From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon <i>Salmo salar</i>

Aykanat, Tutku; Lindqvist, Meri; Pritchard, Victoria L.; Primmer, Craig R.

doi:10.1111/jfb.13149

Cited by 65 publications

(79 citation statements)

References 70 publications

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“…Amplicon sequencing has recently been adopted by multiple genetics laboratories to genotype tens of thousands of individuals for research and monitoring efforts in salmonids (Matala et al, ). Additionally, a number of published studies have highlighted the utility of amplicon sequencing, including an analysis of thousands of Coho salmon ( Oncorhynchus kisutch) for parental based tagging and genetic stock identification (Beacham et al, ,), analysis of Chinook salmon ( O. tshawytscha ) returning to a stream in Idaho over a 19‐year period to evaluate long‐term impacts of supplementation (Janowitz‐Koch, Rabe, & Kinzer, ), genetic monitoring of Atlantic salmon ( Salmo salar ) (Aykanat, Lindqvist, Pritchard, & Primmer, ), evaluating pedigree relationships in kelp rockfish ( Sebastes atrovirens ) using microhaplotypes (Baetscher, Clemento, Ng, Anderson, & Garza, ), and determining allele dosage in Chinook salmon (McKinney, Waples, Pascal, Seeb, & Seeb, ). Larson is also developing amplicon sequencing containing ~500 loci for various management applications in walleye ( Sander vitreus ), cisco, lake sturgeon ( Acipenser fulvescens ), and lake whitefish ( Coregonus clupeaformis ).…”

Section: Amplicon Sequencing and Sequence Capture Facilitate The Tranmentioning

confidence: 99%

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

Meek

Larson

2019

Molecular Ecology Resources

112

118

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The genomics revolution has initiated a new era of population genetics where genome‐wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high‐throughput sequencing (e.g., GTseq), and sequence capture refers to using capture probes to isolate loci from reduced‐representation libraries (e.g., Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research programme. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype <500 loci on many individuals (>1,500) or for species where continued monitoring is anticipated (e.g., long‐term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where >500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.

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Section: Amplicon Sequencing and Sequence Capture Facilitate The Tranmentioning

confidence: 99%

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

Meek

Larson

2019

Molecular Ecology Resources

112

118

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“…There is considerable interest in applying the results of genomewide association analyses to conservation and management (Bernatchez, 2016;Bernatchez et al, 2017;Funk, McKay, Hohenlohe, & Allendorf, 2012;Garner et al, 2016;Harrisson, Pavlova, Telonis-Scott, & Sunnucks, 2014;Hoffmann et al, 2015;Pearse, 2016;Shafer et al, 2015). In fact, identifying the genetic basis of fitness traits has already provided key information for these purposes, including an improved understanding of adaptive divergence (Brieuc, Ono, Drinan, & Naish, 2015;Hornoy, Pavy, Gerardi, Beaulieu, & Bousquet, 2015), the discrimination of ecotypes within a panmictic species (Pavey et al, 2015), detecting polygenic selection to aquatic pollutants (Laporte et al, 2016), and the development of a marker panel for routine trait and population monitoring (Aykanat, Lindqvist, Pritchard, & Primmer, 2016;Barson et al, 2015). As the availability of genomic resources improves, it is important to explore how markers identified by association analyses on natural populations might be applied in different contexts.…”

Section: Introductionmentioning

confidence: 99%

Genomewide association analyses of fitness traits in captive‐reared Chinook salmon: Applications in evaluating conservation strategies

Waters

Hard

Brieuc

et al. 2018

Evolutionary Applications

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A novel application of genomewide association analyses is to use trait‐associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive‐ and wild‐origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha) and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site‐associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait‐associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness‐related traits. Genotypes at trait‐associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad‐scale change was detected across four generations, there were numerous regions where trait‐associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait‐associated—and potentially adaptive—loci. The results will promote the development of trait‐specific tools to better monitor genetic change in captive and wild populations.

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“…Indeed, the application of genomic techniques to the conservation management of salmonids represent key case studies for successful integration into management programmes (Garner et al , ; Aykanat et al , ; Pearse, ). Moving ahead with such genomics research is an important long‐term goal in order to improve salmonid conservation.…”

mentioning

confidence: 99%

“…Genomic methods have led to recent advances in the management of such mixed-stock fisheries (Garner et al, 2015;Bradbury et al, 2016), wherein the identification of stock composition is critical for sustainability. Indeed, the application of genomic techniques to the conservation management of salmonids represent key case studies for successful integration into management programmes (Garner et al, 2015;Aykanat et al, 2016;Pearse, 2016). Moving ahead with such genomics research is an important long-term goal in order to improve salmonid conservation.…”

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confidence: 99%

Conservation genomics: coming to a salmonid near you

Piccolo

2016

Journal of Fish Biology

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Using the examples on hereditary and environmental factors affecting salmonid populations, this paper demonstrates that ecologists have long appreciated the importance of local adaptation and intraspecific diversity for salmonid conservation. Conservationists, however, need to embrace the genomics revolution and use new insights to improve salmonid management. At the same time, researchers must be forthcoming with the uses and limitations of genomics, and conservation must move forward in the face of scientific uncertainty.

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From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon Salmo salar

Cited by 65 publications

References 70 publications

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

Genomewide association analyses of fitness traits in captive‐reared Chinook salmon: Applications in evaluating conservation strategies

Conservation genomics: coming to a salmonid near you

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