Genetic relationships among emu populations in Japanese farms based on mitochondrial and microsatellite DNA polymorphisms

Abstract

Emus (Dromaius novaehollandiae) are expected to become a novel poultry species for producing eggs, meat, and oil. In our previous studies, Japanese emu populations were predicted to have reduced genetic diversity through inbreeding. For a sustainable emu industry in Japan, it is necessary to understand the current genetic structure and relationships in dispersed farms. In this study, we investigated the genetic structure and relationships of six Japanese emu farms based on mitochondrial DNA and microsatellite polymorphisms. We analyzed the DNA sequences of the mitochondrial D-loop region in 157 individuals and detected four haplotypes with four nucleotide substitution sites (Hap-a, Hap-b, Hap-c, and Hap-d). Analysis of molecular variance revealed that 43.6% of total variance was "among population," and the F ST value was 0.436 with significant genetic differentiation (P < 0.001). In microsatellite analysis, the expected (H E ) and observed (H O ) heterozygosities were 0.53-0.64 and 0.44-0.59, respectively. Phylogenetic trees and STRUCTURE analysis revealed that the six Japanese farmed emu populations could be divided into four genetically differentiated groups. Therefore, we identified genetic resources that may be useful in extending the genetic diversity of Japanese farms and are predicted to contribute to the conservation and reconstruction of populations.

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

“…The inbreeding coefficients ( F IS ) of the TSP, OEF2016, OEF2017, FGP, and KGP were 0.320, 0.198, 0.175, 0.237, and 0.305, respectively. These results suggest that all tested Japanese farmed populations tend to inbreed and that TSP is in the most profound condition, consistent with our previous reports 5 , 27 . Pedigree analysis using Colony2 software showed that there were three full-sib pairs and 69 half-sibs in the analyzed 253 individuals (Fig.…”

“…In a previous study, we suggested that TSP and FGP/KGP are genetically different from OEF based on analyses using SSR markers and mtDNA haplotypes 5 . Therefore, we used samples derived from the same populations as in our previous studies and included a large number of individuals with OEF as controls.…”

“…We also found that some farm populations in Japan harbored different genetic components. Our previous study suggested that TSP, FGP, and KGP could be distinct populations from OEF and other two farms 5 . These results indicate that TSP, FGP, and KGP, which are composed of a small number of individuals for ornamental use, could become useful genetic resources for extending the genetic diversity of Japanese production farms.…”

“…The emu ( Dromaius novaehollandiae ) is a ratite species originally found in Australia. For a few decades, the emu has been expected to become a novel poultry breed that produces low-fat meat 1 , hypoallergenic eggs 2 , 3 , and oil containing a high proportion of unsaturated fatty acids 4 , 5 . In particular, emu oil purified from subcutaneous fat has anti-inflammatory properties 6 – 8 and thus has been utilized as a material for skincare products with high economic value 9 .…”

“…Based on mitochondrial DNA (mtDNA) and microsatellite DNA (SSR) polymorphisms, we have previously reported that genetic diversity within populations tends to be reduced through inbreeding 5 , 12 , 13 . We also found that some farm populations in Japan harbored different genetic components.…”