Genetic parameters for economically important traits in yellowtail kingfis Seriola lalandi Paul Whatmore, Nguyen Hong Nguyen,

Adam Miller, Rob Lamont, Dan Powell, Trent D' Antignana, Erin Bubner, Abigail Elizur, Wayne Knibb PII: DOI: Reference: To appear in: Received date: Revised date: Accepted date: S0044-8486(13)00111-7 doi: 10.1016/j.aquaculture.2013.03.002 AQUA 630583 Aquaculture 1 September 2012 27 February 2013 3 March 2013

Please cite this article as: Whatmore, Paul, Nguyen, Nguyen Hong, Miller, Adam, Lam ont, Rob, Powell, Dan, D'Antignana, Trent, Bubner, Erin, Elizur, Abigail, Knibb, Wayne, Genetic parameters for economically important traits in yellowtail kingsh Seriola lalandi, Aquaculture (2013), doi: 10.1016/j.aquaculture.2013.03.002

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Genetic parameters for economically important traits in yellowtail kingfish Seriola lalandi

D'Antignanac, Erin Bubnerd, Abigail Elizura, Wayne Knibba*

The Australian Seafood Cooperative Research Centre.

Clean Seas Tuna Limited, 7 North Quay Boulevard, Port Lincoln, SA 5606, Australia. School of Biological Science, Lincoln Marine Science Centre, Flinders University, PO Box

2023, Port Lincoln, South Australia 5606, Australia

ABSTRACT

The aim of the present study was to estimate genetic parameters for body and carcass traits, visual condition score, and deformity in yellowtail kingfish Seriola lalandi, an emerging aquaculture species in Australia. These novel data and genetic parameters are required to solve the problem of how to conduct efficient selection in this and related species. Analyses were performed on a total of 400 data records collected from a yellowtail kingfish breeding population at Cleanseas Tuna Ltd. farm. They were progeny of 22 full- and half-sib families (eight sires and six dams). Six newly developed and four published microsatellite markers were used to construct the pedigree. Genetic parameters were
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*Corresponding author: Tel: +61 7 5430 2831; e-mail: wknibb@usc.edu.au

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The University of the Sunshine Coast, Maroochydore, Queensland 4558, Australia

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Paul Whatmorea,b, Nguyen Hong Nguyena, Adam Millerc, Rob Lamonta, Dan Powella, Trent

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estimated using average information algorithm in ASReml with a multiple trait model. Fixed effects included sex, seal bite and deformity status. Random effects were the additive genetics of individual animal, and maternal and common environmental effects (i.e., damtank effect arising from a short period of separate rearing of offspring that came from two

moderate (h2 = 0.15 to 0.30, s.e. ranging from 0.09 to 0.19). Fillet fat content showed an

(0.41 0.26) when tank and dam were included as random effects. The estimate for condition score was 0.15 0.11, whereas the heritability for deformity was close to zero (h2 = 0.02). The genetic correlations between body and carcass (fillet weight and fillet yield)

body traits and condition score were moderate to high and positive (i.e. favourable). These results suggest that selection for high growth would result in concomitant increase in fillet

potential for genetic improvement of economically important traits especially growth performance and fillet weight in the current population of yellowtail kingfish. Keywords: selection. Seriola lalandi, kingfish; heritability; genetic correlation; fillet; fat content;

1. Introduction The yellowtail kingfish, Seriola lalandi, is an emerging aquaculture finfish species in Australia, with a current production approaching four thousand tons at a value of 20 million

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weight, a carcass trait of paramount importance. It is concluded that there is substantial

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traits were high and positive (0.57 to 0.94, s.e. 0.05 to 0.46). Genetic correlations between

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unusually high heritability (0.940.21) with a standard animal model, but was only moderate

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different broodstock tanks). The estimates of heritability for body and carcass traits were

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dollars/year (Booth et al., 2010) although aquaculture production on Seriola species in Japan is very large, accounting for most of Japans finfish aquaculture (Statistics Department, Ministry of Agriculture, Forestry and Fisheries, Japan 2002). In South Australia, where the majority of production occurs, it is the second most commercially valuable aquaculture

domestic and export markets with culture technologies being well developed. Yellowtail

fillets, cutlets and loins. In the Japanese sashimi market yellowtail kingfish is an extremely valuable product after tuna. However, with steadily reducing catches and quotas for bluefin tuna, the value and demand for yellowtail kingfish will continue to grow (Love and

known in yellowtail kingfish and there are no reports on genetic associations between body and carcass traits and flesh quality in this species. Genetic associations between

available in the literature for this species (Seriola lalandi). As yellowtail kingfish are group spawners and produce small larvae (about 4mm at hatching), physical tagging of offspring is unfeasible. DNA markers function as naturally occurring biological tags that can be used in lieu of physical tags, with the added benefit of enabling other biological observations to be made, such as management of genetic diversity and inbreeding of stocks (Frost et al., 2006). The application of genetic markers for parentage allocation and pedigree reconstruction have been practiced in other aquaculture species (e.g., Ferguson and Danzmann, 1998; Hara and Sekino, 2003; Sekino et al., 2005; Jerry et al., 2004; Vandeputte et al., 2004; Ninh et al., 2011). The technology has long been recognized as an effective tool to reconstruct the pedigrees of group spawned and communally reared aquaculture populations, allowing high
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performance and fitness related traits (condition score and deformity) were also not

