Detection of whole-genome selection signal in Jinding duck

Chinese indigenous ducks shape the phenotypic diversities of varieties under the influence of natural selection and artificial selection. Selection signatures are genotypic markers formation in the process of species evolution. The detection of selection signatures can reveal the evolutionary direction of species. In this study, restriction-site associated DNA sequencings was performed on four local duck breeds in Fujian Province, and selection signal detection was performed on Jinding duck with Liancheng White duck, Putian black duck and Shanma duck as the reference background to explore the evolutionary direction of this breed. Based on SNP data, selective sweep analysis was performed using population genetic differentiation coefficient（Fst） and nucleotide diversity ratio（π ratio）. The top 5% value was used as the threshold for Fst and π ratio, and the two thresholds were combined to identify selected genomic regions. In the selected regions of the three comparison groups, 349, 185 and 316 candidate genes were detected, respectively. The candidate genes were analyzed by gene ontology（GO） and Kyoto Encyclopedia of Genes and Genomes（KEGG）. The results showed that 129, 27 and 77 genes were significantly enriched in 20, 6 and 14 pathways, respectively（P＜0.05）. The functional genes that may be related to the important economic traits of Jinding ducks were selected from these significantly enriched candidate genes. These candidate genes were mainly involved in metabolic pathways, PI3K-Akt signaling pathways, starch and sucrose metabolism, chemokine signaling pathways and so on, suggesting that Jinding duck has experienced strong artificial selection in egg laying performance, muscle growth and development, heat stress, immunity and fat metabolism. The results of this study provided a reference for the protection and development of genetic resources of Jinding duck.