FN Archimer Export Format
PT J
TI Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout
BT 
AF Smith, Seth R.
   Amish, Stephen J.
   Bernatchez, Louis
   Le Luyer, Jeremy
   Wilson, Chris
   Boeberitz, Olivia
   Luikart, Gordon
   Scribner, Kim T.
AS 1:1,2,3;2:1,2;3:4;4:4,5;5:6;6:7;7:1,2;8:3,7;
FF 1:;2:;3:;4:PDG-RBE-RMPF;5:;6:;7:;8:;
C1 Conservation Genomics Group; Wildlife Biology Program, University of Montana, Missoula, MT, USA
   Flathead Lake Biological Station, Division of Biological Sciences, University of Montana Polson, MT, USA
   Department of Integrative Biology, Michigan State University, East Lansing MI, USA
   Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
   Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française, France
   Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
   Department of Fisheries and Wildlife, Michigan State University, East Lansing MI, USA
C2 UNIV MONTANA, USA
   UNIV MONTANA, USA
   UNIV MICHIGAN STATE, USA
   UNIV LAVAL, CANADA
   IFREMER, FRANCE
   ONTARIO MINIST NATURAL RESOURCES FORESTRY, CANADA
   UNIV MICHIGAN STATE, USA
SI TAHITI
SE PDG-RBE-RMPF
UM EIO
IN WOS Ifremer UMR
   DOAJ
   copubli-int-hors-europe
IF 3.154
TC 8
UR https://archimer.ifremer.fr/doc/00634/74659/74565.pdf
LA English
DT Article
DE ;Linkage map;Salvelinus;QTL;RAD;genomics;lake trout
AB Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus Salvelinus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species. 
PY 2020
PD JUL
SO G3-genes Genomes Genetics
SN 2160-1836
PU Genetics Society of America
VL 10
IS 6
UT 000539281600013
BP 1929
EP 1947
DI 10.1534/g3.120.401184
ID 74659
ER

EF