BACKGROUND
atlantic salmon , an anadromous species found primarily in the northern atlantic ocean, is widely known for its importance in both wild fishing and aquaculture.
according to statistics from the food and agriculture organization , the estimated global economic value of this species in  <dig> was approximately $ <dig>  billion  <cit> .
atlantic salmon is also a model for genomic studies of salmonid species with extensive genomic resources and a recent availability of an assembled reference genome sequence  <cit> .
atlantic salmon breeding programs are the most advanced of all aquaculture species and routinely incorporate genomic information to construct pedigrees, and to improve selection accuracy via marker-assisted or genomic selection  <cit> .
genome-wide association studies  are employed to assess the association between dna sequence variants  dispersed throughout the genome and complex traits of interest.
to date, abundant gwas have been conducted on human  <cit>  and terrestrial livestock species  <cit> , resulting in the discovery of several genes and underlying mutations affecting traits of medical and economic importance.
however, despite the contribution of gwas to terrestrial livestock and human medical research, relatively few gwas have been undertaken in aquaculture species to date, and have typically utilized relatively sparse snp chips .
recently, a high density publicly available snp chip containing ~132 k verified snp markers was developed  <cit>  and gives the opportunity to apply gwas at a resolution previously not possible in salmon.
commercially important traits for salmon farming such as growth and disease resistance are a major focus for scientific research, with several qtl mapping studies performed for growth performance  and disease resistance .
studies of the genetic basis of growth related traits using qtl linkage mapping identified chromosome regions of interest; however, there is a lack of consistency between the location of the qtl in different populations  <cit> .
potentially, gwas may be able to address some of the drawbacks of qtl mapping, such as the possible omission of qtl due to inadequate marker density  <cit> .
additionally, since gwas detects snps in population-wide linkage disequilibrium with qtl affecting the trait, the potential for applying these markers directly in selective breeding is greater.
while single marker-assisted selection is of limited value for polygenic traits, genomic estimated breeding values  can be calculated for candidate breeding animals using marker data, even in the absence of trait and/or pedigree information  <cit> .
studies using simulated data have shown the accuracy of prediction of breeding values using genomic data was significantly higher than using pedigree records alone  <cit> .
few studies of genomic prediction using real data have been performed in aquaculture species, although one recent analysis of a recently admixed farmed atlantic salmon population suggests that a genomic prediction approach can be effective at improving the accuracy of selection compared to pedigree records alone  <cit> .
the objectives of this study were  to use the high density  snp array to estimate genetic parameters for weight and length of juvenile farmed salmon and compare to those based on pedigree;  to detect individual snps/chromosomes associated with these traits;  to estimate breeding values and prediction accuracy for the two traits by applying the pedigree and the genomic relationship matrix across different marker densities;  to identify putative growth candidate genes by annotating the most significant markers from transcribed regions of the genome.
RESULTS
summary statistics and heritability
the final dataset used for the gwas consisted of ~ 112 k qc-filtered snps successfully genotyped in  <dig> fish  with weight and length measurements taken approximately 1 year post-hatching.
sex of the fish was predicted based on the y-specific probes on the snp array  and the population was evenly split between males and females .
the weight and length traits were highly correlated at the phenotypic and genetic level .
the overall heritability for both traits, as estimated by the genomic relationship matrix was ~  <dig> , compared to ~  <dig>  using the pedigree relationship matrix .table  <dig> the heritability and summary statistics of the weight and length phenotypes
aheritability was estimated by the genomic relationship matrix  and pedigree-based relationship matrix  respectively
genome-wide association analysis
to determine which individual snps were associated with weight and length, a gwas was performed on all markers.
no snps reached the genome-wide significance level , whereas one snp mapping to chromosome  <dig> surpassed the chromosome-wide significance level for length and was estimated to explain ~ 7 % of the additive genetic variation .
