A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations

Abstract

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo," cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.

Keywords: SNPs; homozygous-by-descent; runs of homozygosity; selective sweep.

Fig. 1.

Genome-wide SNP statistics and the phylogenetic tree. a) The distribution of SNP numbers in 500 kb window on chromosomes. b) The phylogenetic tree of 83 Muscovy duck individuals.

Fig. 2.

Analysis of the population structure. a) Scatter plots of PCA for 8 Muscovy duck populations. b) The admixture analysis of population structure differences among 83 individuals. c) The comparison of genetic distances between Fujian-bred and Crimo populations. d) The comparison of F_ST between Fujian-bred and Crimo populations.

Fig. 3.

Statistics of ROH and KEGG enrichment analysis. a) The number (log₁₀) of ROH fragments in the whole genome. b) The proportion of different ROH fragment length. (c) The length statistics of ROH in 8 populations. d) The results of KEGG enrichment analysis in commercial population ROH-overlapping genes. e) The results of KEGG enrichment analysis in Fujian-bred population ROH-overlapping genes.

Fig. 4.

Statistics of HBD and KEGG enrichment analysis. a) The number (log₁₀) of HBD fragments in the entire genome. b) The proportion of HBD at different levels. c) The length statistics of HBD in 8 populations. d) The results of KEGG enrichment analysis in the commercial populations in HBD-overlapping genes. e) The results of KEGG enrichment analysis in the Fujian-bred populations in HBD-overlapping genes.

Fig. 5.

Selective sweep unveils selection pressures on TECR. a) The identification of selective regions on chromosome 8 by SweeD. b) XP-CLR value distribution on chromosomes 1–10. c) The pi analysis results of Fujian-bred and commercial populations on chromosome 8. d) The Tajima's D analysis results of Fujian-bred and commercial populations on chromosome 8.