Runs of homozygosity assessment using reduced representation sequencing highlight the evidence of random mating in emu (<i>Dromaius novaehollandiae</i>)

The domestication of emu (<i>Dromaius novaehollandiae)</i> began in the 1970s, but their productive characteristics have not undergone significant genetic enhancement. This study investigated the inbreeding and genetic diversity of 50 emus from various farms in Japan using Double digest restriction-site associated DNA sequencing (ddRAD-seq) markers. Single nucleotide polymorphism (SNP) calling revealed 171 975 high-quality SNPs while runs of homozygosity (ROH) analysis identified 1843 homozygous segments, with an average of 36.86 ROH per individual and a mean genome length of 27 Mb under ROH. The majority (86%) of ROH were short (0.5-1 Mb), indicating ancient or remote inbreeding. The average genomic inbreeding coefficient (<i>F</i>_ROH) was 0.0228, suggesting nearly no inbreeding. Overlapping ROH regions were identified, with top consensus regions found on chromosomes 8 and Z. Seven candidate genes related to egg production, feather development, and energy metabolism were annotated in these regions. The findings highlight the prevalence of genetic diversity and low inbreeding levels in the studied emu population. This research highlights the potentiality of random mating in genetic management and conservation of emus. Further studies should focus on enhancing productive traits through selective breeding while preserving genetic diversity to ensure the sustainable growth of the emu farming.