Genetic structure and origin of emu populations in Japanese farms inferred from large-scale SNP genotyping based on double-digest RAD-seq

• Published in: Scientific reports Vol. 14; no. 1; p. 6982
• Main Authors: Koshiishi, Yuichi, Wada, Kenta
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.03.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208/1348; 631/208/8; Animals; Australia; Dromaiidae; Farm structure; Farms; Genetic diversity; Genetic resources; Genetic structure; Genetic Structures; Genetic Variation; Genotype; Genotyping; Haplotypes; Humanities and Social Sciences; Humans; Inbreeding; Japan; Microsatellite Repeats - genetics; Mitochondrial DNA; multidisciplinary; Phylogeny; Polymorphism, Single Nucleotide; Population genetics; Science; Science (multidisciplinary); Single-nucleotide polymorphism; Wildlife tourism; Australia; Japan
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-57032-y

The emu is a novel poultry species in Japan. However, Japanese farmed emu populations have reduced genetic diversity owing to inbreeding. We have previously suggested that there are genetic resources in the Tohoku Safari Park (TSP) and Fuji/Kakegawa Kachoen Garden Park (FGP/KGP) to extend the genetic diversity of commercial emu farms based on microsatellite (SSR) and mitochondrial DNA. However, those markers provide relatively poor information. Thus, we investigated the genetic structure of farmed Japanese populations based on a large-scale genotyping system using RAD-seq and verified the usefulness of TSP and FGP/KGP as genetic resources for expanding genetic diversity. Admixture, phylogenetic, and principal component analyses based on 28,676 SNPs showed that TSP individuals were ancestors in the Okhotsk Emu Farm (OEF). FGP/KGP individuals showed a unique genetic component that differed from that of the others. We have previously reported that the mitochondrial haplotypes of FGP/KGP were shared with an isolated wild population in eastern Australia. These results suggest that FGP/KGP individuals originated from an eastern Australia isolated population different from other populations including ancestral of OEF/TSP. Our results would provide information for the development of Japanese emu farms and industry and for the conservation of genetic resources in the Australian wild emu.