<dig> of the  <dig>  snps surpassed an  relaxed threshold  and were used for determining putative candidate genes .
the p-value, allele frequency, additive and dominance effect, and proportion of additive genetic variance due to the snp for the top ten markers for weight and length are given in table  <dig>  full lists of the snps surpassing the relaxed threshold are given in additional file 2: appendix  <dig>  the proportion of genetic variation explained by the top ten markers ranged between  <dig>  to  <dig> .
approximately 40 k snps had been assigned to corresponding chromosome using sire-based linkage mapping performed by crimap software  <cit>  as described in houston et al.
<cit>  and using the reference genome sequence .
the quantile-quantile  plots generated using model  in the gwa analysis for weight and length are given in additional file 3: appendix  <dig> table  <dig> the p-value, allele frequency, additive  and dominance  effect, and proportion of additive genetic variance explained for the top ten snp markers associated with weight and length
a
ax87963258
<dig>  e-05
<dig>
<dig>
<dig>
<dig>
<dig>
bold: chromosome-wide significance
asnp appears in the lists for both traits.
pomt1
myh9
gapdh
notch3
wdr35
wdr35
agrn
ax87963258b
rai2
kndc1
txnrd3
arhgef7
dlg5
klhl42
gucy2f
txnrd1
myo18ab
sytl5
gc3
si:ch211-181d <dig>
dlg5a
pgbd4
pgbd4
acorresponding chromosome was based on the atlantic salmon reference genome  and the chromosome assignments given in houston et al.
<cit> , see methods for additional details
bchromosome-wide significance
agrn: agrin; arhgef7: rho guanine nucleotide exchange factor  7; gapdh: glyceraldehyde-3-phosphate dehydrogenase; dlg5: discs, large homolog  <dig> ; rai2: retinoic acid-induced protein 2; kndc1: kinase non-catalytic c-lobe domain  containing 1; gucy2f: guanylate cyclase 2 f, retinal; pomt1: protein-o-mannosyltransferase 1; gc3: guanylate cyclase 2d, membrane ; klhl42: kelch-like family member 42; txnrd1: thioredoxin reductase 1; txnrd3: thioredoxin reductase 3; wdr35: wd repeat domain 35; myh9: myosin, heavy chain  <dig>  non-muscle; notch3: notch 3; myo18ab: myo18ab; sytl5: synaptotagmin-like 5
genomic prediction within population
the use of the snp markers for genomic prediction  of the weight and length traits was assessed and compared to the equivalent model using the pedigree to define relationships between the animals  using a five-fold cross validation design.
the accuracy of the gblup model was approximately 20 % higher than pblup for both traits when using all markers in the model, reaching a value of approximately  <dig>  within this population.
interestingly, while the prediction accuracy was improved by approximately 20 % with increased marker density from  <dig>  k to 5 k snps, there was very little or no improvement in accuracy of prediction with increased marker density beyond this level.
at the lowest marker density analyzed , the accuracy of gblup and pblup had the similar performance in both traits .
however, it should be noted that the training and validation populations used for this analysis will contain closely related animals.fig.
<dig> the estimated prediction accuracy of the  length and  weight traits when applying gblup and pblup across different marker densities
putative gene identification
a large proportion of the snps on the 132 k axiom array were derived from an rna-seq experiment and, therefore, are likely to be located within genes.
<dig> of the  <dig> snps surpassing a nominal significance threshold were matched with salmon fry transcriptome data using blastn alignment.
from these  <dig> transcripts, twelve, seven, and fifteen corresponding unique peptides were identified from human, mouse, and zebrafish database respectively using strict alignment criteria .
five genes were identified in all reference species, while ten, seven, and two genes were detected specifically in the zebrafish, human, and mouse databases respectively.
details including the associated gene name, putative chromosome in atlantic salmon, gene ontology , transcript id and gene id are given in additional file 1: appendix  <dig>  summaries of the identified genes are given in table  <dig> while the effects associated with these genetic markers are given in additional file 2: appendix  <dig>
the single marker that surpassed the chromosome-wide significance level for length  was annotated as retinoic acid-induced protein  <dig> .
retinoic acid is a critical regulator of development, cellular growth, and differentiation  <cit>  although the specific role of this ra induced gene is unknown.
