Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus <i>Salvelinus</i>

Hale, Matthew C.; McKinney, Garrett J.; Bell, Courtney L; Nichols, Krista M.

doi:10.1534/g3.117.300317

Cited by 7 publications

(8 citation statements)

References 62 publications

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“…Synteny analysis between members of Salmonidae also identified a number of Atlantic salmon chromosomes which each show homology to two linkage groups (Sutherland et al . 2016; Hale et al . 2017).…”

Section: Resultsmentioning

confidence: 99%

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A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication

De‐Kayne

Feulner

2018

Preprint

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Genomic datasets continue to increase in size and ease of production for a wider selection of species including non-model organisms. For many of these species highly contiguous and well-annotated genomes are unavailable due to their prohibitive complexity and cost. As a result, a common starting point for genomic work in non-model species is the production of a linkage map, which involves the grouping and relative ordering of genetic markers along the genome. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g. chromosome number and type or sex-related structural differences, to fine scale patterns e.g. recombination rate variation and co-localisation of differentiated regions. Here we present both a sex-averaged and sex-specific linkage maps for Coregonus sp. “Albock” containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring in Lep-MAP3. We discuss the differences between our sex-avagerated and sex-specific maps and identify synteny between C. sp. “Albock” linkage groups and the Atlantic salmon (Salmo salar) genome. Our synteny analysis confirms that many patterns of homology observed between Atlantic salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily.

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Section: Resultsmentioning

confidence: 99%

“…number and length of linkage groups (i.e. chromosomes) and can be used to evaluate synteny with related taxa to investigate genome evolution (Sarropoulou 2011; Hale et al . 2017; Leitwein et al .…”

Section: Introductionmentioning

confidence: 99%

A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication

De‐Kayne

Feulner

2018

Preprint

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“…Comparative analysis of linkage maps and genome assemblies from related species can also shed light on chromosomal evolution and speciation (Rastas et al 2015;Sutherland et al 2016;Hale et al 2017). Chromosomal inversions appear to have played an important role in speciation and adaptive divergence within the salmonid lineage (Miller et al 2012;Sutherland et al 2016, Pearse et al 2019 and within other taxa (Lowry and Willis 2010;Aylala et al 2013;Kupper et al 2016; for review see Wellenruether and Bernatchez 2018).…”

Section: Introductionmentioning

confidence: 99%

“…Linkage maps have been constructed for multiple salmonid species including rainbow trout (Miller et al 2012;Palti et al 2012;Gonzalez-Pena et al 2016), chinook salmon (Brieuc et al 2014;McKinney et al 2016;McKinney et al 2019), coho salmon (Kodama et al 2014), sockeye salmon (Everett, Miller and Seeb 2012;Larson et al 2015;Limborg et al 2015), chum salmon (Waples et al 2016); pink salmon (Spruell et al 1999;Lindner et al 2000), Atlantic salmon (Moen et al 2008;Lien et al 2011;Brenna-Hansen et al 2012;Gonen et al 2014), Arctic char (Nugent et al 2017;Christensen et al 2018a), brook trout (Sauvage et al 2012;Sutherland et al 2016;Hale et al 2017), brown trout (Leitwein et al 2017), European grayling (Sävilammi et al 2019), lake whitefish (Rogers et al 2007;Gagnaire et al 2013a), and European whitefish (De-Kayne et al 2018). No linkage map has been constructed for lake trout (but see May et al 1979, Johnson et al 1987, for work on segregation patterns in lake trout x brook trout hybrids), although the lake trout karyotype has been characterized in multiple previous studies (Phillips and Zajicek 1982;Reed and Phillips 1995) providing a reference for the number of expected chromosomes.…”

Section: Introductionmentioning

confidence: 99%

Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout

Smith

Amish

Bernatchez

et al. 2020

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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.

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“…, number and length of linkage groups ( i.e. , chromosomes) and can be used to evaluate synteny with related taxa to investigate genome evolution (Sarropoulou 2011; Hale et al 2017; Leitwein et al 2017). Linkage maps can be used to associate phenotypes and genotypes through quantitative trait locus (QTL) mapping (Doerge 2002).…”

mentioning

confidence: 99%

A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication

De‐Kayne

Feulner

2018

G3 Genes|Genomes|Genetics

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Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the complexity and cost involved in their assembly. As a result, a common starting point for genomic work in non-model species is the production of a linkage map. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g., chromosome number and type or sex-related structural differences, to fine scale patterns e.g., recombination rate variation and co-localization of differentiated regions. Here we present both sex-averaged and sex-specific linkage maps for Coregonus sp. “Albock”, a member of the European whitefish lineage (C. lavaretus spp. complex), containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring. We discuss the differences between our sex-averaged and sex-specific maps and identify genome-wide synteny between C. sp. “Albock” and Atlantic Salmon (Salmo salar), which have diverged following the salmonid-specific whole genome duplication. Our analysis confirms that many patterns of synteny observed between Atlantic Salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily. We also show that regions known for their species-specific rediploidization history can pose challenges for synteny identification since these regions have diverged independently in each salmonid species following the salmonid-specific whole genome duplication. The European whitefish map provided here will enable future studies to understand the distribution of loci of interest, e.g., FST outliers, along the whitefish genome as well as assisting with the de novo assembly of a whitefish reference genome.

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Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus

Cited by 7 publications

References 62 publications

A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication

A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication

Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout

A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication

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