Genetic Architecture of Migration-Related Traits in Rainbow and Steelhead Trout,<i>Oncorhynchus mykis</i>s

Hecht, Benjamin C.; Thrower, Frank P.; Hale, Matthew C.; Miller, Michael R.; Nichols, Krista M.

doi:10.1534/g3.112.003137

Cited by 106 publications

(158 citation statements)

References 72 publications

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“…Many of these studies have identified QTL or significant associations between markers on Omy5 and life-history traits such as spawn timing [47,65,68], smoltification [42,46] and development rate or early maturation [17,66,67,70]. Thus, this study supports previous suggestions that the LD block on chromosome Omy5 represents a 'master control region' influencing residency and anadromy in O. mykiss [46,72] and is a parallel selected region [21] that has experienced repeated selection in multiple populations.…”

Section: Discussionsupporting

confidence: 87%

“…Our results provide data from natural populations in California and Oregon that support prior studies on diverse O. mykiss lineages using candidate genes, genome wide association and QTL mapping to explore the genetic architecture of traits associated with life history in O. mykiss, including migration [17,32,42,46,48,[65][66][67][68][69][70][71][72][73][74][75][76]. Many of these studies have identified QTL or significant associations between markers on Omy5 and life-history traits such as spawn timing [47,65,68], smoltification [42,46] and development rate or early maturation [17,66,67,70].…”

Section: Discussionsupporting

confidence: 73%

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Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

et al. 2014

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Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) lifehistory strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionsupporting

confidence: 73%

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

et al. 2014

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“…Members of the salmonid family cover a wide range of different life-history strategies (Hutchings and Morris 1985;Crete-Lafreniere et al 2012) and ecological conditions (e.g., Maret et al 1997;Evans et al 2010Evans et al , 2012Hecht et al 2012). Symbiotic microbes may to a large degree reflect these ecological conditions.…”

Section: Discussionmentioning

confidence: 99%

Declining diversity of egg-associated bacteria during development of naturally spawned whitefish embryos (Coregonus spp.)

et al. 2015

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Fish eggs are associated with microbes, whose roles range from mutualism to parasitism. Recent laboratory experiments have shown that the taxonomic composition of associated microbial communities on the egg influences embryonic development. Host genetics also plays an important role in determining the consequences for embryonic growth and survival in this interaction. Moreover, it has been found that the importance of host genetics increases during embryogenesis. These findings suggest that during embryogenesis, the host increasingly influences the composition of its associated microbial community. However, little is known about the composition of microbial communities associated with naturally spawned eggs in the wild. We sampled fertilized whitefish eggs (Coregonus spp.) of different developmental stages from six sub-Alpine lakes and used a universal primer pair and 454 pyrosequencing in order to describe the taxonomic composition of egg-associated bacterial communities. We found bacterial communities on early embryos to be very diverse and to resemble the bacterial composition of the surrounding water environment. The bacterial communities on late embryos were significantly less diverse than on early embryos and displayed a clear shift in taxonomic composition that corresponded poorly with the bacterial composition of the surrounding water environment. The main bacterial components on whitefish eggs in this study were Proteobacteria, Actinobacteria, and Firmicutes, while the five most common families were Leuconostocaceae, Streptococcaceae, Comamonadaceae, Oxalobacteraceae and Moraxellaceae. Their putative relationships with the host are discussed. We conclude that natural symbiotic bacterial communities become more specialized during embryogenesis because of specific interactions with their embryo host.

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“…Genetic maps from NGS have been developed quite extensively for salmonids, for example with RAD sequencing in O. nerka (Everett et al, 2012), O. mykiss (Hecht et al, 2012), and Atlantic salmon (Sm. salar) (Gonen et al, 2014).…”

Section: Genomic Organisationmentioning

confidence: 99%

“…With a similar paired design, Hecht and colleagues sought the genetic loci associated with propensity to migrate using a genome-wide association approach using SNPs of known location from species-specific linkage maps (Hecht et al, 2012;Miller et al, 2012). Genome-wide association analysis suggested different genomic regions underlying different phenotypic components of the migratory phenotype (Hecht et al, 2012(Hecht et al, , 2013. Annotation of genome regions linked to significant SNPs indicated they were likely in regions associated with physiological processes important in migration (Hecht et al, 2013;Hale et al, 2013).…”

Section: Migrationmentioning

confidence: 99%

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

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The past few years have seen an absolute revolution in genomic technologies and their potential applications to ecology and evolutionary biology research. Such advances open up a range of opportunities for research on non-model organisms and individuals drawn from wild populations. This has resulted in exciting new research seeking to identify the genetic polymorphisms important in adaptation and speciation and how they are organised within the genome. Building on this, there is great interest in the extent to which similar evolutionary patterns are found across multiple populations, particularly whether consistent genetic mechanisms are associated with recurrent phenotypes. A powerful context for disentangling these mechanisms is to focus on highly diverse radiations, where phenotypes vary in and across environments. Therefore, the high diversity found within and among species of salmonid fishes such as charr (Salvelinus) make for an ideal 'non'-model for genomic research. This paper outlines some of the current approaches available in ecological genomics and highlights some recent advances in salmonid research. It also suggests avenues for the sort of predictions that can be derived from ecological genomics, with the aim of understanding the genetics behind the fantastic diversity of salmonid fishes.Keywords Ecological genomics Á Transcriptomics Á Speciation Á Genetic mapping Á Salmonid fishes Á Charr Recent advances in the field of molecular biology have exciting implications for research on the ecology and evolution of natural populations. Particularly, high throughput 'next-generation' sequencing (NGS) (also known as 'second-generation', or 'massively parallel' sequencing) can generate huge amounts of genomic or transcriptomic data on almost any organism. NGS is dramatically decreasing in cost and the associated tools and pipelines are within reach of even modest research groups. This is therefore becoming an invaluable tool for understanding the origins and maintenance of biodiversity. These exciting new approaches can address long-standing questions in evolutionary biology, such as: What is the genetic basis of adaptations? How do closely related species differ? Why are some lineages more diverse than others?The challenge for 'omics' of non-model organisms now shifts away from raw data generation to focusing on informative evolutionary, ecological, and environmental contexts in order to most efficiently and

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Genetic Architecture of Migration-Related Traits in Rainbow and Steelhead Trout,Oncorhynchus mykiss

Cited by 106 publications

References 72 publications

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

Declining diversity of egg-associated bacteria during development of naturally spawned whitefish embryos (Coregonus spp.)

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

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