- Population analysis of the Korean native. - Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. - 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. - 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.. - For ex- ample, analysis using sequencing data of a total of 89 indi- viduals in polar bear and brown bear populations was conducted to identify the divergence point of the two bear breeds [5]. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - Full list of author information is available at the end of the article. - The duck is one of the most common domesticated waterfowls and is economically important as a source of meat, eggs, and feathers [11]. - As a result, various genetic studies have been conducted to discover economically valuable genetic characteristics of duck breeds. - Although some recent stud- ies have investigated the unique characteristics of the Korean native duck [17–20], whole genome-level studies for the Korean native duck still lag behind other domes- tic animals and duck breeds.. - To address this, we apply a population-level genome ana- lysis based on whole-genome sequencing data from popula- tions of various duck breeds including KD. - Specifically, we sequenced the whole genomes of 20 KDs, collected whole- genome sequencing data of 14 phenotypically diverse duck breeds (Additional file 1: Table S1), and discovered single nucleotide polymorphisms (SNPs) for 15 duck breed popu- lations including KD. - Additionally, we examined the population structure of 15 duck breeds using various meth- odologies such as principal component analysis (PCA), ad- mixture, and phylogeny estimation. - 1 Appearance of male and female Korean native duck. - genomic regions under high differentiation among duck breeds and performed functional analysis of genes in those regions. - We also anno- tated SNPs and summarized the results for 15 duck breeds. - We also iden- tified the number of SNPs in indigenous duck breeds (Longsheng (LS), Jiding (JD), Loancheng white (LC), Mawang (MW), Puitan black (PT), Shan (SM), Sansui (SS), Shaoxing (SX), Taiwan (TW), Youxian (YX), Ji ’ an red (JA), and Gaoyou (GY. - The Ti/Tv ratio for KD, PK, and MD were and 2.51, respectively, and for the indigenous duck breeds have shown the Ti/Tv ratio ranging from 2.53 to 2.56. - We annotated all SNPs for 15 duck breeds with 19 functional categories, including synonymous, non- synonymous, intron, untranslated regions, and inter- genic (Additional file 3: Table S3).. - Investigation of unique genomic characteristics of Korean native duck. - To investigate the unique genomic characteristics of the Korean native duck (KD), we found 3062 KD genes con- taining unique non-synonymous SNPs (nsSNPs) not ob- served at the same position in other duck breeds (see Methods. - Enriched GO terms in the molecular function and cellu- lar component category are also shown in Additional file 5: Table S5. - In addition, we examined how the amino acid composition of these genes differs from other duck breeds. - In the case of PNPLA8 (Fig. - The ENO1 gene also had other positions where amino acid changes occur due to missense variant in various duck breeds.. - We further filtered the above KD genes and obtained KD-specific genes which have only KD unique nsSNPs, not with nsSNPs of the other duck breeds (see Methods). - Figure 2c shows an example of the change of amino acid composition in the GRIK2 gene. - After filtering out SNPs using various criteria such as minor allele frequency, genotype rate and the Hardy- Table 1 SNP statistics of 15 duck breeds. - Korean native duck (KD . - a Ti/Tv ratio is the ratio of the number of transitions to the number of transversions and standard deviations are in parentheses. - Weinberg equilibrium (see Methods), we obtained a total of 8,769,869 SNPs from 123 individuals of 15 duck breeds. - We first calculated the mean nucleotide diversity (π) [22] for each of 15 duck breeds using the filtered SNPs (Table 2. - MD showed the highest π value (0.1698), which is clearly larger than the values of other duck breeds (from 0.1028 to 0.1384). - We next used two approaches to identify the population structure of 15 duck breeds. - principal component analysis (PCA) to identify genomic relationships among 15 duck breeds. - By the first two principal components, 15 duck breeds were divided into three major clusters (Fig. - Second, we analyzed the popu- lation structure of 15 duck breeds using ADMIXTURE to estimate admixture proportion and individual ances- try based on the called genotypes (see Methods. - At K = 2, similar to the results of PCA, KD and PK were distinguished from the rest of the breeds. - At K = 5, we observed genomic rela- tionships among the 15 duck breeds consistent with the results of PCA. - We then constructed a maximum likeli- hood tree using a subset of 12,566 high-quality SNPs to identify the phylogenetic relationships among 15 duck breeds (Fig. - We confirmed that most of the individ- uals in the same breeds were grouped into one cluster, and these results were also consistent with the PCA result in terms of the first two principal components (Fig. - Bottom panel indicates positions of non-synonymous SNPs and comparison of amino acids among different duck breeds. - Table 2 Nucleotide diversity ( π ) of 15 duck breeds. - In the case of the KD versus PK population, some highly differentiated. - In the case of the KD versus MD population, the MTNR1A and ITPR2 genes were observed in highly differentiated regions (Fig.. - a The principal component analysis plot of 15 duck populations with the first two components. - c Maximum-likelihood phylogenetic tree of 15 duck populations. - Color of each branch corresponds to the color in the PCA plot for each duck population. - In this study, we performed whole-genome resequencing of 20 individual Korean native ducks (KD) using high- throughput next-generation sequencing technologies, and conducted a comparative analysis with 14 duck breeds based on single nucleotide polymorphism (SNP) data. - The 14 duck breeds were selected because they are well categorized according to their phenotypes, and their relationship among Pekin duck (PK), mallard (MD), and