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Langenkamp, 2003). Up to the present, quantitative genetic basis of these traits are not

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kingfish is a premium quality product and is marketed as whole live fish or fresh and frozen

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industry (Fernandes and Tanner, 2008). There is increasing demand for the species in both

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selection intensity in genetic improvement programmes (Doyle and Herbinger, 1995), to account for environmental effects common to full-sibs (Rodzen et al., 2004) and to achieve a high selection responses (Ninh et al., 2011). In the present study, we used a total of 10 microsatellites to construct the pedigrees for the

Specifically we report: i) heritability for body and carcass (fillet weight and fillet yield) traits including fat content, condition score and deformity, and ii) genetic relationships among

of traits in yellowtail kingfish such as whole and fillet weight, traits for which the market pays for, to start a formal breeding program for this species.

2. Materials and methods 2.1 Experimental location

The reproduction, larval rearing, fingerling production and grow-out were conducted at Clean Seas Tuna Ltd., Arno Bay (33 56.202' S 136 34.500' E), South Australia. Cages were towed from Arno Bay to Port Lincoln, South Australia (latitude 34 73' S, longitude 135 86' E) for harvest which is a distance of about 115 km.

2.2 Animal materials The original broodstock were eight wild males and six wild females, presumed to be 6-10 years old and estimated to be >15kg each, caught in the Spencer Gulf (i.e., are presumed to

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traits studied. The main aim of this study was to understand the quantitative genetic basis

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breeding population of yellowtail kingfish from which genetic parameters were estimated.

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come from the same population) and were held into two broodstock tanks at Arno Bay and all broodstock contributed to the offspring. The two tanks spawned a daily average of 1,290,000 and 974,000 eggs. Broodstock were kept at a density of 3-5 kg/m3, fed commercial diets, and mass spawned on several consecutive nights between 19 th and 30th

90/l, and fed rotifers (Artemia) from day 2 until day 15, Artemia was introduced at day 11

rearing, water temperature was maintained at about 24.5oC and 12h photoperiod. The survival rate from hatching to fingerlings varied from 6 to 14%. Fish continued to be reared in the hatchery until around day 70-80 when they reached 6-8 g when they were transferred

427 days post spawning) using standard industry practices. At harvest, four hundred fish were randomly sampled from the sea cage with approximately 40,000 fish and transported

progeny of 22 full-sibs and half-sibs families. As there were eight sires and six dams, typically each sire or dam had three to four half-sib groups, ranging from two to 50 offspring per group.

Phenotyping: Measurements and tissue sampling was completed at the processing factory in Port Lincoln and at the laboratory at the Lincoln Marine Science Centre. Four hundred animals were taken for measuring but some data were not available because of seal bites and availability from the factory. Measurements included weights, lengths (mouth to caudal fork), and condition score (an arbitrary measure to grade the general appearance of the fish

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to the processing factory in Port Lincoln in large, ice-filled containers. They were the G1

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to a sea cage, where they were on-grown to harvest (average body weight of 3.1 kg 0.35;

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and fed until day 25, fish were weaned onto pellet diet around day 22-25. During larval

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October 2011. The larvae were stocked in hatchery rearing tanks (8 14 m3) at a density of

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on a 1 to 5 scale, with 1 being the poorest condition and 5 the best condition; a fish that scored 5 had long, wide and deep body shape, appeared to have a heavy body weight for its length and no deformity, by contrast, a fish that scored 1 had deformity, and short and thin body shape).

which were the prevalent deformities found in these fish. In the present study, deformity was defined as a binary trait (coded as 1 for fish which had either low jaw, nasal erosion or

Both sides of skinless fillets were weighed and used to calculate total fillet weight and percent fillet yield (fillet weight/ slaughter weight). Gonads were bagged and placed on ice for later visual identification of sex. Approximately 20 g of muscle tissue were bagged and

2.3 Chemical analysis of fat

The crude fat content of the flesh was determined with an ethyl acetate extraction method based on the Norwegian Standard method (NS 9402 E) (NSA, 1994). We sampled tissue from approximately the same region in each animal; approximately 30mm inferior and anterior from the dorsal fin. This region showed the least seasonal variation and corresponds with the Mowi cut, which is a standard cut used in examining fat content in salmonids (Bremner, 2010).

