# Whole-Genome Sequencing Identifies Functional Genes for Environmental Adaptability in Chinese Geese

## TL;DR

This study uses whole-genome sequencing to identify genes in Chinese geese that help them adapt to different environmental conditions, such as temperature and precipitation.

## Contribution

The study identifies 447 genes and two non-coding variants associated with environmental adaptability in Chinese geese using multiple genetic-environment association methods.

## Key findings

- 447 genes were identified as being associated with environmental adaptation in Chinese geese.
- Two non-coding variants showed stronger positive selection in breeds living in high-temperature environments.
- The identified genes are enriched in pathways related to metabolism and signaling, such as the GnRH signaling pathway.

## Abstract

Rapid and unprecedented global climate change is posing a significant and multifaceted threat to biodiversity. Investigating the genetic footprints of temperature and precipitation selection can provide insights into local adaptation and is helpful for providing strategies to respond to climate change. As the largest goose-producing country in the world, China accounts for more than 70% of global goose breeds. However, few studies have comprehensively demonstrated the genetic signatures associated with environmental adaptation in Chinese geese. To elucidate the environmental adaptability of the Chinese goose, we used three genetic–environment association analysis methods and identified a range of functional genes with temperature and precipitation based on the whole-genome sequencing data of 239 geese collected from 21 breeds. A total of 447 genes were identified as being associated with environmental adaptation, such as the FAF1 and RSF1 genes, and genes belonging to the solute carrier family and the nicotinamide adenine dinucleotide hydride (NADH) family. Two variants (chr3: 38968547, chr13: 23863699) located in a non-coding region were identified and exhibited stronger signatures for positive selection in the breeds living in higher temperatures.

China is home to a rich diversity of goose genetic resources, with more than 30 distinct breeds. These breeds are widely distributed in various environments with high annual mean temperature differences ranging from about 3.5 °C to 23 °C and annual precipitation differences ranging from about 230 mm to 2200 mm, positioning them as excellent models for studying environmental adaptability. With three genetic–environment association methods, the LFMM, Samβada, and RDA analysis, a total of 447 genes were selected by at least two methods. These genes are significantly enriched in three pathways, including the polycomb repressive complex pathway, the alanine, aspartate, and glutamate metabolism pathway, and the GnRH signalling pathway. The scanning of all candidate single-nucleotide polymorphism variations found that only two variants located in a non-coding region (chr3:38968547, chr13:23863699) showed stronger positive selection in breeds living in a high-temperature environment. This research not only deepens our understanding of the genetic basis of goose adaptation to diverse environments but also provides a valuable resource for future selective breeding programs in the goose industry facing rapid global climate change.