Carlo Biagi - Academia.edu (original) (raw)
Papers by Carlo Biagi
Aquaculture, Aug 1, 2012
Several different transgenic growth hormone (GH) gene constructs have been used to obtain acceler... more Several different transgenic growth hormone (GH) gene constructs have been used to obtain accelerated growth in salmonids. However, there have been limited direct comparisons of these constructs in terms of the ability to achieve maximal growth in fish. We examined the effect of promoter type (sockeye salmon metallothionein-B or histone 3) fused to a growth hormone-1 coding region from the same species (OnMTGH1 and OnH3GH1 constructs respectively) on growth and plasma growth hormone (GH) and insulin-like growth factor-I (IGF-I) in multiple strains of GH transgenic coho salmon (Oncorhynchus kisutch). Salmon transgenic for the OnMTGH1 construct had consistently greater overall weight than those containing the OnH3GH1 construct, although both groups possessed greatly accelerated growth over non-transgenic fish. However, there were strong strain effects, where some OnH3GH1 strains had similar weight to OnMTGH1 strains while others did not. Triploidy diminished growth acceleration and decreased condition factors in both a fast growing MT strain and slower growing H3 strain. Plasma GH levels did not correlate to weight in transgenic strains, and all but one transgenic strain had plasma GH levels similar to equal sized non-transgenic fish. In contrast, plasma IGF-I content correlated well to size in transgenic strains. The mechanism by which accelerated growth in transgenic fish is obtained appears to be due in part to an upregulation of GH action through increased circulating IGF-I levels, and promoter-type appears to influence potential for growth.
Aquaculture, Jun 1, 2004
Transgenic coho salmon strains containing an all-salmon growth hormone (GH) gene construct (OnMTG... more Transgenic coho salmon strains containing an all-salmon growth hormone (GH) gene construct (OnMTGH1) have been examined. The transgene utilized is comprised of the metallothionein-B promoter driving the expression of the type-I growth hormone gene from sockeye salmon. Transgene DNA is integrated into the salmon genome, but is transmitted at low frequency from founder transgenic animals consistent with late integration following microinjection resulting in mosaic animals, whereas subsequent generations transmit transgene DNA as a stable Mendelian trait. Different families established from separate founder animals yield lines with unique growth characteristics suggesting important site-of-integration effects on transgene expression. Growth enhancement of transgenic salmon is initiated early, with advanced hatch timing but occurring also throughout the life history, particularly during the early phase in fresh water. GH transgenic fish showed precocious smoltification and onset of sexual maturation, but approximately normal adult body size, indicating that compression of the normal coho salmon life history is occurring. The viability of diploid GH transgenic salmon ranges from reductions to greater than that of controls among strains, and triploid transgenic animals had normal viability relative to diploid transgenic salmon. Triploid transgenic salmon display a reduction in growth rate relative to transgenic diploids, but are still significantly growth enhanced compared with nontransgenic controls. The distinct phenotypic characteristics of GH transgenic families suggest that evaluation for aquaculture and for risk assessments requires examination of strains on a case-by-case basis. Furthermore, strong effects of size at maturity in culture conditions were observed for nontransgenic wild strain coho salmon which were not apparent in GH transgenic salmon,
Transactions of The American Fisheries Society, Mar 1, 2006
Selective breeding for enhanced growth in Pacific salmon Oncorhynchus spp. and other fish typical... more Selective breeding for enhanced growth in Pacific salmon Oncorhynchus spp. and other fish typically involves use of the largest mature individuals to breed for future generations of aquaculture broodstock. Owing to an altered selection regime, faster‐growing fish may not be as adapted to the natural environment as wild fish. To increase understanding of the genetic changes underlying selection for enhanced growth that results in phenotypic differentiation of farmed from wild Pacific salmon, multiple generations of pure and hybrid families were generated for coho salmon O. kisutch, including pure farm (D), pure native (Ch; a natural strain propagated by wild and hatchery production), F1 and F2 hybrids, and F1 × wild backcross (BCh) genotypes. The family groups were reared in the laboratory under controlled conditions as (1) individual genotypic groups, (2) mixed groups under culture conditions, and (3) mixed groups under enriched (seminatural) conditions. The growth of the fish was tracked until smoltification. There was a significant genotype effect on growth performance (mass and length), with rankings as follows: D > F2 > F1 > BCh > Ch. This ranking remained the same in all three rearing environments. Behavioral differences were observed among the families, the fast‐growing domesticated families showing a reduced antipredator response relative to the slow‐growing wild families. Expression of the phenotypic differences in the hybrids and backcrosses, together with the results from a joint‐scale analysis on line means, suggests that additive genetic effects contribute significantly to the divergence between the fast‐ and slow‐growing strains. As phenotypic differences between strains are largely a consequence of additive gene action, the phenotypic effects of domestication are largely diluted within two generations of backcrossing to wild salmon. Knowledge of the genetic changes responsible for altered growth rates is crucial to our ability to predict the consequences of introgression of domestic strains into wild populations of salmon.