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placed on ice for flesh quality assessment (analysis of fat content).

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operculum, and coded as 0 if these clinical signs were absent).

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Deformity was visually recorded and categorised as lower jaw, nasal erosion or operculum,

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2.4 Marker development 2.4.1 Primer design: For this study we used four published microsatellite primer pairs (references following) and developed primers for six additional microsatellite loci from S. lalandi transcriptome sequences. Primers for 25 published microsatellites from two other

four candidates were selected based on polymorphism and scoring accuracy. These four

Sdu46 (Renshaw et al., 2007). These were tested and validated using the protocols outlined by Renshaw et al. (2007).

Transcriptome sequences from S. lalandi liver and digestive systems were generated using

Facility. Microsatellite sequences were identified using the QDD pipeline (Meglecz et al., 2010) which includes primer design using Primer3 (Rozen and Skaletsky, 2000). Of the

70 were found to have a suitable number of repeat motifs (over 20) and suitable flanking regions on which to design primers. Of these 70 microsatellite sequences, 31 candidate primer pairs with similar Tm (around 60C) and minimal dimer interaction were selected for further testing. Forward primers for these 31 microsatellites were tagged with the M13(21) universal sequence 5-TGT AAA ACG ACG GCC AGT -3 to enable two-stage labelling with the use of an additional fluorescent dye labelled M13(21) primer. Primers were optimised by testing under a range of thermal and reaction parameters and a final six of the most specific and polymorphic microsatellites were selected for production. These loci in addition to the four published microsatellites are Sel001, Sel002, Sel008, Sel011, Sel017 and Sel019.

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41,765 reads generated, 250 contigs containing microsatellites were identified, from which

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the Roche 454 FLX next generation sequencing platform at the Australian Genome Research

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microsatellites were Sequ38 (Ohara et al., 2003), Sdu21 (Renshaw et al. 2006), Sdu32 and

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Seriola species (S. quinqueradiata and S. dumerili) were tested on S. lalandi broodstock and

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A total of six loci developed from our laboratory in addition to four published loci made up a total of 10 microsatellites for parentage assignments. The thermal parameters for primers with M13 sequences were: 94C for 3 minutes, 20 cycles of 94C for 30 seconds, 60C for 30 seconds (decreasing by 0.5C for each cycle), 72C for 45 seconds, 20 cycles of 94C for 30

M13 sequences the parameters were: 94C for 3 minutes, 40 cycles of 94C for 30 seconds,

average number of alleles detected was 102.10, the average observed heterozygosity was 0.70.05 and the polymorphic information content average was 0.66.06.

2.4.2 DNA extraction and PCR Reactions: DNA was extracted from caudal fin clips from

Microsatellite markers were amplified using a two-stage touchdown protocol with an initial 20 cycles running at an annealing temperature of 60C reducing by 0.5C every cycle, and

primers. PCR reactions were performed using 1.25 l of 10x reaction buffer, 1 l of 2.5mM dNTPs, 0.75 l of 25mM MgCl2, 0.05 l of Taq and 1 l of genomic DNA. For reactions using M13 tailed primers, three primers are included: equimolar reverse primer and M13 fluorescently labelled primers, and a M13 tailed forward primer that has 25% concentration of the other two primers (Schuelke, 2000). For our reactions this was 0.5 l of both the M13 fluorescently tagged primer and the reverse primer, and 0.125 l of the M13 tailed forward primer. To reach a final reaction volume of 13 l, 7.825 l of DNAse free water was added.

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then another 20 cycles run at 50C. This protocol is specifically optimised for M13 tailed

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broodstock and muscle tissue from G1 animals using a Qiagen DNeasy Blood and tissue kit.

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52C for 30 seconds, 72C for 45 seconds, 72C for 10 minutes. Considering all 10 loci, the

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seconds, 50C for 30 seconds, 72C for 45 sec, 72C for 10 minutes. For the primers without

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2.4.3 Genotyping and analysis: All genotyping was performed at the University of the Sunshine Coast on an Applied Biosystems 3500 Genetic Analyzer (Life Technologies). The G5 standard dye set was used on this platform (FAM-blue, NED-yellow, VIC-green, PET-red) with GeneScan LIZ 600 V2.0 (orange) as the size marker. Samples were prepared for use on

Genemarker software (SoftGenetics, USA). Only clear, high quality and easy to score peaks

markers was further validated by repeat genotyping of 100 samples. Of the 100 genotypes were that repeated, including a repeated PCR step, all match exactly at all 10 loci which suggest a high accuracy of scoring. This was done to minimise genotyping error and produce

MICROCHECKER (van Oosterhout et al., 2004) to check for null alleles, large allele dropout and scoring errors. Linkage disequilibrium between loci and deviation from Hardy-Weinberg