indigenous duck breeds is well studied [23].. - We detected and annotated a total of high-quality SNPs from the 15 duck breeds, and identified two types of gene sets based on the existence of non-synonymous SNPs (nsSNPs) in order to find unique genetic characteristics of the KD breed compared to other duck breeds. - Although no significantly enriched function has been identified in the 103 KD- specific genes, these genes may underlie a difference be- tween KD and other breeds. - The mean nucleotide diversity (π) of duck breeds was between 0.1028 to 0.1384, and MD showed exceptionally higher nucleotide diversity than domesticated breeds.. - We also performed population ana- lyses of 15 duck breeds including KD, and found similar patterns for duck breeds used in the previous study [23].. - In the highly differentiated regions. - The MITF gene plays an important role in the melanogenesis pathway [31, 32] and is involved in functions such as melanocyte differentiation (GO:0030318) and pigmen- tation (GO:0043473). - The ITPR2 gene plays a crucial role in the regulation of intracellular calcium transportation and the process of eggshell calcification related to eggshell quality [36]. - We suggest that these genes in the highly differentiated regions could be candidates for improving reproductivity, meat quality, and egg quality. - Genes related with these functions may have created difference between KD and other 14 duck breeds. - Zhou et al. - compared populations of MD, PK, and indigenous-breed ducks, and found a regulatory mutation in a long-distance upstream re- gion of the IGF2BP1 gene [23]. - The long-distance mutation may have a potential to induce continuous expression of the IGF2BP1 gene, which is related to large body size in PK. - The long-distance regulatory region and the IGF2BP1 gene were not included in the differentiated genomic regions obtained from the comparison between KD versus PK and KD versus MD in our study.. - In summary, our study represents the first population- level analysis of 15 duck breeds including Korean native duck (KD) based on whole-genome sequencing data.. - Our results include candidate genes associated with unique characteristics of KD, and the genetic relation- ship among the 15 duck breeds. - As a result, our research provides a comprehensive overview of the population structure and genetic diversity of 15 duck breeds, and will help further investigate the genetic information underlying commercially valuable traits in the KD breed.. - We generated whole-genome resequencing data from a population of Korean native duck (KD. - The Ko- rean duck samples were collected from Myeongbawi- nongsan (Yongin, Korea) in compliance with relevant guidelines, using protocols approved by the Committee on the Ethics of Animal Experiments of the National In- stitute of Animal Science (Permit Number: NIAS2015–. - Additional file 2:. - Table S2 for accession numbers of the data). - A total 103 public sequencing data of various duck breeds and 20 resequencing data of KD were aligned to the chromosome-level duck reference genome (assembly version IASCAAS_PekingDuck_PBH1.5. - Finally, raw calling data was filtered using the same criteria as in the previ- ous filtering step.. - We built a database with the NCBI RefSeq gene annota- tion data (duck annotation release 103) of the reference duck assembly (IASCAAS_PekingDuck_PBH1.5) [37], and performed variant annotation for the final SNPs of 15 duck breeds using SnpEff v4.3 [41]. - We also calculated the transition-to-transversion ratio (Ti/Tv) to evaluate the quality of the SNPs. - Note that these genes can have unique nsSNPs of other duck breeds or common nsSNPs among other duck breeds. - Therefore, we further reduced those KD genes to KD-specific genes which have only KD unique nsSNPs, not with nsSNPs of other duck breeds. - Functional analysis of the above KD genes and KD-specific genes was performed by g:Profiler with default parameters [42].. - Genes in the genomic regions with high Z-transformed Fst value (>. - The results of population differen- tiation were visualized in the form of a Manhattan plot by the qqman R package [52]. - Phenotypic information of 15 duck breeds.. - Functional categories of annotated SNPs of 15 duck breeds.. - A list of 3062 genes containing locus where only KD had non-synonymous SNPs compared to other duck breeds.. - The principal component analysis plot of 15 duck populations for all pairs of four components.. - Maximum likelihood phylogenetic tree of 15 duck breeds with Muscovy duck as an outgroup. - Color of each branch corresponds to the color in the PCA plot (Fig. - Manhattan plot of Z-transformed Fst (ZFst) between Korean native duck and other 14 duck breeds in sliding window 40 Kb with 10 Kb steps across the autosomal chromosomes. - PJ01040601, PJ01040606 and PJ01334302) of the National Institute of Animal Science funded by Rural Development Administration (RDA), a grant (2019R1F1A1042018) funded by. - The funding bodies played no role in the design of the study and collection, analysis and interpretation of data and in writing the manuscript.. - All SNPs of 15 duck breeds discovered in this study have been submitted to the European Variation Archive database (https://www.ebi.ac.uk/eva/. - This study was approved by the local committees and the research ethics committees of the National Institute of Animal Science, Republic of Korea.. - Verbal consent was obtained from the farm at which the Korean native ducks were sampled, which was sufficient to inform owners of the animals.. - The experimental protocols were approved by the Committee on the Ethics of Animal Experiments of the National Institute of Animal Science (Permit Number: NIAS2015 – 775). - Strong signatures of selection in the domestic pig genome. - Gene expression patterns in Korean native ducks (Anas platyrhynchos) with different apparent metabolisable energy (AME) levels. - Characterization of the human patatin-like phospholipase family. - Polymorphism of the melatonin receptor 1A (MNTR1A) gene and association with seasonality of reproductive activity in a local Greek sheep breed
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