discussion
genome wide association study
a high density snp array  <cit>  was applied to estimate genetic parameters and map snps associated with early growth of farmed salmon, as reflected by weight and length measurements at 1 year of age.
the estimates of trait heritability when using the genomic relationship matrix was comparable but slightly higher than the equivalent model using the pedigree relationships .
while no snps surpassed the stringent genome-wide significance threshold, one snp surpassed the chromosome-wide threshold for length .
therefore, the gwas results suggest that early growth in salmon is highly heritable but with a polygenic architecture and no evidence for major qtl.
based on previous linkage mapping and the current salmon reference genome assembly , the individual snps with the lowest p value for the growth traits were located on chr.
<dig>   <dig>   <dig>   <dig>   <dig> and  <dig>  qtl associated with growth traits have been reported on the same chromosomes in some  previous studies in atlantic salmon .
the proportion of variance explained  by each individual marker was relatively small  for the growth traits.
the data in the current study support previous studies suggesting that there is a lack of consistent, cross-population, major qtl affecting growth in atlantic salmon.
previous studies have performed gwa analyses to identify genetic variants associated with complex traits such as flesh texture, fat content and sexual maturation by using a ~ 6 k snp array in farmed atlantic salmon  <cit> .
in the current study, we used a substantially higher density of snps , which may have facilitated the detection of qtl in regions not covered by previous lower density snp platforms.
assessment of genomic prediction
due to practical and financial limitations, such as the previous lack of a high density genotyping platform, relatively few studies into genomic prediction have been undertaken using real data in aquaculture species.
a recent study by odegard et al.
<cit>  showed prediction accuracies of  <dig>  and  <dig>  for the traits of sea lice resistance and fillet colour respectively when using pblup, whereas gblup improved the accuracies by 32 % to 51 % for sea lice resistance, and up to 22 % for fillet colour.
previous studies applying simulated data have also indicated that gblup would have significantly higher accuracy compared to the equivalent model using pedigree records in the typical half/full-sibling family structure of salmon breeding programs .
our results also show that the blup model applying genomic data had higher accuracy than using pedigree information for both the weight and length traits, with an improvement of approximately 20 % to values close to  <dig> .
this is promising for the application of genomic prediction within salmon breeding programs, where it may be most effective for traits evaluated in siblings or other close relations of the selection candidates.
it is also noteworthy that ~  <dig> high quality informative snps are sufficient to achieve this increase in prediction accuracy in this population.
genotyping and field data collection are costly and the relative advantage of using snp data in selection depends on these costs versus the value of the extra improvement in the traits of interest.
therefore, while the high density snp array is more than adequate for within-population genomic prediction, the use of a cheaper and lower density snp platform is likely to be most cost-effective.
the cost-benefit is also likely to be most favourable for traits with high economic value and that cannot be measured directly on the selection candidates .
however, it is important to note that  this is a relatively small dataset for assessing genomic prediction and  the training and validation population will contain closely related animals.
as such, genomic prediction in this dataset will be based on both linkage and linkage disequilibrium information, which is likely to result in increased accuracy of prediction and reduced need for high density markers compared to scenarios where the training and validation populations are distantly related to each other.
it is plausible that with more distant relationships between the populations, a higher marker density and larger sample size would be required to achieve improvements in selection accuracy over traditional blup.
further, the high levels of linkage disequilibrium will result in greater power to detect qtl via gwas, but lower resolution to estimate qtl position.
simulation studies are generally consistent with the results based on real data presented in the current study: vela-avitua et al.
<cit>  reported that the prediction accuracy using sparse genomic data was equivalent or lower than using the classical pedigree model with sparse markers  across traits with different heritabilities , while hickey et al.
<cit>  demonstrated that increasing marker density above ~ 10 k results in little or no improvement in prediction accuracy in maize populations, while the results of gorjanc et al.
<cit>  also show only minor increases in accuracy above this level in simulated livestock datasets.
finally, odegard et al.