Aquaculture, Jun 1, 2010
The present study has assessed the efficacy of spontaneous and pressure-shock-induced triploidy a... more The present study has assessed the efficacy of spontaneous and pressure-shock-induced triploidy among 60,366 transgenic coho salmon progeny derived from crosses between homozygous growth hormone (GH) transgenic fathers and wild-type mothers. Trials found no effect of pressure, treatment timing postfertilization, treatment duration, or incubation temperature on the presence of diploid exception frequency, whereas older eggs (held in vivo or in vitro) were found to have lower frequencies of triploid failure. High temperature and young egg age were found to reduce survival of treated eggs, and family effects influenced survival in many treatments. Spontaneous triploidy was found to be rare (0.06% and 0.22% when eggs were stored in vivo or in vitro, respectively). Three larger scale trials (n = 15,814, 10,419, and 19,593) using normal pressure, high pressure, or high pressure plus aged eggs, yielded triploidy frequencies of 99.8%, 97.6%, and 97.0%, respectively. Overall, among all pressure-treated groups (n = 54,787 fish), 1.1% exceptional diploids were detected. If families with obvious high levels (N2%) of diploids are excluded, the frequency of diploid exceptions is 0.32%. Analyses of maternal genetic contributions to shocked progeny were consistent with 100% retention of the second polar body both in diploid exceptional individuals and in triploids. However, diploid exceptions did not consistently possess paternal genetic information (for GH transgene and microsatellite loci), and appeared to be either diploids or hyperdiploid aneuploids (i.e. possessing some but not all of the paternal marker loci). Thus, although sperm appear to fertilize and activate egg development in diploid exceptions, paternal chromosomes are not consistently contributed to the developing zygote's genome. It will be important to assess the fertility of these exceptional "diploid" individuals to determine whether rare cytological events occurring at fertilization may influence the utility of pressure-shock-induced triploidy for biocontainment purposes.
Aquaculture, Nov 1, 2020
Abstract Aquaculture continues to be the fastest-growing animal food sector and accounts for over... more Abstract Aquaculture continues to be the fastest-growing animal food sector and accounts for over 50% of the world's fish consumption. This trend is projected to continue, highlighting the role that the aquaculture industry will play in ensuring future global food security. Enhancement of growth rates of fish can optimize aquaculture production and has been achieved through selective breeding programs producing fast-growing domesticated strains, or the development of growth hormone (GH) transgenic strains. Although the ability of selectively-bred domesticated and GH transgenic salmon to outgrow wild-type salmon is well documented, very little research has been reported that directly compares the growth rates of domesticated and GH transgenic strains. The aim of the present study was to compare the growth and survival of selectively-bred domesticated and GH transgenic coho salmon across a range of experimental conditions. We performed four experiments investigating the growth rates of domesticated and GH transgenic salmon by comparing these strains at different developmental stages and under different experimental rearing conditions, as well as under conditions when strains were competing and when they were reared separately. Results from all experiments showed that GH transgenic coho salmon grew faster and to a larger size than the selectively-bred domesticated coho salmon. This was true whether fish groups were reared post-smolt in freshwater or seawater, whether reared together or separately, and whether manipulated to be size-matched at early stages. Thus, GH transgenesis could become a viable complement to selective breeding to produce fast-growing salmon for aquaculture systems. While further research can continue to optimize the development and use of transgenic strains, the data presented here also are important for environmental risk assessments by providing data on the relative fitness and ecological consequences of selectively-bred domesticated and GH transgenic fish should they enter nature.
