025-00986-y.