<cit>  detected little increase in accuracy with increases in marker density above 22 k for fillet colour or lice resistance in a commercial salmon population.
putative gene identification
the single snp exceeding the chromosome-wide significance level for length was mapped to chr.
<dig>  and its predicted location is within the retinoic acid-induced protein  <dig> gene .
although the function of rai <dig> is not yet clear, this gene is suggested to be involved in the control of cellular growth and embryo development  <cit> .
retinoic acid is well established as a key regulator of growth and differentiation in early life  <cit> , and is involved in the regulation of bone formation and mineralization in salmon  <cit> .
therefore, rai <dig> can be considered both a positional and a biological candidate for an effect on regulation of growth in juvenile salmon.
genes associated with the other markers discovered surpassing the arbitrary relaxed significance threshold  were also identified by aligning with human, mouse, and zebrafish databases .
amongst these was a snp in pomt <dig>  which produces the pomt enzyme complex, dysregulation of which can contribute to the formation of abnormal basement membranes, which can lead to muscular dystrophy  <cit> .
interestingly, the agrn  gene also appears to have a key regulatory role in basement membranes of neuromuscular junctions, and is involved in the inhibition, storage, activation of varied growth factors  <cit> , clustering of voltage-gated sodium channels, and g-protein coupled acetylcholine receptor signaling pathway  <cit> , all of which are essential for fundamental cell development.
in addition, notch <dig>  and the notch <dig> receptor have critical roles in the development and maintenance of vascular smooth muscle cells  <cit> .
finally, genes associated with atp binding and motor activity, such as myh <dig>  and myo18ab were also identified amongst the nominally significant markers.
while a proportion of the nominally significant snps  will clearly be false positives, highlighting these genes provides the opportunity to cross-reference with future studies to identify with higher confidence the putative candidates underlying growth in salmon.
CONCLUSIONS
the results of the current study show that early growth traits are highly heritable in farmed atlantic salmon, and that the heritability can be estimated by using either the genomic or the pedigree relationship matrix.
the gwa analysis showed that there are likely to be small effect qtl on several chromosomes, but there was no evidence for major qtl and these traits appear to be highly polygenic in nature.
a snp in the retinoic acid-induced protein  <dig> gene on chromosome  <dig> reached chromosome-wide significance, and is a plausible positional and functional candidate gene.
other genes identified from nominally significant snps will be useful for cross-referencing with similar studies in salmon and may form candidates for follow up studies to assess their function in regulation of growth in salmon.
for breeding value prediction using genomic and pedigree data, gblup had better accuracy than pblup in general with accuracy of ~  <dig>  attained for early growth traits using gblup in this population.
as few as 5 k snps gives close to maximal accuracy within population, suggesting that only moderate marker density is likely to be suitable for gs breeding programs for similar highly heritable but polygenic traits where the discovery populations have close relationships with the selection candidates.
however, it is important to note that increased marker density is likely to be advantageous, alongside larger sample size, when attempting to predict genomic breeding values in more distantly related animals.