Aquaculture, Mar 1, 1999
The organization of growth hormone GH genes has been examined in two closely related Ž. Ž species... more The organization of growth hormone GH genes has been examined in two closely related Ž. Ž species of salmonids from Japan, masu salmon Oncorhynchus masou and amago salmon O.. Ž. Ž. rhodurus. In two other species of salmonid, coho O. kisutch and chinook O. tshawytscha , a type-2 GH pseudogene sequence has been identified on the Y chromosome, and this sequence also appears to be located on the Y chromosome of O. masou. Interestingly, despite the close relationship between amago and masu salmon based on mtDNA sequence data, a Y-linked GH sequence was not observed in O. rhodurus and thus provides a molecular marker that can distinguish males of these two species. In addition, the Y-linked GH sequence in masu salmon provides a useful tool for the production of monosex all-female populations for aquaculture.
G3: Genes, Genomes, Genetics
Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to ... more Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant ann...
G3 Genes|Genomes|Genetics
Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that retur... more Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly. We also resequenced the genomes of 83 coho salmon across the North American range to identify nucleotide variants and understand the demographic histories of these salmon by modeling effective population size from genome-wide data. From demographic history modeling, we observed reductions in effective population sizes between 3,750 and 8,000 years ago for several northern sampling sites, which may correspond to bottleneck events during recolonization after glacial retreat.
North American Journal of Aquaculture
Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that retur... more Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated two chromosome-level genome assemblies and sequenced 24 RNA-seq libraries to better annotate the coho salmon genome assemblies. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, characterize the broad effects of isolation-by-distance using a genome-wide association analysis approach, and understand the demographic histories of these salmon by modeling population size from genome-wide data. We observed that more than 13% of all SNPs were associated with latitude (before multiple test correction), likely an...
Canadian Journal of Fisheries and Aquatic Sciences, 2022
Salmonids possess straying abilities that allows them to exploit open territory and establish new... more Salmonids possess straying abilities that allows them to exploit open territory and establish new populations. Atlantic salmon (Salmo salar) are expanding their distribution primarily as first-generation escapes from aquaculture, whereas Pacific salmon (Oncorhynchus spp.) are expanding their range in polar and temperate regions due to both anthropogenic and natural influences. Here we utilize artificial intergeneric reciprocal crosses to assess the ability of seven species of Pacific salmon to hybridize with Atlantic salmon. Most cross types were found to produce low numbers of hatched embryos, but none survived to sexual maturation. Survivors consisted of diploids and triploids containing both Atlantic and Pacific salmon parental genomes. Thus, introgression of DNA between Pacific and Atlantic salmon may occur to form F1 hybrids, but transmission to subsequent generations is expected to be rare and occur only over evolutionary time scales. Further, the low viability observed for th...
Canadian Journal of Fisheries and Aquatic Sciences, 2021
Many natural and managed organisms will require substantial functional genetic variation to respo... more Many natural and managed organisms will require substantial functional genetic variation to respond to selection in the face of rapid environmental change. Pacific salmon have experienced strong fluctuations in critical fitness traits over the past five decades. We examined genetic and phenotypic variability over three generations in a pedigreed hatchery population of coho salmon (Oncorhynchus kisutch) by monitoring seven fitness-related traits. Three-year-old adult return numbers varied more than fivefold, and jack (2-year-old males) numbers varied 13-fold. Body sizes of Inch Creek coho salmon decreased consistently such that fish were only 40.7% as heavy in 2015 as in 2006, and female reproductive traits also decreased. During the study period, the majority of families produced returning adult progeny, and effective population size was relatively constant. Heritability estimates for phenotypic traits were significantly greater than zero except for condition factor, and the estimat...
Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to... more Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a comb...
Canadian Journal of Fisheries and Aquatic Sciences, 2016
Two entries of data in Table A1 were placed in an incorrect column. Fish with ovaries from the Ba... more Two entries of data in Table A1 were placed in an incorrect column. Fish with ovaries from the Babine and Kitsumkalum Rivers (n = 25 and 24, respectively) were identified as being of GH-Y+; OtY1M genotype when in fact they are GH-Y-; OtY1F. These data should have been in one column to the right. This typographical mistake would lead a reader to believe that phenotypic females from these two populations carry the GH-Y and OtY1 Y-chromosomal markers when in fact they do not.
Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous... more Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids,. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on ...
Aquaculture, Aug 1, 2012
Several different transgenic growth hormone (GH) gene constructs have been used to obtain acceler... more Several different transgenic growth hormone (GH) gene constructs have been used to obtain accelerated growth in salmonids. However, there have been limited direct comparisons of these constructs in terms of the ability to achieve maximal growth in fish. We examined the effect of promoter type (sockeye salmon metallothionein-B or histone 3) fused to a growth hormone-1 coding region from the same species (OnMTGH1 and OnH3GH1 constructs respectively) on growth and plasma growth hormone (GH) and insulin-like growth factor-I (IGF-I) in multiple strains of GH transgenic coho salmon (Oncorhynchus kisutch). Salmon transgenic for the OnMTGH1 construct had consistently greater overall weight than those containing the OnH3GH1 construct, although both groups possessed greatly accelerated growth over non-transgenic fish. However, there were strong strain effects, where some OnH3GH1 strains had similar weight to OnMTGH1 strains while others did not. Triploidy diminished growth acceleration and decreased condition factors in both a fast growing MT strain and slower growing H3 strain. Plasma GH levels did not correlate to weight in transgenic strains, and all but one transgenic strain had plasma GH levels similar to equal sized non-transgenic fish. In contrast, plasma IGF-I content correlated well to size in transgenic strains. The mechanism by which accelerated growth in transgenic fish is obtained appears to be due in part to an upregulation of GH action through increased circulating IGF-I levels, and promoter-type appears to influence potential for growth.
Aquaculture, Jun 1, 2004
Transgenic coho salmon strains containing an all-salmon growth hormone (GH) gene construct (OnMTG... more Transgenic coho salmon strains containing an all-salmon growth hormone (GH) gene construct (OnMTGH1) have been examined. The transgene utilized is comprised of the metallothionein-B promoter driving the expression of the type-I growth hormone gene from sockeye salmon. Transgene DNA is integrated into the salmon genome, but is transmitted at low frequency from founder transgenic animals consistent with late integration following microinjection resulting in mosaic animals, whereas subsequent generations transmit transgene DNA as a stable Mendelian trait. Different families established from separate founder animals yield lines with unique growth characteristics suggesting important site-of-integration effects on transgene expression. Growth enhancement of transgenic salmon is initiated early, with advanced hatch timing but occurring also throughout the life history, particularly during the early phase in fresh water. GH transgenic fish showed precocious smoltification and onset of sexual maturation, but approximately normal adult body size, indicating that compression of the normal coho salmon life history is occurring. The viability of diploid GH transgenic salmon ranges from reductions to greater than that of controls among strains, and triploid transgenic animals had normal viability relative to diploid transgenic salmon. Triploid transgenic salmon display a reduction in growth rate relative to transgenic diploids, but are still significantly growth enhanced compared with nontransgenic controls. The distinct phenotypic characteristics of GH transgenic families suggest that evaluation for aquaculture and for risk assessments requires examination of strains on a case-by-case basis. Furthermore, strong effects of size at maturity in culture conditions were observed for nontransgenic wild strain coho salmon which were not apparent in GH transgenic salmon,
Transactions of The American Fisheries Society, Mar 1, 2006
Selective breeding for enhanced growth in Pacific salmon Oncorhynchus spp. and other fish typical... more Selective breeding for enhanced growth in Pacific salmon Oncorhynchus spp. and other fish typically involves use of the largest mature individuals to breed for future generations of aquaculture broodstock. Owing to an altered selection regime, faster‐growing fish may not be as adapted to the natural environment as wild fish. To increase understanding of the genetic changes underlying selection for enhanced growth that results in phenotypic differentiation of farmed from wild Pacific salmon, multiple generations of pure and hybrid families were generated for coho salmon O. kisutch, including pure farm (D), pure native (Ch; a natural strain propagated by wild and hatchery production), F1 and F2 hybrids, and F1 × wild backcross (BCh) genotypes. The family groups were reared in the laboratory under controlled conditions as (1) individual genotypic groups, (2) mixed groups under culture conditions, and (3) mixed groups under enriched (seminatural) conditions. The growth of the fish was tracked until smoltification. There was a significant genotype effect on growth performance (mass and length), with rankings as follows: D > F2 > F1 > BCh > Ch. This ranking remained the same in all three rearing environments. Behavioral differences were observed among the families, the fast‐growing domesticated families showing a reduced antipredator response relative to the slow‐growing wild families. Expression of the phenotypic differences in the hybrids and backcrosses, together with the results from a joint‐scale analysis on line means, suggests that additive genetic effects contribute significantly to the divergence between the fast‐ and slow‐growing strains. As phenotypic differences between strains are largely a consequence of additive gene action, the phenotypic effects of domestication are largely diluted within two generations of backcrossing to wild salmon. Knowledge of the genetic changes responsible for altered growth rates is crucial to our ability to predict the consequences of introgression of domestic strains into wild populations of salmon.
