AUTHOR=Dong Hong , Dong Zheng , Wang Fuwen , Wang Gang , Luo Xiaoyu , Lei Chuzhao , Chen Jingbo 

TITLE=Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids

JOURNAL=Frontiers in Genetics

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.818420

DOI=10.3389/fgene.2022.818420

ISSN=1664-8021

ABSTRACT=<p>The diversity of livestock coat color results from human positive selection and is an indispensable part of breed registration. As an important biodiversity resource, Asiatic wild ass has many special characteristics, including the most visualized feature, its yellowish-brown coat color, and excellent adaptation. To explore the genetic mechanisms of phenotypic characteristics in Asiatic wild ass and its hybrids, we resequenced the whole genome of one Mongolian Kulan (a subspecies of Asiatic wild ass) and 29 Kulan hybrids (Mongolian Kulan ♂×Xinjiang♀), and the ancestor composition indicated the true lineage of the hybrids. XP-EHH (Cross Population Extended Haplotype Homozygosity), θπ-ratio (Nucleotide Diversity Ratio), CLR (Composite Likelihood Ratio) and θπ (Nucleotide Diversity) methods were used to detect the candidate regions of positive selection in Asiatic wild ass and its hybrids. Several immune genes (<italic>DEFA1</italic>, <italic>DEFA5</italic>, <italic>DEFA7</italic>, <italic>GIMAP4</italic>, <italic>GIMAP1</italic>, <italic>IGLC1</italic>, <italic>IGLL5</italic>, <italic>GZMB</italic> and <italic>HLA</italic>) were observed by the CLR and θπ methods. XP-EHH and θπ-ratio revealed that these genes are potentially responsible for coat color (<italic>KITLG</italic>) and meat quality traits (<italic>PDE1B</italic> and <italic>MYLK2</italic>). Furthermore, the heatmap was able to show the clear difference in the haplotype of the <italic>KITLG</italic> gene between the Kulan hybrids and Asiatic wild ass group and the Guanzhong black donkey group, which is a powerful demonstration of the key role of <italic>KITLG</italic> in donkey color. Therefore, our study may provide new insights into the genetic basis of coat color, meat quality traits and immunity of Asiatic wild ass and its hybrids.</p>