 atlantic salmon, an anadromous species found primarily in the northern atlantic ocean, is widely known for its importance in both wild fishing and aquaculture. according to statistics from the food and agriculture organization, the estimated global economic value of this species in was approximately $ billion. atlantic salmon is also a model for genomic studies of salmonid species with extensive genomic resources and a recent availability of an assembled reference genome sequence. atlantic salmon breeding programs are the most advanced of all aquaculture species and routinely incorporate genomic information to construct pedigrees, and to improve selection accuracy via marker-assisted or genomic selection. genome-wide association studies are employed to assess the association between dna sequence variants dispersed throughout the genome and complex traits of interest. to date, abundant gwas have been conducted on human and terrestrial livestock species, resulting in the discovery of several genes and underlying mutations affecting traits of medical and economic importance. however, despite the contribution of gwas to terrestrial livestock and human medical research, relatively few gwas have been undertaken in aquaculture species to date, and have typically utilized relatively sparse snp chips. recently, a high density publicly available snp chip containing ~132 k verified snp markers was developed and gives the opportunity to apply gwas at a resolution previously not possible in salmon. commercially important traits for salmon farming such as growth and disease resistance are a major focus for scientific research, with several qtl mapping studies performed for growth performance and disease resistance. studies of the genetic basis of growth related traits using qtl linkage mapping identified chromosome regions of interest; however, there is a lack of consistency between the location of the qtl in different populations. potentially, gwas may be able to address some of the drawbacks of qtl mapping, such as the possible omission of qtl due to inadequate marker density. additionally, since gwas detects snps in population-wide linkage disequilibrium with qtl affecting the trait, the potential for applying these markers directly in selective breeding is greater. while single marker-assisted selection is of limited value for polygenic traits, genomic estimated breeding values can be calculated for candidate breeding animals using marker data, even in the absence of trait and/or pedigree information. studies using simulated data have shown the accuracy of prediction of breeding values using genomic data was significantly higher than using pedigree records alone. few studies of genomic prediction using real data have been performed in aquaculture species, although one recent analysis of a recently admixed farmed atlantic salmon population suggests that a genomic prediction approach can be effective at improving the accuracy of selection compared to pedigree records alone. the objectives of this study were to use the high density snp array to estimate genetic parameters for weight and length of juvenile farmed salmon and compare to those based on pedigree; to detect individual snps/chromosomes associated with these traits; to estimate breeding values and prediction accuracy for the two traits by applying the pedigree and the genomic relationship matrix across different marker densities; to identify putative growth candidate genes by annotating the most significant markers from transcribed regions of the genome.  summary statistics and heritability the final dataset used for the gwas consisted of ~ 112 k qc-filtered snps successfully genotyped in fish with weight and length measurements taken approximately 1 year post-hatching. sex of the fish was predicted based on the y-specific probes on the snp array and the population was evenly split between males and females. the weight and length traits were highly correlated at the phenotypic and genetic level. the overall heritability for both traits, as estimated by the genomic relationship matrix was ~ , compared to ~  using the pedigree relationship matrix.table the heritability and summary statistics of the weight and length phenotypes aheritability was estimated by the genomic relationship matrix and pedigree-based relationship matrix respectively genome-wide association analysis to determine which individual snps were associated with weight and length, a gwas was performed on all markers. no snps reached the genome-wide significance level, whereas one snp mapping to chromosome surpassed the chromosome-wide significance level for length and was estimated to explain ~ 7 % of the additive genetic variation. of the snps surpassed an relaxed threshold and were used for determining putative candidate genes. the p-value, allele frequency, additive and dominance effect, and proportion of additive genetic variance due to the snp for the top ten markers for weight and length are given in table  full lists of the snps surpassing the relaxed threshold are given in additional file 2: appendix the proportion of genetic variation explained by the top ten markers ranged between to. approximately 40 k snps had been assigned to corresponding chromosome using sire-based linkage mapping performed by crimap software as described in houston et al. and using the reference genome sequence. the quantile-quantile plots generated using model in the gwa analysis for weight and length are given in additional file 3: appendix table the p-value, allele frequency, additive and dominance effect, and proportion of additive genetic variance explained for the top ten snp markers associated with weight and length a ax87963258 e-05 bold: chromosome-wide significance asnp appears in the lists for both traits. pomt1 myh9 gapdh notch3 wdr35 wdr35 agrn ax87963258b rai2 kndc1 txnrd3 arhgef7 dlg5 klhl42 gucy2f txnrd1 myo18ab