Genome-Wide Detection of Structural Variations Reveals New Regions Associated with Domestication in Small Ruminants

被引:7
作者
Cumer, Tristan [1 ]
Boyer, Frederic [1 ]
Pompanon, Francois [1 ]
机构
[1] Univ Grenoble Aloes, Univ Savoie Mt Blanc, LECA, CNRS, Grenoble, France
来源
GENOME BIOLOGY AND EVOLUTION | 2021年 / 13卷 / 08期
关键词
domestication; goat; population genomics; sheep; SNP; structural variations; L1; INSERTION; SPEF2; GENE; EXPRESSION; MUTATION; RESOLUTION; SIGNATURE; DISCOVERY; DELETION; PATTERN; MODELS;
D O I
10.1093/gbe/evab165
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
During domestication processes, changes in selective pressures induce multiple phenotypical, physiological, and behavioral changes in target species. The rise of next-generation sequencing has provided a chance to study the genetics bases of these changes, most of the time based on single nucleotide polymorphisms (SNPs). However, several studies have highlighted the impact of structural variations (SVs) on individual fitness, particularly indomestic species. We aimedat unraveling the role of SVs during the domestication and later improvement of small ruminants by analyzing whole-genome sequences of 40 domestic sheep and 11 of their close wild relatives (Ovis orientalis), and 40 goats and 18 of their closewild relatives (Capra aegagrus). Using a combination of detection tools, we called 45,796 SVs in Ovis and 15,047 SVs in Capra genomes, including insertions, deletions, inversions, copy number variations, and chromosomal translocations. Most of these SVs were previously unreported in small ruminants. 69 and 45 SVs in sheep and goats, respectively, were in genomic regions with neighboring SNPs highly differentiated between wilds and domestics (i.e., putatively related to domestication). Among them, 25 and 20 SVs were close to or overlapping with genes related to physiological and morpho-anatomical traits linked with productivity (e.g., size, meat or milk quality, wool color), reproduction, or immunity. Finally, several of the SVs differentiated between wilds and domestics would not have been detected by screening only the differentiation of SNPs surrounding them, highlighting the complementarity of SVs and SNPs based approaches to detect signatures of selection.
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页数:10
相关论文
共 55 条
[1]   Convergent genomic signatures of domestication in sheep and goats [J].
Alberto, Florian J. ;
Boyer, Frederic ;
Orozco-terWengel, Pablo ;
Streeter, Ian ;
Servin, Bertrand ;
de Villemereuil, Pierre ;
Benjelloun, Badr ;
Librado, Pablo ;
Biscarini, Filippo ;
Colli, Licia ;
Barbato, Mario ;
Zamani, Wahid ;
Alberti, Adriana ;
Engelen, Stefan ;
Stella, Alessandra ;
Joost, Stephane ;
Ajmone-Marsan, Paolo ;
Negrini, Riccardo ;
Orlando, Ludovic ;
Rezaei, Hamid Reza ;
Naderi, Saeid ;
Clarke, Laura ;
Flicek, Paul ;
Wincker, Patrick ;
Coissac, Eric ;
Kijas, James ;
Tosser-Klopp, Gwenola ;
Chikhi, Abdelkader ;
Bruford, Michael W. ;
Taberlet, Pierre ;
Pompanon, Francois .
NATURE COMMUNICATIONS, 2018, 9
[2]   The genomic signature of dog domestication reveals adaptation to a starch-rich diet [J].
Axelsson, Erik ;
Ratnakumar, Abhirami ;
Arendt, Maja-Louise ;
Maqbool, Khurram ;
Webster, Matthew T. ;
Perloski, Michele ;
Liberg, Olof ;
Arnemo, Jon M. ;
Hedhammar, Ake ;
Lindblad-Toh, Kerstin .
NATURE, 2013, 495 (7441) :360-364
[3]   The challenges and importance of structural variation detection in livestock [J].
Bickhart, Derek M. ;
Liu, George E. .
FRONTIERS IN GENETICS, 2014, 5
[4]   A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses [J].
Brooks, S. A. ;
Lear, T. L. ;
Adelson, D. L. ;
Bailey, E. .
CYTOGENETIC AND GENOME RESEARCH, 2007, 119 (3-4) :225-230
[5]   Cloning and sequence comparison of sheep CD28 and CTLA-4 [J].
Chaplin, PJ ;
Pietrala, LN ;
Scheerlinck, JPY .
IMMUNOGENETICS, 1999, 49 (06) :583-584
[6]  
Chen K, 2009, NAT METHODS, V6, P677, DOI [10.1038/NMETH.1363, 10.1038/nmeth.1363]
[7]   Detection and validation of structural variations in bovine whole-genome sequence data [J].
Chen, Long ;
Chamberlain, Amanda J. ;
Reich, Coralie M. ;
Daetwyler, Hans D. ;
Hayes, Ben J. .
GENETICS SELECTION EVOLUTION, 2017, 49
[8]   Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog [J].
Clark, LA ;
Wahl, JM ;
Rees, CA ;
Murphy, KE .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (05) :1376-1381
[9]   The population genetics of structural variation [J].
Conrad, Donald F. ;
Hurles, Matthew E. .
NATURE GENETICS, 2007, 39 (Suppl 7) :S30-S36
[10]  
Cumer T, 2020, BIORXIV