Whole-genome Resequencing And Transcriptome Sequencing Reveal Population Structure And Domestication Signature Of Ducks

Duck meat is well-known for its flavor and aroma,high composition of essential amino acids and high percentage of polyunsaturated fatty acids.China is not only the country with the largest number of ducks in the world and a long history of duck raising,but also one of the earliest regions in the world to domesticate wild ducks.Domestic ducks are quite different in appearance and behavior from their wild ancestors because they are bred by humans for two specific purpose,egg laying and meat production.However,little is known about the genetic changes during duck domestication.The genome of wild and native ducks provide a unique opportunity for tracing the history of domestication and identifying signatures of artificial selection.Here we used whole-genome resequencing approach and transcriptome sequencing method to explore the genetic relationship among wild ducks and domestic ducks,and to identify genomic footprints left by selection during the domestication of native ducks.Our experimental design involved the resequencing of ducks representing three populations of domestic ducks,Shaoxing Duck(SX),Shanma Duck(SM)and Cherry Valley Duck(CV),as well as two populations of wild ducks,Spot-billed Duck(Anas poecilorhyncha)(SB)and Mallard Duck(Anas platyrhnchos)(MA).Sequencing of sixty individuals from six duck populations generated a total of 397.88 GB of clean data and average of 6.63 Gb for each individual.This reads mapped to 95.09% of the reference genome assembly with 6.52-fold average depth.We called 2,809,077 high quality single nucleotide polymorphic sites(SNP)for 60 ducks,and the six populations shared 838,413 SNP.The neighbour-joining(NJ)tree,principal component analysis as well as population structure plots were implemented to examine the genome-wide relationships and divergence among six populations.The results of this analyses revealed a clear split between six populations.The excess of ABAB sites indicated that the CV population had a stronger signal of introgression from MA population,as well as SX population and SB population,which indicate that Spot-billed Duck has a contribution in the formation of Chinese native ducks.We employed the pairwise sequentially Markovian coalescent(PSMC)method to examine changes in effective population size of the ancestral population of both wild and domestic ducks response to Quaternary climatic change.The ancestral of SB showed a peak at 20,000 years ago,while the ancestral of other populations showed a peak at 40,000 to 60,000 years ago coinciding with the last glaciation.We detected genomic regions that have been subject to selection as inferred from high wild/domestic ? log-ratios and an extreme divergence of allele frequencies of wild and domestic ducks.We identified 17 shared potential selective-sweep genes in SX,SM and CV populations.These genes involved in cardiovascular development,smooth muscle proliferation,insulin function regulation,blood phosphorus metabolism and other physiological activities.The results of muscle,liver and cerebellum in transcriptome of SX and MA populations showed that a total of 731,733,980 high quality clean reads were detected in two populations.According to |log2Ratio| ? 1and q < 0.05,319,161 and 28 differentially expressed genes were identified in muscle,liver and cerebellum between SX and MA,respectively.Gene ontology annotation related to cellular process,single-organism process,biological regulation,bingding and catalytic.And the pathway analysis revealed that these genes belong to oxidative phosphorylation and fatty acid degradation.