Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae)

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

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.

Carcass traits and fat quality of breeding emu (Dromaius novaehollandiae) in northern Japan

Characterization of carcass traits and fat quality is important to effectively produce and genetically improve emus. We investigated carcass traits in 309 emus. The meat production of female emus showed a significantly higher value than that of males (P < 0.01). The fat weight of male (9.232 ± 3.156 kg) was larger than that of the female (7.772 ± 2.697 kg). The fat yield (fat weight per kg of body weight) was strongly correlated to body weight (r = 0.79 and r = 0.75 in male and female, respectively). The fat melting points of females and males were 19.19 ± 3.39°C and 19.39 ± 3.39°C, respectively, without significant difference. Since the fat melting point did not correlate to body and fat weights, we predicted that it was an independent trait from body growth and was highly influenced by genetic elements. Percentages of palmitic, stearic, oleic, linoleic, and α-linolenic acids were 22.27 ± 3.50%, 9.37 ± 1.90%, 54.11 ± 5.17%, 13.54 ± 7.80% and 0.71 ± 0.59%, respectively. Among them, linoleic acid contents showed a wide individual difference (range 0.3–19.9%). The oleic/stearic acid ratio showed a negative correlation to the fat melting point. These results suggest that the fat melting point is a good indicator of C18:1/C18:0 ratio in emu fat.

Seasonal and sexual variation in mRNA expression of selected adipokine genes affecting fat deposition and metabolism of the emu (Dromaius novaehollandiae)

Emus are farmed for fat production. Oil rendered from their back and abdominal fat pads has good anti-oxidant and anti-inflammatory properties and has ingredients that promote cell growth. Our objective is to examine the mRNA expression of 7 emu adipokine genes (eFABP4, eSCD1, eAdipoQ, eAdipoR1, eAdipoR2, eLEP and eLepR) to identify gene markers that may help improve emu fat production. Back and abdominal fat tissues from 11 adult emus were biopsied at four time points (April, June, August and November). Total RNA was isolated and cDNA was synthesized. Gene specific primers were designed for partial cloning fragments to amplify the open reading frame of the 7 genes. eLEP was not expressed in emu fat tissue. Nucleotides and amino acids sequences of the 6 expressed gene were compared with homologs from other species and phylogenetic relationships established. Seasonal mRNA expression of each gene was assessed by quantitative RT-PCR and differential expression analysed by the 2^−ΔΔC_T method. The 6 expressed genes showed seasonal variation in expression and showed association of expression level with back fat adiposity. More whole-genome scanning studies are needed to develop novel molecular markers that can be applied to improve fat production in emus.

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.

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

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.