Aquaculture, Jun 1, 2010
The present study has assessed the efficacy of spontaneous and pressure-shock-induced triploidy a... more The present study has assessed the efficacy of spontaneous and pressure-shock-induced triploidy among 60,366 transgenic coho salmon progeny derived from crosses between homozygous growth hormone (GH) transgenic fathers and wild-type mothers. Trials found no effect of pressure, treatment timing postfertilization, treatment duration, or incubation temperature on the presence of diploid exception frequency, whereas older eggs (held in vivo or in vitro) were found to have lower frequencies of triploid failure. High temperature and young egg age were found to reduce survival of treated eggs, and family effects influenced survival in many treatments. Spontaneous triploidy was found to be rare (0.06% and 0.22% when eggs were stored in vivo or in vitro, respectively). Three larger scale trials (n = 15,814, 10,419, and 19,593) using normal pressure, high pressure, or high pressure plus aged eggs, yielded triploidy frequencies of 99.8%, 97.6%, and 97.0%, respectively. Overall, among all pressure-treated groups (n = 54,787 fish), 1.1% exceptional diploids were detected. If families with obvious high levels (N2%) of diploids are excluded, the frequency of diploid exceptions is 0.32%. Analyses of maternal genetic contributions to shocked progeny were consistent with 100% retention of the second polar body both in diploid exceptional individuals and in triploids. However, diploid exceptions did not consistently possess paternal genetic information (for GH transgene and microsatellite loci), and appeared to be either diploids or hyperdiploid aneuploids (i.e. possessing some but not all of the paternal marker loci). Thus, although sperm appear to fertilize and activate egg development in diploid exceptions, paternal chromosomes are not consistently contributed to the developing zygote's genome. It will be important to assess the fertility of these exceptional "diploid" individuals to determine whether rare cytological events occurring at fertilization may influence the utility of pressure-shock-induced triploidy for biocontainment purposes.
Aquaculture, Nov 1, 2020
Abstract Aquaculture continues to be the fastest-growing animal food sector and accounts for over... more Abstract Aquaculture continues to be the fastest-growing animal food sector and accounts for over 50% of the world's fish consumption. This trend is projected to continue, highlighting the role that the aquaculture industry will play in ensuring future global food security. Enhancement of growth rates of fish can optimize aquaculture production and has been achieved through selective breeding programs producing fast-growing domesticated strains, or the development of growth hormone (GH) transgenic strains. Although the ability of selectively-bred domesticated and GH transgenic salmon to outgrow wild-type salmon is well documented, very little research has been reported that directly compares the growth rates of domesticated and GH transgenic strains. The aim of the present study was to compare the growth and survival of selectively-bred domesticated and GH transgenic coho salmon across a range of experimental conditions. We performed four experiments investigating the growth rates of domesticated and GH transgenic salmon by comparing these strains at different developmental stages and under different experimental rearing conditions, as well as under conditions when strains were competing and when they were reared separately. Results from all experiments showed that GH transgenic coho salmon grew faster and to a larger size than the selectively-bred domesticated coho salmon. This was true whether fish groups were reared post-smolt in freshwater or seawater, whether reared together or separately, and whether manipulated to be size-matched at early stages. Thus, GH transgenesis could become a viable complement to selective breeding to produce fast-growing salmon for aquaculture systems. While further research can continue to optimize the development and use of transgenic strains, the data presented here also are important for environmental risk assessments by providing data on the relative fitness and ecological consequences of selectively-bred domesticated and GH transgenic fish should they enter nature.
