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Cheng-Fei Sun, Xin-Hui Zhang, Jun-Jian Dong, Xin-Xin You, Yuan-Yuan Tian, Feng-Ying Gao, He-Tong Zhang, Qiong Shi, Xing Ye. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (Micropterus salmoides). Zoological Research, 2023, 44(1): 78-89. doi: 10.24272/j.issn.2095-8137.2022.274
Citation: Cheng-Fei Sun, Xin-Hui Zhang, Jun-Jian Dong, Xin-Xin You, Yuan-Yuan Tian, Feng-Ying Gao, He-Tong Zhang, Qiong Shi, Xing Ye. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (Micropterus salmoides). Zoological Research, 2023, 44(1): 78-89. doi: 10.24272/j.issn.2095-8137.2022.274

Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (Micropterus salmoides)

doi: 10.24272/j.issn.2095-8137.2022.274
Raw reads from Illumina sequencing were deposited in the China National Genebank database (CNGBdb) under Accession No. CNP0003162, National Center for Biotechnology Information (NCBI) under BioProjectID PRJNA856472, Genome Sequence Archive (GSA) under Accession No. CRA013093, and Science Data Bank (SDB) under DOI:10.57760/sciencedb.03591.
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
X.Y. and Q.S. conceived and designed the research. X.H.Z., C.F.S., J.J.D., and X.X.Y. performed data analyses. C.F.S., J.J.D., F.Y.G., H.T.Z., and Y.Y.T. prepared the samples. X.H.Z. and C.F.S. wrote the manuscript. Q.S. and X.Y. revised the manuscript. All authors read and approved the final version of the manuscript.
#Authors contributed equally to this work
Funds:  This study was supported by the Key-Area Research and Development Program of Guangdong Province (2021B0202020001), China Agriculture Research System of MOF and MARA (CARS-46), Central Public-interest Scientific Institution Basal Research Fund of CAFS (2020TD23, 2020ZJTD-02), Project of Construction of Guangdong Aquatic Seed Industry Demonstration Base 2021, and Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (KJYF202101-02)
More Information
  • Largemouth bass (Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (psst1 and grb10), early development (klf9, sp4, and sp8), and immune traits (pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
  • Raw reads from Illumina sequencing were deposited in the China National Genebank database (CNGBdb) under Accession No. CNP0003162, National Center for Biotechnology Information (NCBI) under BioProjectID PRJNA856472, Genome Sequence Archive (GSA) under Accession No. CRA013093, and Science Data Bank (SDB) under DOI:10.57760/sciencedb.03591.
    Supplementary data to this article can be found online.
    The authors declare that they have no competing interests.
    X.Y. and Q.S. conceived and designed the research. X.H.Z., C.F.S., J.J.D., and X.X.Y. performed data analyses. C.F.S., J.J.D., F.Y.G., H.T.Z., and Y.Y.T. prepared the samples. X.H.Z. and C.F.S. wrote the manuscript. Q.S. and X.Y. revised the manuscript. All authors read and approved the final version of the manuscript.
    #Authors contributed equally to this work
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