1995). Parentage assignment was completed using Cervus software (Kalinowski et al., 2007), and validated by comparing all broodstock genotypes to designated cohort of 90 G1 individuals known to be offspring from one of the two production broodstock tanks. Over 98% of these G1 animals was correctly assigned to their known parental group. Confidence scores for parentage assignments were calculated from likelihood-odds ratios and only assignments scoring over either 80% or 95% confidence were included in the pedigree, those below 80% were excluded. In total, 84% of parental assignments scored greater than a 95% confidence, and 8% scored between 80% and 95% confidence, thus 92% scores over 80% confidence. Those scoring between 80% and 95% confidence were confirmed by

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Equilibrium (HWE) at each locus was calculated using GENEPOP 4.1 (Raymond and Rousset,

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high confidence results. Validation of individual microsatellite loci was performed by using

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were accepted, with lower quality results discarded and/or repeated, and accuracy of

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this instrument as per the manufacturers instructions. Genotypes were scored using

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visually scoring individual alleles. The pedigree comprised only one generation of offspring and parents. Genotyping and molecular data analysis were conducted at University of the Sunshine Coast (USC) in Sippy Downs, Queensland, Australia.

2.5 Statistical analysis

2.5.1 Linear mixed model: Uni- and multi-trait linear mixed models were applied to estimate heritability and correlations for all the traits studied, respectively. The ASReml package was used (Gilmour et al., 2009). In a matrix notation, the model is written as the

y = Xb + Za + Wc + e where y is a vector of observations for traits studied, X, Z and W are the incidence matrices related to the fixed, additive genetic and common full-sib effects, and b is the vector of fixed

deformity status (yes or no), a is the additive genetic effect of individual animal for traits studied, and c is the vector of common full-sib effects [i.e., dam nested within spawning batch (tank), c2]. Due to a short period of about two-week early rearing before communal grow-out of all families was practised, the c2 effect was included as the second random term in the model. The c2 effect was however not significant. When it was added to the model, there were no (or only trivial) changes in logarithmic likelihood (LogL) value to all traits including fat content. Therefore, all traits observed were also analysed with a model that omitted the c2 effect.
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effects including sex (female and male), seal bite (fish were bitten by seal or not) and

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following:

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2 A Under the full model, heritabilities for traits were calculated as h 2 , where the P 2
2 2 phenotypic variance ( P ) was the sum of the additive genetic variance ( A ), maternal and

2 ) and the residual variance ( e2 ), i.e. common environmental variance ( C

2 2 2 2 . The estimated heritability for deformity was transformed from observed P A C e

(0, 1) scale to the underlying liability scale using the classical formula of Dempster and

2 2 is the estimate of heritability on the underlying normal scale; hO is the estimate of where hL

with observations of 1; and z is the height of the ordinate at the truncation point for an area of p under the normal curve.

linear mixed model with the fixed and random effects as described above. ASReml allows to specify different random effects for different traits in the model. For traits that had zero c2 estimates (from univariate analysis), this effect was omitted in multi-variate models. Correlations were calculated as the covariance divided by the product of the standard deviations of traits: r

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Genetic and phenotypic correlations were estimated from a series of bivariate and trivariate

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12 12 22

phenotypic covariance between the two traits, and 12 and 22 are the additive genetic or phenotypic variances of traits 1 and 2, respectively.

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heritability from the linear model with binomial observations; p is the fraction of deformity

where 12 was the estimated additive genetic or

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ho2 p(1 p) h z2
2 L

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Lerner (1950) as follows.

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2.5.2 Generalized linear mixed model (GLMM): In addition to standard linear mixed model as described above, deformity was also analysed by GLMM sire model. Under logit model, the assumption was that the data followed a binomial distribution, and the probability can

= ex /(1 +ex)) where p is the probability of fish deformity be obtained by logistic function ( p

effects of sex (j = female and male) and seal bite (the fish were bitten by seal or not). With GLMM sire model, heritability was calculated using the variance of the logit link function, which implies that residuals have a mean of 0 and a variance of 2/3.
4 s2

h2

s2 e

2 2

The mathematical form of the generalized linear mixed model with a logit link function used

where Bi, and Sk are the fixed effects of seal bite and sex respectively, al is the random effect of sire and eijkl is the error term of the model, and p is the probability of fish deformity recorded at harvest. Deformity was also analysed using probit threshold model. The statistical model was the same as described for logit model. However, the probit link function 1 ( pi ) is used, with inverse link pi ( )

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pijklm log( ) = + Bi + Sk + al + eijklm 1 pijklm

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to estimate variance components for deformity is as the followings:

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1 e 2

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where e2 1

dx , where is the cumulative normal density

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recorded at harvest and x is a linear predictor. The effects fitted in the model included the

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function, and pi denotes the probability of deformity for fish i. Under the probit threshold model, the heritability was calculated as

3.1 Descriptive statistics

The number of actual observations, means, standard deviations and coefficients of variation for traits studied is given in Table 1. The body weight of the fish at harvest averaged 3.1 kg,

yellowtail kingfish fillet sampled from approximately the same region (about 30mm inferior and anterior from the dorsal fin) was 4.9%. The coefficient of variation (CV) for fat content

deformities in this population was about 20%.

