Genomic analyses reveal the origin of domestic ducks and identify
different genetic underpinnings of wild ducks
Abstract
Domestic ducks are considered to have been tamed from the mallard or a
descendant of the mallard and the spot-billed duck. Domestic ducks show
remarkable phenotypic variation in morphology, physiology and behaviour.
However, the molecular genetics of the origin and phenotypic variation
of ducks are still poorly studied. Here, we present mallard and
spot-billed genomes and perform whole-genome sequencing on eight
domestic duck breeds and eight wild duck species. Surprisingly, analyses
of these data support a model in which domestic ducks diverged from
their closest wild lineage (mallard ducks and spot-billed ducks) at the
last glacial period (LGP, 100-300 kilo years ago (Kyr)). The wild
lineage further speciated into mallard ducks and spot-billed ducks
approximately 70 Kyr, whereas the domestic lineage population decreased
through the LGP. A scan of wild duck genomes compared with domestic duck
genomes identified numerous loci that may have been affected by positive
selection in ancestral wild ducks after their divergence from domestic
lineages. Function analyses suggested that genes usually affecting organ
development and energy metabolism may involve long-distance flight
ability. Further selective sweep analyses identified two genes
associated with egg production and three genes related to feeding
modulation under selection in domestic ducks. These analyses unravel a
distinct evolutionary pattern of ducks and two wild duck de novo
genomes, thus providing a novel resource for speciation studies.