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

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

doi:10.3389/fgene.2021.671686

Guangqi Lyu, Chunyu Feng + Show 6 more

Open Access

https://doi.org/10.3389/fgene.2021.671686

Copy DOI

Abstract

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 FST, Hp and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). 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.

Highlights

As our best friend, dogs are crucial to modern human society and are involved in many aspects of our life
Due to human imposed artificial selection, some Shiba Inus have body sizes that are smaller than their ancestors
Study, we conducted whole-genome pool sequencing on two breeds of primitive Japanese dogs, Shiba Inu and Mame Shiba Inu, to investigate the molecular mechanisms responsible for the differences in their body size, and to identify candidate genes that may regulate body size in all dogs

Summary

INTRODUCTION

Dogs are crucial to modern human society and are involved in many aspects of our life. Shiba Inus typically range in height from 34 to 41 cm (Figure 1A) in recent years, artificial selection has been imposed to yield smaller individuals, which are called mini or Mame Shiba Inu (Mame is a Japanese word for “bean,” representing “small”). The change in body size between Shiba Inu and Mame Shiba Inu is relatively mild, but distinct, making them good source for investigating mechanisms that change body size These breeds are highly divergent from the other domesticated dogs. Regulation of dog body size, or weight, in the dog has been extensively researched, with many studies conducted at the genomic level (Ostrander et al, 2017) Through these works, many genes and loci have been identified as associated with the regulation of body size in the dog. Using a GWAS analyses of 690 dogs, three genes (IRS4, IGSF1, and ACSL4) were found to be associated with body weight, where IRS4 and IGSF1 are both involved in the GH/IGF1 and thyroid hormonal pathways involved in body size regulation (Plassais et al, 2017)

Ethics Statement

RESULTS

DATA AVAILABILITY STATEMENT