AUTHOR=Lyu Guangqi , Feng Chunyu , Zhu Shiyu , Ren Shuang , Dang Wanyi , Irwin David M. , Wang Zhe , Zhang Shuyi 

TITLE=Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.671686

DOI=10.3389/fgene.2021.671686

ISSN=1664-8021

ABSTRACT=<p>Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the “Mame Shiba Inu” breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including <italic>F</italic><sub>ST</sub>, <italic>H</italic><sub>p</sub> and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (<italic>PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141</italic>, and <italic>ENSCAFG00000018533</italic>). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.</p>