Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout

Liu, Sixin; Vallejo, Roger L.; Palti, Yniv; Gao, Guangtu; Marancik, David; Hernández, Álvaro Gonzalez; Wiens, Gregory D.

doi:10.3389/fgene.2015.00298

Cited by 59 publications

(54 citation statements)

References 24 publications

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“…) and cortisol response (Liu et al . ) in rainbow trout, and thermal tolerance and growth in Oncorhynchus nerka , the sockeye salmon (Larson et al . ).…”

Section: Applications Of Rad Sequencing In Aquaculturementioning

confidence: 99%

Applications of genotyping by sequencing in aquaculture breeding and genetics

Robledo

Palaiokostas

Bargelloni

et al. 2017

Reviews in Aquaculture

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Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

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“…) and cortisol response (Liu et al . ) in rainbow trout, and thermal tolerance and growth in Oncorhynchus nerka , the sockeye salmon (Larson et al . ).…”

Section: Applications Of Rad Sequencing In Aquaculturementioning

confidence: 99%

Applications of genotyping by sequencing in aquaculture breeding and genetics

Robledo

Palaiokostas

Bargelloni

et al. 2017

Reviews in Aquaculture

219

172

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“…Several genome-wide association studies (GWAS) that match genetic variants, with or without pedigree records, with the observed phenotype have identified significant loci associated with economically important traits in livestock (Kadarmideen, 2014; Sharma et al, 2015). The aquaculture research community is following this trend, and interesting examples are available for growth and disease resistance traits in Atlantic Salmon (e.g., Correa et al, 2015; Gutierrez et al, 2015), rainbow trout (e.g., Kocmarek et al, 2015; Liu et al, 2015b; Palti et al, 2015b), and catfish (e.g., Geng et al, 2015). …”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

et al. 2016

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Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance. The GWAS analysis was performed using the weighted single-step GBLUP method (wssGWAS). Phenotypic records of 1447 fish (1.5 kg at harvest) from 299 full-sib families in three successive generations, of which 875 fish from 196 full-sib families were genotyped, were used in the GWAS analysis. A total of 38,107 polymorphic SNPs were analyzed in a univariate model with hatch year and harvest group as fixed effects, harvest weight as a continuous covariate, and animal and common environment as random effects. A new linkage map was developed to create windows of 20 adjacent SNPs for use in the GWAS. The two windows with largest effect for FY and FW were located on chromosome Omy9 and explained only 1.0–1.5% of genetic variance, thus suggesting a polygenic architecture affected by multiple loci with small effects in this population. One window on Omy5 explained 1.4 and 1.0% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17, and Omy9 (same window detected for FY) explained 1.7, 1.7, and 1.0%, respectively, of genetic variance for CAR. Among the detected 100 SNPs, 55% were located directly in genes (intron and exons). Nucleotide sequences of intragenic SNPs were blasted to the Mus musculus genome to create a putative gene network. The network suggests that differences in the ability to maintain a proliferative and renewable population of myogenic precursor cells may affect variation in growth and fillet yield in rainbow trout.

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“…It has also facilitated the identification of individual loci or regions of the genome directly under natural selection. "Top-down" approaches, such as genome-wide association studies and quantitative trait locus mapping, enable the discovery of regions of the genome associated with ecologically important traits (e.g., Jones et al 2012;Küpper et al 2015;Liu et al 2015;Pavey et al 2015;Comeault et al 2016). Alternatively, using "bottom-up" (or genome-scanning) approaches, it is possible to statistically detect loci under divergent selection between populations, and to use this information to identify candidate phenotypes previously not known to be under selection (Turner et al 2010;Fumagalli et al 2015;Kardos et al 2015;Manel et al 2016).…”

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confidence: 99%

Genomic associations with bill length and disease reveal drift and selection across island bird populations

et al. 2018

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Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterized genetic diversity and population structuring that supported previous inferences of a history of recent colonizations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands, and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in nonequilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.

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Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout

Cited by 59 publications

References 24 publications

Applications of genotyping by sequencing in aquaculture breeding and genetics

Applications of genotyping by sequencing in aquaculture breeding and genetics

Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

Genomic associations with bill length and disease reveal drift and selection across island bird populations

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