Whole-genome Resequencing Reveals Signatures Of Selection And Timing Of Duck Domestication

Animal domestication was one of the major contributory factors to the agricultural revolution during the Neolithic period,which has significantly changed the earth's biosphere and resulted in a shift in human lifestyle from hunting to farming.Domesticated animals provide us stable sources of animal protein,such as meat,eggs,and milk,which contributing to the progress of human civilization and the growth of the world's population.Compared with their wild progenitors,domesticated animals showed notable changes in behavior,morphology,physiology,and reproduction.Detecting domestication-mediated selective signatures is important for understanding the genetic basis of both adaptation to new environments and rapid phenotype change.Mallards(Anas platyrhynchos)are the world's most widely distributed and agriculturally important waterfowl species,and are of particular economic importance in Asia.In the absence of archaeological evidence,the exact timing of domestication remains unknown.Moreover,domesticated mallards show many important behavioral and morphological differences from their wild ancestors,particularly related to plumage and neuroanatomy.However,the genetic basis of these phenotypic differences are still poorly understood.In order to determine the timing of duck domestication in China and the timing of meat and egg type ducks split,as well as identify the genomic regions under selection during domestication,we performed whole genome resequencing from 22 mallards belonging to two geographically distinct wild populations and 56 domesticated ducks belonging to seven different duck breeds(three for meat breeds,three for egg breeds,and one dual-purpose breed).A total of 535 billion high quality paired end sequence reads were recovered across 78 ducks with an average of 6.42 and a volume of 613.37 Gb in total,resulting in a mean coverage of 96.6%for the whole duck genome.Across samples,we identified a total of 39.2 million(M)variants,consisting of 36.1 M SNPs(average per sample = 4.5 M SNPs;range = 2.34-9.52 M SNPs)and 3.1 M INDELs(average per sample = 0.4 M INDELs;range = 0.21-0.89 M INDELs).Using this powerful dataset and a suite of cutting-edge population genetic and demographic analyses,we show that duck domestication was a recent and complex process,occurring only 2000 years ago,with the rapid subsequent selection for separate meat and egg breeds roughly 100 generations later.Gene flow estimates were relatively high,with 1 and 4 migrants per generation from the meat and egg breeds,respectively,into the wild population.Genomic comparison of wild to domesticated populations suggest that genes affecting brain and neuronal development have undergone strong positive selection during domestication.Our FST analysis also indicates that the duck white plumage is the result of selection at the MITF(melanogenesis associated transcription factor)locus.Taken together,our results show that duck domestication was a relatively recent and complex process,and the genetic basis of domestication traits show many striking overlaps with other vertebrate domestication events.And,the whole genome resequencing data of nine duck populations and SNPs and INDELs variant datasets are valuable resources for researchers studying evolution,domestication or trait discovery,and for breeders of Anas platyrhynchos.Furthermore,the data represent a foundation for development of new,ultrahigh density variant screening arrays for duck population level trait analysis and genomic selection.