sytl5 gc3 si:ch211-181d dlg5a pgbd4 pgbd4 acorresponding chromosome was based on the atlantic salmon reference genome and the chromosome assignments given in houston et al., see methods for additional details bchromosome-wide significance agrn: agrin; arhgef7: rho guanine nucleotide exchange factor 7; gapdh: glyceraldehyde-3-phosphate dehydrogenase; dlg5: discs, large homolog; rai2: retinoic acid-induced protein 2; kndc1: kinase non-catalytic c-lobe domain containing 1; gucy2f: guanylate cyclase 2 f, retinal; pomt1: protein-o-mannosyltransferase 1; gc3: guanylate cyclase 2d, membrane; klhl42: kelch-like family member 42; txnrd1: thioredoxin reductase 1; txnrd3: thioredoxin reductase 3; wdr35: wd repeat domain 35; myh9: myosin, heavy chain non-muscle; notch3: notch 3; myo18ab: myo18ab; sytl5: synaptotagmin-like 5 genomic prediction within population the use of the snp markers for genomic prediction of the weight and length traits was assessed and compared to the equivalent model using the pedigree to define relationships between the animals using a five-fold cross validation design. the accuracy of the gblup model was approximately 20 % higher than pblup for both traits when using all markers in the model, reaching a value of approximately within this population. interestingly, while the prediction accuracy was improved by approximately 20 % with increased marker density from  k to 5 k snps, there was very little or no improvement in accuracy of prediction with increased marker density beyond this level. at the lowest marker density analyzed, the accuracy of gblup and pblup had the similar performance in both traits. however, it should be noted that the training and validation populations used for this analysis will contain closely related animals.fig. the estimated prediction accuracy of the length and weight traits when applying gblup and pblup across different marker densities  putative gene identification a large proportion of the snps on the 132 k axiom array were derived from an rna-seq experiment and, therefore, are likely to be located within genes. of the snps surpassing a nominal significance threshold were matched with salmon fry transcriptome data using blastn alignment. from these transcripts, twelve, seven, and fifteen corresponding unique peptides were identified from human, mouse, and zebrafish database respectively using strict alignment criteria. five genes were identified in all reference species, while ten, seven, and two genes were detected specifically in the zebrafish, human, and mouse databases respectively. details including the associated gene name, putative chromosome in atlantic salmon, gene ontology, transcript id and gene id are given in additional file 1: appendix summaries of the identified genes are given in table  while the effects associated with these genetic markers are given in additional file 2: appendix the single marker that surpassed the chromosome-wide significance level for length was annotated as retinoic acid-induced protein. retinoic acid is a critical regulator of development, cellular growth, and differentiation although the specific role of this ra induced gene is unknown. discussion genome wide association study a high density snp array was applied to estimate genetic parameters and map snps associated with early growth of farmed salmon, as reflected by weight and length measurements at 1 year of age. the estimates of trait heritability when using the genomic relationship matrix was comparable but slightly higher than the equivalent model using the pedigree relationships. while no snps surpassed the stringent genome-wide significance threshold, one snp surpassed the chromosome-wide threshold for length. therefore, the gwas results suggest that early growth in salmon is highly heritable but with a polygenic architecture and no evidence for major qtl. based on previous linkage mapping and the current salmon reference genome assembly, the individual snps with the lowest p value for the growth traits were located on chr. and qtl associated with growth traits have been reported on the same chromosomes in some previous studies in atlantic salmon. the proportion of variance explained by each individual marker was relatively small for the growth traits. the data in the current study support previous studies suggesting that there is a lack of consistent, cross-population, major qtl affecting growth in atlantic salmon. previous studies have performed gwa analyses to identify genetic variants associated with complex traits such as flesh texture, fat content and sexual maturation by using a ~ 6 k snp array in farmed atlantic salmon. in the current study, we used a substantially higher density of snps, which may have facilitated the detection of qtl in regions not covered by previous lower density snp platforms. assessment of genomic prediction due to practical and financial limitations, such as the previous lack of a high density genotyping platform, relatively few studies into genomic prediction have been undertaken using real data in aquaculture species. a recent study by odegard et al. showed prediction accuracies of and for the traits of sea lice resistance and fillet colour respectively when using pblup, whereas gblup improved the accuracies by 32 % to 51 % for sea lice resistance, and up to 22 % for fillet colour. previous studies applying simulated data have also indicated that gblup would have significantly higher accuracy compared to the equivalent model using pedigree records in the typical half/full-sibling family structure of salmon breeding programs. our results also show that the blup model applying genomic data had higher accuracy than using pedigree information for both the weight and length traits, with an improvement of approximately 20 % to values close to. this is promising for the application of genomic prediction within salmon breeding programs, where it