3.2 Fixed effects The fixed effects included in statistical models for the analysis of traits studied were sex, seal bite and deformity. The least square means for sex, seal bite and deformity status are shown in Table 2. Of particular interest is that in yellowtail kingfish sex dimorphism does not exist at the size evaluated (3.1 kg). Between-sex differences were not statistically significant for all traits studied.

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was 43.3%, markedly greater than that for body and fillet traits (10-15%). The proportion of

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corresponding to a fillet weight of 1.8 kg and fillet yield of 61%. The fillet fat content of

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3. Results

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h2

4 s2 s2 1

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The effect of seal bite was statistically significant for carcass traits only (i.e., fillet weight, fillet yield and fat content). On the other hand, deformity had significant effect ( P < 0.05 to 0.001) on the majority of growth and carcass performance traits in yellowtail kingfish, except for fillet yield (Table 2). Deformed fish grew slower and had smaller fillet weights and

3.3 Heritabilities

Single trait analysis of heritabilities, and maternal and common environmental variances in proportion to phenotypic variances (c2) is presented in Table 3. The estimates of heritability for body and carcass traits including fillet fat content were moderate (0.15 to 0.41). Condition score was heritable (0.15). Overall, the estimates for heritability for all traits were

shallowness of the pedigree. Heritability for deformity obtained from both nonlinear (generalized) mixed model using logit and probit link functions and standard animal mixed

The c2 were low, only 5% for body weight, but were essentially zero for other traits. One exception was the moderate c2 for fat content. The heritability of 0.94 for fat content from the model without maternal and common environmental effect hence may be overestimated. Among body and carcass traits, multivariate analyses increased albeit marginally heritability estimates for body and fillet weight relative to single trait models, 0.30 vs. 0.26 and 0.34 vs. 0.31, respectively (results not shown). However these differences were not significant.

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were low, close to zero.

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associated with high standard errors (0.03 to 0.26), likely due to the limited sample size and

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lower visual condition score than normal (non-deformed) counterparts.

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3.4 Correlations among body and fillet traits Table 4 presents phenotypic and genetic correlations among body and carcass traits. Measurements of body traits (weight and length) were genetically highly correlated (r g= 0.57 0.28). The genetic correlations between fillet weight and body measurements were

be simultaneously improved. Fillet weight showed slightly greater correlations with body weight than with fork length (0.96 vs. 0.91), suggesting that harvest weight is the most effective selection criterion to improve both growth and fillet weight in practical breeding programs. The genetic correlation of fillet yield with body weight were moderate (0.57), but those with fork length were not significant different from zero (-0.19 and 0.24, respectively).

weight (rg = 0.72). Breeding objectives for increased fillet weight are thus expected to result in improvement in fillet yield. Overall, condition score show favourable phenotypic and genetic correlations with body and carcass traits.

3.5 Correlations between fillet fat content and body and carcass traits Phenotypic and genetic correlations of body and carcass traits with muscle fat content are shown in Table 5. At both phenotypic and genetic levels, all the estimates were moderately positive and significant, except for the genetic correlations between length and fillet yield with fat content that were not significant due to their high standard errors.
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There was also a moderate and positive genetic correlation between fillet yield and fillet

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also very high (close to unity, 0.91 to 0.96), indicating that both growth and fillet weight can

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4. Discussion

The fillet yield of yellowtail kingfish Seriola lalandi in our study (61%) falls in the high range

the present study we report skinless fillet yield which is higher than the average value of the same species reported in other studies (Burke, 2011), and remarkably higher than other

trout and Atlantic salmon (Kause et al., 2007; Powell et al., 2008; Le Boucher et al., 2011). The fat content of 4.9% in the yellowtail kingfish population in our present study is generally

Tobin et al., 2006) report that fat content varies largely with fish tissues (fillet cuts, adipose and intestinal tissues, viscera or liver). Within a fillet, the distribution of fat also differs, that

muscle tissue sampled in the present study showed the least variation in fat content.

