Genomic analyses reveal the origin of domestic ducks and identify different genetic underpinnings of wild ducks

Abstract

19Domestic ducks are considered to have been tamed from the mallard or a descendant 20 of the mallard and the spot-billed duck. Domestic ducks show remarkable phenotypic 21 variation in morphology, physiology and behaviour. However, the molecular genetics 22 of the origin and phenotypic variation of ducks are still poorly studied. 23 Here, we present mallard and spot-billed genomes and perform whole-genome 24 sequencing on eight domestic duck breeds and eight wild duck species. Surprisingly, 25 analyses of these data support a model in which domestic ducks diverged from their 26 closest wild lineage (mallard ducks and spot-billed ducks) at the last glacial period 27 (LGP, 100-300 kilo years ago (Kyr)). The wild lineage further speciated into mallard 28 ducks and spot-billed ducks approximately 70 Kyr, whereas the domestic lineage 29 population decreased through the LGP. A scan of wild duck genomes compared with 30 domestic duck genomes identified numerous loci that may have been affected by 31 positive selection in ancestral wild ducks after their divergence from domestic 32 lineages. Function analyses suggested that genes usually affecting organ development 33 and energy metabolism may involve long-distance flight ability. Further selective 34 sweep analyses identified two genes associated with egg production and three genes 35 related to feeding modulation under selection in domestic ducks. These analyses 36 unravel a distinct evolutionary pattern of ducks and two wild duck de novo genomes, 37 thus providing a novel resource for speciation studies.38 40 41 65 zonorhyncha, refer as spot-billed)(Steve, 1992). Those are mainly based on their 66 similar outlooks, habits, and distributions. Moreover, there are broad phenotypic 67 4 differences between domestic ducks and their wild relatives, such as loss of flight and 68 migration ability, reduced brain size, and increased body size and fertility. Although 69 researches of steamer ducks on flightless and genetic association with selected traits 70 on domestic ducks have been performed (Zhang et al., 2018; Zhou et al., 2018). They 71 revealed diverse mechanisms from others and It indicating a historical context would 72 be important in understanding functional changes and its ecology factors (Burga et al., 73 2017; Campagna, McCracken, & Lovette, 2019). However, the demographic 74 inference suffered from lacking of solid history information, too many possibilities, 75 complex history and no robust mutation rates. The historical relationships of ducks, 76 like many other domestic animals, are still unclear (Albarella, 2005; Larson & Fuller, Despite, lots of efforts have committed and traditional domestication hypotheses have 79 been found incompatible with genetic data, and the direct ancestors of domesticated 80 animals are still unclear (Frantz et al., 2015; Freedman et al., 2014). Nevertheless, 81 some genetic analyses were still conducted under the pre-assumption of some 82 untested recoding and questionable hypothesis (Irving-Pease, Frantz, Sykes, Callou, 83 &...

Chromosomal-level reference genome of a wild North American mallard (Anas platyrhynchos)

“…To date, there are 9 mallard genomes published on NCBI ( Huang et al 2013 ; Zhou et al 2018 ; Liu et al 2020 ; Li et al 2021 ; Zhu et al 2021 ), with all of these being from Eurasian mallards that are either of known domestic origins, and with the 2 “wild” mallard genomes being the result of multiple sample poolings (i.e. CAU-Wild GenBank Accession ID GCA_008746955.1 ; Zhou et al 2018 ) and/or of un-vetted origins (i.e.…”

“…CAU-Wild GenBank Accession ID GCA_008746955.1 ; Zhou et al 2018 ) and/or of un-vetted origins (i.e. ASM222489V1 GenBank Accession ID GCA_002224895.1 ; Liu et al 2020 ; Xi et al 2021 ). Understandably, genomes have focused on domestic over wild mallards due to their agricultural and medical importance, including understanding gene linkage of favorable agricultural traits ( Zhang et al 2018 ; Zhou et al 2018 ) and disease resistance in the poultry industry more broadly ( Munster et al 2006 ; Skinner et al 2009 ).…”