may be most effective for traits evaluated in siblings or other close relations of the selection candidates. it is also noteworthy that ~  high quality informative snps are sufficient to achieve this increase in prediction accuracy in this population. genotyping and field data collection are costly and the relative advantage of using snp data in selection depends on these costs versus the value of the extra improvement in the traits of interest. therefore, while the high density snp array is more than adequate for within-population genomic prediction, the use of a cheaper and lower density snp platform is likely to be most cost-effective. the cost-benefit is also likely to be most favourable for traits with high economic value and that cannot be measured directly on the selection candidates. however, it is important to note that this is a relatively small dataset for assessing genomic prediction and the training and validation population will contain closely related animals. as such, genomic prediction in this dataset will be based on both linkage and linkage disequilibrium information, which is likely to result in increased accuracy of prediction and reduced need for high density markers compared to scenarios where the training and validation populations are distantly related to each other. it is plausible that with more distant relationships between the populations, a higher marker density and larger sample size would be required to achieve improvements in selection accuracy over traditional blup. further, the high levels of linkage disequilibrium will result in greater power to detect qtl via gwas, but lower resolution to estimate qtl position. simulation studies are generally consistent with the results based on real data presented in the current study: vela-avitua et al. reported that the prediction accuracy using sparse genomic data was equivalent or lower than using the classical pedigree model with sparse markers across traits with different heritabilities, while hickey et al. demonstrated that increasing marker density above ~ 10 k results in little or no improvement in prediction accuracy in maize populations, while the results of gorjanc et al. also show only minor increases in accuracy above this level in simulated livestock datasets. finally, odegard et al. detected little increase in accuracy with increases in marker density above 22 k for fillet colour or lice resistance in a commercial salmon population. putative gene identification the single snp exceeding the chromosome-wide significance level for length was mapped to chr. and its predicted location is within the retinoic acid-induced protein gene. although the function of rai is not yet clear, this gene is suggested to be involved in the control of cellular growth and embryo development. retinoic acid is well established as a key regulator of growth and differentiation in early life, and is involved in the regulation of bone formation and mineralization in salmon. therefore, rai can be considered both a positional and a biological candidate for an effect on regulation of growth in juvenile salmon. genes associated with the other markers discovered surpassing the arbitrary relaxed significance threshold were also identified by aligning with human, mouse, and zebrafish databases. amongst these was a snp in pomt which produces the pomt enzyme complex, dysregulation of which can contribute to the formation of abnormal basement membranes, which can lead to muscular dystrophy. interestingly, the agrn gene also appears to have a key regulatory role in basement membranes of neuromuscular junctions, and is involved in the inhibition, storage, activation of varied growth factors, clustering of voltage-gated sodium channels, and g-protein coupled acetylcholine receptor signaling pathway, all of which are essential for fundamental cell development. in addition, notch and the notch receptor have critical roles in the development and maintenance of vascular smooth muscle cells. finally, genes associated with atp binding and motor activity, such as myh and myo18ab were also identified amongst the nominally significant markers. while a proportion of the nominally significant snps will clearly be false positives, highlighting these genes provides the opportunity to cross-reference with future studies to identify with higher confidence the putative candidates underlying growth in salmon.  the results of the current study show that early growth traits are highly heritable in farmed atlantic salmon, and that the heritability can be estimated by using either the genomic or the pedigree relationship matrix. the gwa analysis showed that there are likely to be small effect qtl on several chromosomes, but there was no evidence for major qtl and these traits appear to be highly polygenic in nature. a snp in the retinoic acid-induced protein gene on chromosome reached chromosome-wide significance, and is a plausible positional and functional candidate gene. other genes identified from nominally significant snps will be useful for cross-referencing with similar studies in salmon and may form candidates for follow up studies to assess their function in regulation of growth in salmon. for breeding value prediction using genomic and pedigree data, gblup had better accuracy than pblup in general with accuracy of ~  attained for early growth traits using gblup in this population. as few as 5 k snps gives close to maximal accuracy within population, suggesting that only moderate marker density is likely to be suitable for gs breeding programs for similar highly heritable but polygenic traits where the discovery populations have close relationships with the selection candidates. however, it is important to note that increased marker density is likely to be advantageous, alongside larger sample size, when attempting to predict genomic breeding values in more distantly related animals. 