4.2 Heritabilities The extent of genetic variation in body traits and fillet weight for yellowtail kingfish in our study is also consistent with those reported for sea bream (Knibb, 2000), rainbow trout (Kause et al., 2005), Atlantic salmon (Gjerde and Gjedrem, 1984), tilapias (Nguyen et al., 2007; Ponzoni et al., 2011; Bentsen et al., 2012), common carp (Ninh et al., 2011) and crustaceans species (Gitterle et al., 2005; Kenway et al., 2006; Jurez et al., 2007; Hung, D., pers. comm.). The high standard errors associated with our estimates were likely due to the

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is, higher fat content in anterior ventral than posterior dorsal sections (Burke, 2011). The

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in line with other reports for Seriola lalandi (e.g., Bowyer et al., 2012). Several studies (e.g.,

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fishes such as tilapia (Nguyen et al., 2010b; Gjerde et al., 2012) or equivalent to rainbow

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reported for marine species in the literature, from 43 to 69% (e.g. Navarro et al., 2009). In

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4.1 Carcass characteristics of yellowtail kingfish

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limited sample size, single generation data, mass spawning practices as well as impacts of other environmental factors during rearing and growout. Though the data were somewhat limited (n = 400), the animals did come from a number of half-sib families and the genetic parameters estimates were usually statistically significant. Overall, our estimates together

improvement for body traits can be achieved through conventional selection in properly

Our current estimate of heritability for fillet yield in yellowtail kingfish was 0.19 0.11, in good agreement with the results reported by Nguyen et al. (2010b) in GIFT tilapia where h2 for fillet yield was at 0.250.07. Some other studies, however, showed low heritability

Pangasianodon hypophthalmus (Sang et al., 2012), gilthead seabream (Navarro et al., 2009), rainbow trout and Atlantic salmon (Gjerde and Gjedrem, 1984).

potential for genetic improvement of this trait. The estimates of heritability for fat content range from 0.17 to 0.33 in salmonids (Gjerde and Schaeffer, 1989; Iwamoto et al., 1990; Rye and Gjerde 1996; Kause et al., 2002; Tobin et al., 2006; Niera et al., 2004; Quinton et al., 2005; Viera et al., 2007; Powell et al., 2008) and from 0.06 to 0.48 in tilapia (Nguyen et al., 2010a and b; Hamzah, A. per. comm.). The number of fillet samples analysed for fat content in our study is generally comparable with those studies reported in the literature (e.g., n= 514 in tilapia reported by Nguyen et al., 2010a). On both observed and underlying liability scales, the heritability for deformity is not significantly different from zero. Perhaps since our measures of deformity include a range of

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In the present population of yellowtail kingfish fillet fat content is highly heritable, showing

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estimates for fillet yield or carcass ratio traits (0.03-0.05) such as in striped catfish

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designed breeding program.

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with the moderate to high heritabilities across farmed aquaculture species indicates that

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traits, a low or negligible heritability is expected. The heritability on the underlying scale for skeletal deformities is 0.25 0.03 for European seabass (Bardon et al., 2009; Karahan et al., 2012), 0.36 0.14 for Atlantic salmon (Gjerde et al., 2005), 0.64 for sire and 0.36 for dam components of variance on the underlying liability scale in another salmon study (McKay

additive genetic component for deformity which would allow scope for selection and

4.3 Common environmental effects

The common environmental differences between full-sib and half-sib families had significant effects on growth performance on farmed aquaculture species (e.g., Winkelman and

depend on mating strategy, rearing environment, data and family structure, and they are not easily separated from maternal genetic and non-genetic components unless there is a

that by the application of early communal rearing of all families pooled as soon as hatching, the common environmental effects (c2) was minimized. The logarithmic likelihood ratio test showed that the c2 effect was not significant for all body traits (Chi-square test with one degree of freedom, P > 0.05). Ninh et al. (2011) also report a close to zero c2 in communal early rearing of a common carp population in Vietnam. Similar findings were reported in other species (Fishback et al., 2002; Vandeputte et al., 2004; Kocour et al., 2007).

4.4 Correlations

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good depth in the pedigree and ideal data structure. In our present study we demonstrated

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Peterson, 1994). The extent of common environmental effects on body traits generally

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improvement through conventional selective breeding approach.

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and Gjerde, 1986), and 0.27 in cod (Kolstad et al., 2006). These results show that there is

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The high positive genetic correlations among body traits and fillet weight in this current study suggests that all of the above body traits were closely genetically correlated and are likely to be controlled by similar sets of genes. Hence, any one of these traits tested could be used, on its own or simultaneously, to improve overall growth performance of the

weight is reported to be the best predictor of fillet weight, with R 2 = 0.94 and a correlation

correlation of fillet weight with body weight was higher than for fillet weight with other body traits (Nguyen et al., 2010b). In practical selection programs live weight is recommended due to its greater heritability and the ease and accuracy of measurements

can be improved simultaneously.

