IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0228964.html
   My bibliography  Save this article

Genetic characteristics of Jiaji Duck by whole genome re-sequencing

Author

Listed:
  • Lihong Gu
  • Feng Wang
  • Zhemin Lin
  • Tieshan Xu
  • Dajie Lin
  • Manping Xing
  • Shaoxiong Yang
  • Zhe Chao
  • Baoguo Ye
  • Peng Lin
  • Chunhui Hui
  • Lizhi Lu
  • Shuisheng Hou

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.

Suggested Citation

  • Lihong Gu & Feng Wang & Zhemin Lin & Tieshan Xu & Dajie Lin & Manping Xing & Shaoxiong Yang & Zhe Chao & Baoguo Ye & Peng Lin & Chunhui Hui & Lizhi Lu & Shuisheng Hou, 2020. "Genetic characteristics of Jiaji Duck by whole genome re-sequencing," PLOS ONE, Public Library of Science, vol. 15(2), pages 1-15, February.
    • Handle: RePEc:plo:pone00:0228964
    DOI: 10.1371/journal.pone.0228964
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228964
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0228964&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0228964?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Erik Axelsson & Abhirami Ratnakumar & Maja-Louise Arendt & Khurram Maqbool & Matthew T. Webster & Michele Perloski & Olof Liberg & Jon M. Arnemo & Åke Hedhammar & Kerstin Lindblad-Toh, 2013. "The genomic signature of dog domestication reveals adaptation to a starch-rich diet," Nature, Nature, vol. 495(7441), pages 360-364, March.
    2. Qiang Qiu & Lizhong Wang & Kun Wang & Yongzhi Yang & Tao Ma & Zefu Wang & Xiao Zhang & Zhengqiang Ni & Fujiang Hou & Ruijun Long & Richard Abbott & Johannes Lenstra & Jianquan Liu, 2015. "Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions," Nature Communications, Nature, vol. 6(1), pages 1-7, December.
    3. Ravi K Patel & Mukesh Jain, 2012. "NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-7, February.
    4. Zhengkui Zhou & Ming Li & Hong Cheng & Wenlei Fan & Zhengrong Yuan & Qiang Gao & Yaxi Xu & Zhanbao Guo & Yunsheng Zhang & Jian Hu & Hehe Liu & Dapeng Liu & Weihuang Chen & Zhuqing Zheng & Yong Jiang &, 2018. "An intercross population study reveals genes associated with body size and plumage color in ducks," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jun Gojobori & Nami Arakawa & Xiayire Xiaokaiti & Yuki Matsumoto & Shuichi Matsumura & Hitomi Hongo & Naotaka Ishiguro & Yohey Terai, 2024. "Japanese wolves are most closely related to dogs and share DNA with East Eurasian dogs," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Dongya Wu & Enhui Shen & Bowen Jiang & Yu Feng & Wei Tang & Sangting Lao & Lei Jia & Han-Yang Lin & Lingjuan Xie & Xifang Weng & Chenfeng Dong & Qinghong Qian & Feng Lin & Haiming Xu & Huabing Lu & Lu, 2022. "Genomic insights into the evolution of Echinochloa species as weed and orphan crop," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Christian Rellstab & Stefan Zoller & Andrew Tedder & Felix Gugerli & Martin C Fischer, 2013. "Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-1, November.
    4. Xinfeng Liu & Wenyu Liu & Johannes A. Lenstra & Zeyu Zheng & Xiaoyun Wu & Jiao Yang & Bowen Li & Yongzhi Yang & Qiang Qiu & Hongyu Liu & Kexin Li & Chunnian Liang & Xian Guo & Xiaoming Ma & Richard J., 2023. "Evolutionary origin of genomic structural variations in domestic yaks," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Abrar E Al-Shaer & George R Flentke & Mark E Berres & Ana Garic & Susan M Smith, 2019. "Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-25, April.
    6. Feng Zhu & Zhong-Tao Yin & Zheng Wang & Jacqueline Smith & Fan Zhang & Fergal Martin & Denye Ogeh & Maxwell Hincke & Fang-Bing Lin & David W. Burt & Zheng-Kui Zhou & Shui-Sheng Hou & Qiang-Sen Zhao & , 2021. "Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    7. Wei Ding & Shougang Wang & Peng Qin & Shen Fan & Xiaoyan Su & Peiyan Cai & Jie Lu & Han Cui & Meng Wang & Yi Shu & Yongming Wang & Hui-Hui Fu & Yu-Zhong Zhang & Yong-Xin Li & Weipeng Zhang, 2023. "Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    8. Terence C. Burnham & Jay Phelan, 2021. "Ordinaries," Journal of Bioeconomics, Springer, vol. 23(2), pages 125-149, July.
    9. Tsukasa Yoshidomi & Kazuaki Tanaka & Tatsuya Takizawa & Satoshi Nikaido & Tetsuya Ito & Mai Kamikawa & Kensuke Hirose, 2021. "Copy number variation of amylase alpha 2B gene is associated with feed efficiency traits in Large White pigs," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 66(12), pages 495-503.
    10. Xue Gao & Sheng Wang & Yan-Fen Wang & Shuang Li & Shi-Xin Wu & Rong-Ge Yan & Yi-Wen Zhang & Rui-Dong Wan & Zhen He & Ren-De Song & Xin-Quan Zhao & Dong-Dong Wu & Qi-En Yang, 2022. "Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Irene Stefanini & Monica Di Paola & Gianni Liti & Andrea Marranci & Federico Sebastiani & Enrico Casalone & Duccio Cavalieri, 2022. "Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes," IJERPH, MDPI, vol. 19(13), pages 1-15, July.
    12. Matteo Bianchi & Stina Dahlgren & Jonathan Massey & Elisabeth Dietschi & Marcin Kierczak & Martine Lund-Ziener & Katarina Sundberg & Stein Istre Thoresen & Olle Kämpe & Göran Andersson & William E R O, 2015. "A Multi-Breed Genome-Wide Association Analysis for Canine Hypothyroidism Identifies a Shared Major Risk Locus on CFA12," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-16, August.
    13. Srijana Joshi & Lily Shrestha & Neha Bisht & Ning Wu & Muhammad Ismail & Tashi Dorji & Gauri Dangol & Ruijun Long, 2020. "Ethnic and Cultural Diversity amongst Yak Herding Communities in the Asian Highlands," Sustainability, MDPI, vol. 12(3), pages 1-25, January.
    14. Pingfen Zhu & Weiqiang Liu & Xiaoxiao Zhang & Meng Li & Gaoming Liu & Yang Yu & Zihao Li & Xuanjing Li & Juan Du & Xiao Wang & Cyril C. Grueter & Ming Li & Xuming Zhou, 2023. "Correlated evolution of social organization and lifespan in mammals," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0228964. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.