Genomic Analyses Reveal The Evolution And Domestication Process Of Ducks

The duck is one of the most economically important waterfowl as a source of meat,eggs and feathers.Duck is also a kind of highly ornamental value that is stocked in lakes,parks and other human recreational places.In gerneral,the duck was considered to be domesticated from the mallard or the descendant of the mallard and spot-billed duck.However,domestic ducks showed significantly phenotypic diversity from these two wild populations.For example,the mallard and spot-billed make seasonal migrations.In contrast,domestic ducks are tame in behavior,and can't migrate which require the capacity for long time sustained flight,orientation and navigation.Recent Beijing duck whole genome sequence provide an important resource for functional analysies.However,The molecular genetics about ducks' origin and their phenotype variation are still poorly studied.In this study,cooperating with BGI colleagues,I sequenced the whole genome of a female mallard and a female spot-billed duck using methods similar to those applied to the Beijing duck genome.I generated a high-quality mallard assembly and a high-quality spot-billed assembly with three short insert size libraries(250 bp,500 bp,800 bp)and four mate-pair libraries(2 kbp,5 kbp,10 kbp,20 kbp).The contig N50 and scaffold N50 values of mallard genome assembly and spot-billed genome assembly were 37.78 kbp,33.30 kbp and 2.05 Mb,2.48 Mb respectively.Moreover,we found that the two wild duck genome assemblys had a high heterozygosity rate(3.59x 10-3,3.53x 10-3)and TE(repetitive elements)content(136 Mb,139 Mb)than beijing duck genome(2.61 × 10-3,80 Mb)?Moreover,I performed whole-genome sequencing on 7 domestic breeds and 8 wild populations of duck,together with taihu geese and muscovy as outgroups.Surprisingly,my date indicated that the ancestors of domestic ducks diverged from their closely wild relative lineage(mallard and spot-billed ducks)at the last glacial period(LGP,100?200 kilo years ago).Subsequently,the wild lineage was under the adaption selection,which might contribute to prevent the decrease in their population size.We found genes in or closet to these selective sweep regions were related to the development and morphogenesis of limb,lung,cardiac ventricle and respiratory system,energy metabolism and determination of body shape formation.Further analysis suggest that these selective sweeps might the main drive of the speciation of mallard and spot-billed.However,the domestic lineage seemed didn't advantage from such an adaption,and thus decreased continuously their population size during the LGP.Detail selective sweep analyses on domestic ducks identified 91 protein coding genes located around 73 regions that probably represent targets for selection during the initial stage of domestication.These genes were enrichment on the feeding behavior,courtship behavior and androgen metabolic process and nervous system development which might contribute to the tame behavior and ornamental value in domestic ducks.We thus proposed that the domestic ducks may have been subjected to human-derived selection for view and tame pet purpose during the initial stage of domestication.We also found that genes related to lipid,carbohydrate and protein metabolic process were under selection.This may due to domestic ducks have the plenty of food resource after they living with human.Furthermore,we performed luciferase reporter assays on six condidate casual variants that were considered to be functional important in the evolution of ducks.Four of the six candidate casual variants showed significant different effects on luciferase reporter activity.In summary,we generated high-quality assemblies of mallard and spot-billed respectively.I used high-coverage whole-genome sequencing to generate comprehensive genetic variation in wild and domestic duck populations.Detailed analyses suggested that ducks presented a distinct domestic model,which give an new example to understand animal domestication.Moreover,I inferred that mallard ducks diverged from spot-billed ducks at about 20 kyr which are in very recent specation stage.I demonstrated that the genomic landscape of ducks divergence provided important resource for speciation study.In addition,I found that genetic variation in non-coding regions might accelerated genomic diversity and specation process.