Population analysis of the Korean native duck using whole-genome sequencing data

Abstract

Background: Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. The objective of this study is to perform population and functional analyses of Korean native duck, which has a distinct meat flavor and texture phenotype, using whole-genome sequencing data. To study the distinct genomic features of Korean native duck, we conducted population-level genomic analysis of 20 Korean native ducks together with 15 other duck breeds. Results: A total of 15.56 million single nucleotide polymorphisms were detected in Korean native duck. Based on the unique existence of non-synonymous single nucleotide polymorphisms in Korean native duck, a total of 103 genes related to the unique genomic characteristics of Korean native duck were identified in comparison with 15 other duck breeds, and their functions were investigated. The nucleotide diversity and population structures among the used duck breeds were then compared, and their phylogenetic relationship was analyzed. Finally, highly differentiated genomic regions among Korean native duck and other duck breeds were identified, and functions of genes in those regions were examined. Conclusions: This is the first study to compare the population of Korean native duck with those of other duck breeds by using whole-genome sequencing data. Our findings can be used to expand our knowledge of genomic characteristics of Korean native duck, and broaden our understanding of duck breeds.

Whole-genome sequencing identifies potential candidate genes for egg production traits in laying ducks (Anas platyrhynchos)

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Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population

“…This study examined positive selection by scanning both single locus and genomic blocks to obtain comprehensive and reliable genes with selection signatures. VCFtools ( Danecek et al., 2011 ) was used to calculate population Fst statistic as previously described between different populations ( Cagan and Blass, 2016 ; Lee et al., 2020 ; Wang et al., 2021a ) and the per-site Fst value was calculated between two populations with the parameter “–weir-fst-pop”. The R packages “GeneNet” ( Schaefer et al., 2015 ) was implemented to get the Z-transform Fst value for visualization in Manhattan plots by the R package “CMplot” in Figure 5 .…”

Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies

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