In the present population of yellowtail kingfish, the estimated genetic correlation of fillet

striped catfish, Sang (2010) found low genetic correlations between fillet yield and body weight or between fillet yield and fillet weight. Realised correlated response to selection for body weight was also reported to be negligible for fillet yield in this species or in tilapia where the fish were slaughtered at an average weight of 500 g (Nguyen et al., 2010b). Hence, direct improvement of fillet yield in farmed aquaculture species is predicted to be difficult because ratios have been long known to lead statistical hurdles. This is due to the likely disproportionate nature by which selection pressure is exerted on component traits (Gunsett et al., 1987; Simm et al., 1987). However, we may be able to overcome some of these issues relating to ratios by selection on fillet weight adjusted for body weight. In this

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yield with body weight was moderate and positive (0.57 0.28). By contrast in a study of

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relative to other body traits (length or width). Therefore both performance and fillet weight

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between observed and predicted value of 0.97 in tilapia (Nguyen et al., 2008). The genetic

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animals without a requirement for making different measurements. However, harvest

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case indirect improvement in fillet yield to selection for increased body weight may be expected as calculated using selection index theory by Nguyen et al. (2010b). The positive genetic correlations of body and fillet weight with fat content (0.92 and 0.98 respectively) indicated that selection for increased growth can result in increased fat

ranges, from 0.11 to 0.80, reported in salmonids (Neira et al., 2004; Quinton et al., 2005;

pers. comm). The great range of values may reflect slightly different practices in the methods. In any case, such a large range makes it difficult to determine if our values are typical or not. In this study, we examine total fat content from the same region of the fillet,

rainbow trout (Oncorhynchus mykiss) breeding program, Kause et al. (2007) measured muscle (dissected above the lateral line of the fish) and body lipid (samples of un-gutted

visceral weight were different. Therefore, fillet fat contents should be measured as a genetically different trait from the fat deposits at other body locations. Gjerde and Schaeffer (1989), Kause et al. (2002) and Tobin et al. (2006) also proposed that fat deposits at different body locations should be measured as genetically different traits. In the present study, only fillet fat content was examined due to the high costs of chemical analysis and labours involved (fats of other body compartments were not analysed). The present estimates of the genetic correlation of body weight with fat content, are generally in line with other fish species in which either fillet or whole body fat contents were measured (0.36, Iwamoto et al., 1990; 0.73, Neira et al., 2004; 0.31, Quinton et al., 2005; 0.80, Powell et al., 2008; 0.11, Vieira et al., 2007).
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fish) as two different traits. Across studies, the percentages of fat deposits in fish fillet and

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whereas different measurements of fat are reported in the literature. For instance in a

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Powell et al., 2008; Vieira et al., 2007) and from 0.16 0.40 reported in tilapia (Hamzah, A.

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content. The reported genetic correlation between fat and body weight was at the high end

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In our study, the genetic correlations between body traits and deformity were weak (0.09 to 0.34) and not significant due to their large standard errors (results not shown). In Atlantic cod, Kolstard et al. (2006) also reported a low genetic correlation between growth and various measures of deformities. The genetic relationship between growth and deformity

2012, but negative in Atlantic salmon, Gjerde et al., 2005), history of populations, and

breeding programs for farmed aquaculture species, this trait (deformity) should be closely monitored.

Although our study showed that deformity had a low heritability and no significant

scheme, the breeding objective and the selection index to ensure the sustainability of long term genetic improvement programs for yellowtail kingfish. In farmed animals, high

diseases such as mastitis in dairy cattle, leg weakness in pigs or egg defects in layers chicken. Both allocation resource and selection theories (Beilhharz et al., 1993) suggests that fitness related traits may show a tendency to decline due to selection for other traits and due to inbreeding depression (Goddard, 2009). They thus merit further considerations in practical selective breeding programs to meet future demands of the aquaculture industry.

In summary, there is large potential for genetic improvement to increase productivity for production traits in yellowtail kingfish in Australia. Among these traits, body and fillet weights are of particular interest because the fish are priced on the basis of their wet body weight or fillet weight. Fillet weight can be indirectly improved through selection for
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performing individuals resulted from long term selection programs tend to prone to

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correlation with other traits, this character probably should be included in any recording

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rearing phases (Vehvilainen et al., 2012) to which the fish subject. In practical selective

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reported in the literature vary with species (positive in European sea bass, Karahan et al.

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increased growth due to the strong positive genetic correlation between the traits. Alternatively a linear index combining measurements of available body dimensions can be applied (Nguyen et al., 2010b). For some species such as tuna, fat can be a factor in the value of a fish. Should there be consumer and or market demand to increase the fat content

recording on a large scale for genetic evaluation and selection in kingfish, cheap and non-

meters, near infrared spectroscopy or computerised tomography (Cozzorino and Murray, 2012).

associations with body and carcass traits are reported for the first time in yellowtail kingfish. Selection for improving body weight, fillet weight and fat content could be effective as

weight, fillet and fat) are positive and high, i.e. desirable. Our present results provide a basic genetic inheritance for traits of economic importance, and thus should be useful for the design and conduct of practical selective breeding programs in yellowtail kingfish. Due to the limited number of parents and families involved in the present study, frequent update of the genetic parameters would be necessary to guide future breeding programs in this population of yellowtail kingfish.