Aquaculture, Mar 1, 1999
The organization of growth hormone GH genes has been examined in two closely related Ž. Ž species... more The organization of growth hormone GH genes has been examined in two closely related Ž. Ž species of salmonids from Japan, masu salmon Oncorhynchus masou and amago salmon O.. Ž. Ž. rhodurus. In two other species of salmonid, coho O. kisutch and chinook O. tshawytscha , a type-2 GH pseudogene sequence has been identified on the Y chromosome, and this sequence also appears to be located on the Y chromosome of O. masou. Interestingly, despite the close relationship between amago and masu salmon based on mtDNA sequence data, a Y-linked GH sequence was not observed in O. rhodurus and thus provides a molecular marker that can distinguish males of these two species. In addition, the Y-linked GH sequence in masu salmon provides a useful tool for the production of monosex all-female populations for aquaculture.
G3: Genes, Genomes, Genetics
Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to ... more Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant ann...
G3 Genes|Genomes|Genetics
Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that retur... more Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly. We also resequenced the genomes of 83 coho salmon across the North American range to identify nucleotide variants and understand the demographic histories of these salmon by modeling effective population size from genome-wide data. From demographic history modeling, we observed reductions in effective population sizes between 3,750 and 8,000 years ago for several northern sampling sites, which may correspond to bottleneck events during recolonization after glacial retreat.
North American Journal of Aquaculture
Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that retur... more Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated two chromosome-level genome assemblies and sequenced 24 RNA-seq libraries to better annotate the coho salmon genome assemblies. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, characterize the broad effects of isolation-by-distance using a genome-wide association analysis approach, and understand the demographic histories of these salmon by modeling population size from genome-wide data. We observed that more than 13% of all SNPs were associated with latitude (before multiple test correction), likely an...
Canadian Journal of Fisheries and Aquatic Sciences, 2022
Salmonids possess straying abilities that allows them to exploit open territory and establish new... more Salmonids possess straying abilities that allows them to exploit open territory and establish new populations. Atlantic salmon (Salmo salar) are expanding their distribution primarily as first-generation escapes from aquaculture, whereas Pacific salmon (Oncorhynchus spp.) are expanding their range in polar and temperate regions due to both anthropogenic and natural influences. Here we utilize artificial intergeneric reciprocal crosses to assess the ability of seven species of Pacific salmon to hybridize with Atlantic salmon. Most cross types were found to produce low numbers of hatched embryos, but none survived to sexual maturation. Survivors consisted of diploids and triploids containing both Atlantic and Pacific salmon parental genomes. Thus, introgression of DNA between Pacific and Atlantic salmon may occur to form F1 hybrids, but transmission to subsequent generations is expected to be rare and occur only over evolutionary time scales. Further, the low viability observed for th...
Canadian Journal of Fisheries and Aquatic Sciences, 2021
Many natural and managed organisms will require substantial functional genetic variation to respo... more Many natural and managed organisms will require substantial functional genetic variation to respond to selection in the face of rapid environmental change. Pacific salmon have experienced strong fluctuations in critical fitness traits over the past five decades. We examined genetic and phenotypic variability over three generations in a pedigreed hatchery population of coho salmon (Oncorhynchus kisutch) by monitoring seven fitness-related traits. Three-year-old adult return numbers varied more than fivefold, and jack (2-year-old males) numbers varied 13-fold. Body sizes of Inch Creek coho salmon decreased consistently such that fish were only 40.7% as heavy in 2015 as in 2006, and female reproductive traits also decreased. During the study period, the majority of families produced returning adult progeny, and effective population size was relatively constant. Heritability estimates for phenotypic traits were significantly greater than zero except for condition factor, and the estimat...
Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to... more Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a comb...
Canadian Journal of Fisheries and Aquatic Sciences, 2016
Two entries of data in Table A1 were placed in an incorrect column. Fish with ovaries from the Ba... more Two entries of data in Table A1 were placed in an incorrect column. Fish with ovaries from the Babine and Kitsumkalum Rivers (n = 25 and 24, respectively) were identified as being of GH-Y+; OtY1M genotype when in fact they are GH-Y-; OtY1F. These data should have been in one column to the right. This typographical mistake would lead a reader to believe that phenotypic females from these two populations carry the GH-Y and OtY1 Y-chromosomal markers when in fact they do not.
Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous... more Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids,. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on ...