recently, high density snp arrays have become available for atlantic salmon, which facilitates genomic prediction and association studies using genome-wide markers and economically important traits. the aims of this study were to use a high density snp array to investigate the genetic architecture of weight and length in juvenile atlantic salmon; to assess the utility of genomic prediction for these traits, including testing different marker densities; to identify potential candidate genes underpinning variation in early growth. a pedigreed population of farmed atlantic salmon were measured for weight and length traits at one year of age, and genotyped for segregating snp markers using a high density snp array. the high density snp array can effectively capture the additive genetic variation in complex traits. however, the traits of weight and length both appear to be very polygenic with only one snp surpassing the chromosome-wide threshold. the results of the gwa analysis pointed to a polygenic genetic architecture, with no snps surpassing the genome-wide significance threshold, and one snp associated with length at the chromosome-wide level. the results have practical relevance for genomic selection in salmon and may also provide insight into variation in the identified genes underpinning body growth and development in salmonid species. the genetic architecture of complex traits in farmed animal populations is of interest from a scientific and practical perspective. genomic prediction using the array is effective, leading to an improvement in accuracy compared to pedigree methods, and this improvement can be achieved with only a small subset of the markers in this population. atlantic salmongwasgenomic-wide association analysisgenomic predictiongrowthissue-copyright-statement© the author 2015 the use of genetic markers to predict the genetic merit of individuals is commonplace in modern farm animal breeding schemes. snps surpassing an arbitrary threshold of significance were aligned to an atlantic salmon reference transcriptome, identifying snps in transcribed regions that were annotated by alignment to human, mouse and zebrafish protein databases.
 the genetic architecture of complex traits in farmed animal populations is of interest from a scientific and practical perspective. the use of genetic markers to predict the genetic merit of individuals is commonplace in modern farm animal breeding schemes. recently, high density snp arrays have become available for atlantic salmon, which facilitates genomic prediction and association studies using genome-wide markers and economically important traits. the aims of this study were to use a high density snp array to investigate the genetic architecture of weight and length in juvenile atlantic salmon; to assess the utility of genomic prediction for these traits, including testing different marker densities; to identify potential candidate genes underpinning variation in early growth.  a pedigreed population of farmed atlantic salmon were measured for weight and length traits at one year of age, and genotyped for segregating snp markers using a high density snp array. the heritability of both traits was estimated using pedigree and genomic relationship matrices, and was comparable at around and respectively. the results of the gwa analysis pointed to a polygenic genetic architecture, with no snps surpassing the genome-wide significance threshold, and one snp associated with length at the chromosome-wide level. snps surpassing an arbitrary threshold of significance were aligned to an atlantic salmon reference transcriptome, identifying snps in transcribed regions that were annotated by alignment to human, mouse and zebrafish protein databases. prediction of breeding values was more accurate when applying genomic than pedigree relationship matrices and snps were sufficient for obtaining this accuracy increase over pblup in this specific population.  the high density snp array can effectively capture the additive genetic variation in complex traits. however, the traits of weight and length both appear to be very polygenic with only one snp surpassing the chromosome-wide threshold. genomic prediction using the array is effective, leading to an improvement in accuracy compared to pedigree methods, and this improvement can be achieved with only a small subset of the markers in this population. the results have practical relevance for genomic selection in salmon and may also provide insight into variation in the identified genes underpinning body growth and development in salmonid species. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords atlantic salmongwasgenomic-wide association analysisgenomic predictiongrowthissue-copyright-statement© the author 2015 