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evidenced by their moderate heritability. Genetic correlations among these traits (body

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Genetic properties of muscle fat content, condition score and deformity and their genetic

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5. Conclusions

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invasive measurements of fats on live animals should be considered such as using fat-

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of kingfish, it may be possible to achieve this with genetic selection. To enable routine data

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Acknowledgements This work was supported financially by the Australian Seafood Cooperative Research Centre

management for Southern Bluefin Tuna and Yellowtail Kingfish). Facilities, fish and

technical input and other advice from Jane Quinn (at USC), Morten Deichmann and Craig Foster (CST). References

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Table 1a: Means, standard deviations (SD), coefficient of variation (CV, %) for traits studied Traits WT LG FW FY FC CS DF
a

Unit Kg Cm Kg % % Score %

N 385 385 385 341 379 385 385

Mean 3.1 59.7 1.8 60.7 4.9 3.8

SD

CV 11.4 3.7 15.4 8.3 43.3 15.1 200.2

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WT = weight, LG = Length, FW = Fillet weight, FY = Fillet yield, FC = Fillet Fat content, CS =

Visual condition score and DF = Deformity. Some data were not taken in the case of FY when there was seal bight or when factory operations prevented timely data acquisition.

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2.20 0.28 5.06 2.14 0.57 40.1

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Table 2a, b, c: Least squares means of fixed effects Traits Female WT LG FW FY FC CS DF
a

Gender Male Yes

Seal bite No

Deformity

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Yes -

No

59.10.224 59.00.233 1.600.024 1.580.025 53.10.313 53.10.326 4.230.226 4.090.232 3.570.056 3.620.058 17.50.278 16.10.290

59.20.354 1.300.038 43.80.493 3.260.354 -d

59.40.144 1.850.015 60.30.201 4.800.143 3.620.040 23.70.145

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3.000.036 2.970.038

2.980.057

3.060.023

3.060.023 3.130.057 58.50.296 60.00.185 1.500.032 1.650.020 51.80.413 52.40.258 3.610.298 4.150.184 3.380.072 3.870.036 -

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Between gender difference was not significant for all traits (P > 0.05) Seal bite has significant effect (P<0.001) on fillet weight (FW), fillet yield (FY) and fat

content (FC)
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Effect of deformity was statistically significant (P< 0.001) for all traits, except for FY not estimated for cases with seal bite

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Table 3a,b,c,d: Heritability (h2), and maternal and common environmental effects (c2) for economically important traits in yellowtail kingfish Traits Model 1 h2 SE WT LG FW FY FC CS DF1 DF2 DF3
a

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c2 SE

Model 2 h2 SE 0.17 0.16

-2(LogLModel2 LogLModel1)

0.26 0.13 0.15 0.09 0.31 0.15 0.19 0.11 0.94 0.21 0.15 0.11

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0.05 0.09 0.00 0.04 0.09 0.00 0.29 0.20 0.00 0.00

0.21 0 0.15 0 2.3 0 0

0.15 0.09

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Model 1 (standard animal model): Spawning batch (tank) was not included. bModel 2:

Spawning batch (tank) nested with dam as a random factor in addition to the additive genetic effect. Chi-square test (i.e. -2LogL difference between models 2 and 1) with one degree was not significant for all traits (P > 0.05).
c

DF1 estimated from linear animal model. The heritability from linear model transformed to

liability scale was 0.0006.

d

DF2 estimated from logit threshold sire model

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0.023 0.11 0.021 0.11

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0.24 0.19 0.19 0.11 0.41 0.26 0.15 0.11 0.001 0.027

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DF3 estimated from probit threshold sire model

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Table 4: Phenotypic (above) and genetic (below the diagonal) correlations among body and fillet traits, using model 1 Traits WT LG FW FY CS WT LG FW FY CS 0.57 0.27 0.96 0.05 0.57 0.28 0.94 0.35 0.91 0.05 -0.19 0.46 0.23 0.44 0.80 0.02 0.92 0.008 0.83 0.03 0.14 0.06 0.69 0.04 0.45 0.05 0.63 0.04 0.06 0.07

0.72 0.22

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0.95 0.19

Model 1: Standard animal model with only the additive genetic effect.

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0.07 0.05 0.47 0.05

0.24 0.46

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Table 5: Phenotypic (rP) and genetic correlations (rG) of body and carcass traits with fillet fat content Traits WT LG FW FY rP 0.52 0.07 0.24 0.07 0.54 0.07 0.24 0.06 rG

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0.92 0.13 0.37 0.43 0.78 0.14 0.98 0.20

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Highlights

We found body fat is highly heritable in kingfish. We report genetic parameter estimates from industrial crops of kingfish. We report the application of new microsatellites to establish kingfish pedigrees.

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