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Lee D, Lee J, Heo KN, Kwon K, Moon Y, Lim D, Lee KT, Kim J. Population analysis of the Korean native duck using whole-genome sequencing data. BMC Genomics 2020; 21:554. [PMID: 32787779 PMCID: PMC7430827 DOI: 10.1186/s12864-020-06933-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/20/2020] [Indexed: 11/10/2022] Open
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.
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Affiliation(s)
- Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kang-Neung Heo
- National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngbeen Moon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dajeong Lim
- National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Kyung-Tai Lee
- National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Gu L, Wang F, Lin Z, Xu T, Lin D, Xing M, Yang S, Chao Z, Ye B, Lin P, Hui C, Lu L, Hou S. Genetic characteristics of Jiaji Duck by whole genome re-sequencing. PLoS One 2020; 15:e0228964. [PMID: 32049997 PMCID: PMC7015413 DOI: 10.1371/journal.pone.0228964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Abstract
Jiaji Duck (JJ) is a Muscovy duck species that possesses many superior characteristics, and it has become an important genetic resource in China. However, to date, its genetic characteristics and genetic relationship with other duck breeds have not been explored yet, which greatly limits the utilization of JJ. In the present study, we investigated the genome sequences of 15 individual ducks representing five different duck populations, including JJ, French Muscovy duck (FF), mallard (YD), hong duck (HD) and Beijing duck (BD). Moreover, we investigated the characteristics of JJ-specific single nucleotide polymorphisms (SNPs) and compared the genome sequences of JJ vs. YD and JJ vs. BD using integrated strategies, including mutation detection, selective screening, and Gene Ontology (GO) analysis. More than 40 Gb of clean data were obtained for each population (mean coverage of 13.46 Gb per individual). A total number of 22,481,367 SNPs and 4,156,829 small insertion-deletions (Indels) were identified for the five duck populations, which could be used as molecular markers in breeding and utilization of JJ. Moreover, we identified 1,447,932 JJ-specific SNPs, and found that genes covering at least one JJ-specific SNP mainly involved in protein phosphorylation and dephosphorylation, as well as DNA modification. Phylogenetic tree and principal components analysis (PCA) revealed that the genetic relationship of JJ was closest to FF, while it was farthest to BD. A total of 120 and 111 genes were identified as positive selection genes for JJ vs. BD and JJ vs. YD, respectively. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the positive selection genes for JJ vs. BD ducks mainly involved in pigmentation, muscle contraction and stretch, gland secretion, and immunology, while the positive selection genes obtained from JJ vs. YD ducks mainly involved in embryo development, muscle contraction and stretch, and gland secretion. Taken together, our findings enabled us to better understand the characteristics of JJ and provided a molecular basis for the breeding and hybrid utilization of JJ in the future.
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Affiliation(s)
- Lihong Gu
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Feng Wang
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Zhemin Lin
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Tieshan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, P. R. China
| | - Dajie Lin
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Manping Xing
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Shaoxiong Yang
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Zhe Chao
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Baoguo Ye
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Peng Lin
- Hainan Chuanwei Muscovy Duck Breeding Co., Ltd, Wenchang, P. R. China
| | - Chunhui Hui
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Lizhi Lu
- Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Shuisheng Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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Xu T, Gu L, Yu H, Jiang X, Zhang Y, Zhang X, Rong G, Zhou Z, Schachtschneider KM, Hou S. Correction: Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection. PLoS One 2019; 14:e0220996. [PMID: 31381595 PMCID: PMC6681946 DOI: 10.1371/journal.pone.0220996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0211908.].
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