Genetic structure of Japanese farmed emu population based on flexible-ddRAD

The emu (Dromaius novaehollandiae) is expected to become a novel poultry species in Japan. The genetic structure is one of the most important information for rapid genetic improvement in livestock. We aimed to reveal the genetic structure of Japanese emu populations and find genetic resources for extending the genetic diversity. This is sequence data of RAD-seq including Japanese 4 emu populations that Okhotsk Emu Farm (OEF; Abashiri, Hokkaido, Japan), Tohoku Safari Park (TSP), Fuji Kachoen Garden Park(FGP) and Kakegawa Kachoen Garden Park (KGP). The genomic DNA was isolated from liver tissues and feather pulp using ISOGENOME (Nippon Gene, Tokyo, Japan) according to the manufacturer's instructions. A sequence library was constructed using the flexible ddRAD-seq method. Extracted DNAs (10-100 ng) were digested using two kinds of restriction enzymes, Eco RI (5' GAATTC3') and Hind III (5' AAGCTT3'), for 2 h at 37 °C. Digested DNA fragments were ligated to custom adaptors that have cleavage site of Hind III anneals P5 adaptor (5'- AGC TCT GTC TCT TAT ACA CAT CTG ACG CTG CCG ACG A-3' [underline indicated annealing site]), and the site of EcoRI anneals P7 adaptor (5'- AAT TCT GTC TCT TAT ACA CAT CTA ATC A-3' [underline indicated annealing site]) by T4 DNA ligase (Takara Bio, Otsu, Japan). The adaptor-ligated DNA fragments were amplified via PCR using PrimeSTAR HS (Takara Bio, Shiga, Japan) with a unique dual-index primer. Following library construction, DNA libraries were sequenced on a NextSeq 1000 (Illumina, San Diego, CA, USA) using 150-bp paired-end reads with custom primers.