A dense brown trout (Salmo trutta) linkage map reveals recent chromosomal rearrangements in the Salmo genus and the impact of selection on linked neutral diversity

ABSTRACTHigh-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socio-economically important species heavily impacted by human activities. A total of 3,977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species Salmo salar revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3,721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high density linkage map provides a useful genomic resource for future aquaculture, conservation and eco-evolutionary studies in brown trout.

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A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in theSalmoGenus and the Impact of Selection on Linked Neutral Diversity

G3 Genes|Genome|Genetics ◽

10.1534/g3.116.038497 ◽

2017 ◽

Vol 7 (4) ◽

pp. 1365-1376 ◽

Cited By ~ 19

Author(s):

Maeva Leitwein ◽

Bruno Guinand ◽

Juliette Pouzadoux ◽

Erick Desmarais ◽

Patrick Berrebi ◽

...

Keyword(s):

Linkage Map ◽

Brown Trout ◽

Salmo Trutta ◽

Chromosomal Rearrangements ◽

Brown Trout Salmo Trutta ◽

The Impact

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High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

International Journal of Molecular Sciences ◽

10.3390/ijms22115723 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5723

Author(s):

Yuan-Yuan Xu ◽

Sheng-Rui Liu ◽

Zhi-Meng Gan ◽

Ren-Fang Zeng ◽

Jin-Zhi Zhang ◽

...

Keyword(s):

Qtl Mapping ◽

Linkage Map ◽

Genetic Map ◽

Expression Patterns ◽

High Density ◽

Poncirus Trifoliata ◽

Leaf Abscission ◽

Comparative Genomic ◽

Map Comparison ◽

Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

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Higher mortality of the less suitable brown trout host compared to the principal Atlantic salmon host when infested with freshwater pearl mussel (Margaritifera margaritifera) glochidia

Parasitology Research ◽

10.1007/s00436-021-07145-4 ◽

2021 ◽

Author(s):

Janhavi Marwaha ◽

Per Johan Jakobsen ◽

Sten Karlsson ◽

Bjørn Mejdell Larsen ◽

Sebastian Wacker

Keyword(s):

Atlantic Salmon ◽

Brown Trout ◽

Host Species ◽

Salmo Trutta ◽

The Other ◽

Margaritifera Margaritifera ◽

Pearl Mussel ◽

Suitable Host ◽

Freshwater Pearl Mussel ◽

Host Interaction

AbstractThe freshwater pearl mussel (Margaritifera margaritifera) is a highly host-specific parasite, with an obligate parasitic stage on salmonid fish. Atlantic salmon (Salmo salar) and brown trout (Salmo trutta f. trutta and Salmo trutta f. fario) are the only hosts in their European distribution. Some M. margaritifera populations exclusively infest either Atlantic salmon or brown trout, while others infest both hosts with one salmonid species typically being the principal host and the other a less suitable host. Glochidial abundance, prevalence and growth are often used as parameters to measure host suitability, with the most suitable host species displaying the highest parameters. However, it is not known if the degree of host specialisation will negatively influence host fitness (virulence) among different host species. In this study we examined the hypothesis that glochidial infestation would result in differential virulence in two salmonid host species and that lower virulence would be observed on the most suitable host. Atlantic salmon and brown trout were infested with glochidia from two M. margaritifera populations that use Atlantic salmon as their principal host, and the difference in host mortality among infested and control (sham infested) fish was examined. Higher mortality was observed in infested brown trout (the less suitable host) groups, compared to the other test groups. Genetic assignment was used to identify offspring from individual mother mussels. We found that glochidia from individual mothers can infest both the salmonid hosts; however, some mothers displayed a bias towards either salmon or trout. We believe that the differences in host-dependent virulence and the host bias displayed by individual mothers were a result of genotype × genotype interactions between the glochidia and their hosts, indicating that there is an underlying genetic component for this parasite-host interaction.

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Resource partitioning between lake-dwelling Atlantic salmon (Salmo salar L.) parr, brown trout (Salmo trutta L.) and Arctic charr (Salvelinus alpinus (L.))

Ecology Of Freshwater Fish ◽

10.1111/j.1600-0633.2000.eff090402.x ◽

2000 ◽

Vol 9 (4) ◽

pp. 202-209 ◽

Cited By ~ 7

Author(s):

L. Jorgensen ◽

M. Halvorsen ◽

P.-A. Amundsen

Keyword(s):

Atlantic Salmon ◽

Salmo Salar ◽

Brown Trout ◽

Resource Partitioning ◽

Salmo Trutta ◽

Salvelinus Alpinus ◽

Arctic Charr ◽

Atlantic Salmon Salmo Salar ◽

Brown Trout Salmo Trutta

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River bed construction: impact and habitat restoration for juvenile Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L.

Aquaculture Research ◽

10.1111/j.1365-2109.1992.tb00792.x ◽

1992 ◽

Vol 23 (4) ◽

pp. 489-498 ◽

Cited By ~ 3

Author(s):

N. A. HVIDSTEN ◽

B.O. JOHNSEN

Keyword(s):

Atlantic Salmon ◽

Salmo Salar ◽

Brown Trout ◽

Salmo Trutta ◽

Habitat Restoration ◽

Atlantic Salmon Salmo Salar ◽

Juvenile Atlantic Salmon ◽

River Bed ◽

Brown Trout Salmo Trutta

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Unidirectional Natural Hybridization between Brown Trout (Salmo trutta) and Atlantic Salmon (S. salar) in Newfoundland

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f92-216 ◽

1992 ◽

Vol 49 (9) ◽

pp. 1953-1958 ◽

Cited By ~ 51

Author(s):

Colin McGowan ◽

William S. Davidson

Keyword(s):

Atlantic Salmon ◽

Brown Trout ◽

Salmo Trutta ◽

Dna Analysis ◽

Juvenile Fish ◽

Natural Hybridization ◽

Major Influence ◽

Isolating Mechanisms ◽

Brown Trout Salmo Trutta ◽

Sexually Mature

Protein electrophoresis and mitochondrial DNA analysis were used to detect the frequency and direction of natural hybridization between brown trout (Salmo trutta) and Atlantic salmon (S. salar) in nine Newfoundland rivers. In total, 37 hybrids were discovered in a sample of 792 juvenile fish for a regional frequency of 4.67%. Local frequencies ranged from 0.00 to 18.75% and were significantly heterogeneous. All of the hybrids sampled were produced from matings between female brown trout and male Atlantic salmon. Possible reasons for the breakdown of prereproductive isolating mechanisms between these species are considered. Reproductive characteristics of the populations involved appear to have a major influence on the dynamics of hybridization between these species in Newfoundland. It is proposed that an abundance of sexually mature Atlantic salmon parr in Newfoundland streams is responsible for both the frequency and direction of hybridization observed in this study.

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