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Knibb W.,University of The Sunshine Coast | Whatmore P.,University of The Sunshine Coast | Whatmore P.,The Australian Seafood Cooperative Research Center | Lamont R.,University of The Sunshine Coast | And 6 more authors.
Aquaculture | Year: 2014

This study assesses the changes in genetic diversity using two different methods in eight captive bred lines of banana shrimp (Fenneropenaeus merguiensis) that had been mass selected for length for up to 14 generations.Specifically, mitochondrial D-loop DNA sequencing and genotyping using five DNA microsatellite loci were used to document changes in haplotype diversity and allelic diversity numbers at several time points during and up to 14 generations of captive bred lines, typically maintained without intercrossing among lines. Data from eight of the lines were compared with each other and to a reference sample of wild caught animals.As each wild animal had a unique mtDNA haplotype, we estimate that there were 20 different mtDNA haplotypes in each of the two different founding stocks. The average number of haplotypes was 1.8 after 11 or more generations of captive breeding. Similarly, whereas the wild reference stock had an average number of more than 13 microsatellite alleles per locus, the descendent lines had an average of 5.6 per locus after 11 or more generations. These declines were evident despite strategies that had been put in place to maintain genetic variation, including the use of up to 1000 brood stock per generation. The loss of genetic variation was unequivocal being evident for both DNA methods and in all the different lines.Effective population size (Ne), as derived from linkage disequilibrium, was estimated to average about nine after 11-13 generations in the captively bred lines, compared with 263 estimated in the wild samples. This corresponds to a rate of inbreeding of about 4% per generation for the captively bred lines. Additive genetic variance of the captively bred lines, estimated under the assumption of neutrality, ranged from about 75% to 25% that in the wild samples.We therefore conclude that mass selection, even when using a relatively large number of broodstock, still results in substantial loss of allelic diversity within lines over generations, and a reduction of effective population size and genetic variance, to the degree that productivity could have been compromised compared with similarly selected but outbred stocks. Loss occurred relatively consistently among the different lines.It was common for different microsatellite alleles or mtDNA haplotypes to have persisted in the different lines, such that the total number of haplotypes and allele types among all lines was much greater than that within given single lines, and the number of alleles among lines approximated that found in the wild. This observation, evident because many different lines were monitored, suggests that under certain circumstances (fixation and selection), more net genetic variability can be maintained over many generations of selection by keeping multiple different and independent lines rather than one large single line. Accordingly, if multiple lines are maintained, there could be some practical options to reconstitute allelic and haplotype variation without new introductions of genetically unimproved stock from the wild. © 2014 Elsevier B.V.

Knibb W.,University of The Sunshine Coast | Quinn J.,University of The Sunshine Coast | Lamont R.,University of The Sunshine Coast | Whatmore P.,University of The Sunshine Coast | And 3 more authors.
Aquaculture | Year: 2014

The purpose of this paper was to determine aspects of the reproductive biology of captively bred Fenneropenaeus merguiensis under commercial broodstock production conditions that relate to the design and implementation of genetic improvement programmes for this species.First, we tested whether there is evidence for polygamy vs monogamy by genotyping females, the material found in their thelycums, and material that leaches out of the thelycum using DNA microsatellite loci. All genotypes in all animals and tissues tested could be accounted for using a monogamy model.Second we compared the accuracy of pedigrees formed under assumptions of monogamy vs polygamy. Pedigrees were formed using microsatellite genotypes from 73 dams and 400 offspring. Sibship groups and dam-offspring groups from pedigrees developed assuming monogamy almost always had the same mtDNA haplotypes, suggesting a high accuracy of the pedigrees, but those formed under the assumption of polygamy were less accurate, and together these results also support the monogamy model.Third, we assessed the between family variance in offspring family numbers from two sets of mass spawnings of about 40 inseminated females per spawn. About half of the offspring originated from just 20 percent of the dams, i.e. many dams contributed few offspring. These data can help predict optimal sample sizes required for accurate future estimates of genetic parameters. © 2014 Elsevier B.V.

Nguyen N.H.,University of The Sunshine Coast | Quinn J.,University of The Sunshine Coast | Powell D.,University of The Sunshine Coast | Elizur A.,University of The Sunshine Coast | And 5 more authors.
BMC Genetics | Year: 2014

Background: Banana shrimp Fenneropenaeus merguiensis has emerged as an important aquacultured shrimp species in South East Asia and Australia. However, the quantitative genetic basis of economically important traits in this species are currently not available, while for body colour, cooked or uncooked, there are no genetic parameter estimates for any shrimp or indeed any decapod crustacean. In this study, we report for banana shrimp genetic parameters for morphometric traits and, the first time for any shrimp, parameter estimates for body colour. Ten highly polymorphic microsatellite markers were developed from genomic sequences and used to construct a pedigree for 2000 offspring from approximately 60 female and 60 male parents that were sampled from a single routine commercial production pond. Results: Restricted maximum likelihood method applied to a single trait mixed model was used to estimate heritabilities, while correlations were estimated using the multi-trait approach. The estimates of heritability for morphometric traits were moderate to high (h2 = 0.14 - 0.50). Body colour of uncooked shrimp showed a heritable additive genetic component (h2 = 0.03 - 0.55), and those estimates obtained for cooked shrimp were significantly different from zero. Genetic correlations among morphometric traits were all positive and very high (close to unity, rg =0.85 - 0.99). The genetic correlations of body traits (weight, length and width) were positive with both colour after cooking (0.74 - 0.84) and body colour measured on live shrimp (0.59 to 0.70). The positive genetic correlations between the cooked body colour and uncooked body colour (0.64 ± 0.20) suggests these two traits can be simultaneously improved in practical selective breeding programs. This first ever report of genetic parameters for cooked or uncooked colour in crustacean indicates there is potential for genetic improvement of both growth and body colour through selection. Conclusions: In the present study we demonstrated for banana shrimp that genetic parameters can be estimated from commercial samples (using pedigrees based on DNA markers), that selection for shrimp colour should be successful under such commercial conditions. © 2014 Nguyen et al.; licensee BioMed Central Ltd.

Knibb W.,University of The Sunshine Coast | Quinn J.,University of The Sunshine Coast | Kuballa A.,University of The Sunshine Coast | Powell D.,University of The Sunshine Coast | And 2 more authors.
Journal of Invertebrate Pathology | Year: 2015

Hepatopancreatic parvo-like virus (HPV) has been reported from a variety of shrimp species around the world, including Australia, and thought to impact negatively on production, but until now there was scant information available on variation of HPV over time, ponds and shrimp lineages or families, information that could be used to manage or reduce virus levels.Here we report HPV copy number estimated using qPCR from 1500 individual shrimp sampled over three years and encompassing 91 ponds, 21 breeding groups or lineages and 40 families.HPV copy number variation between ponds was used by farm management as a criterion to choose prospective broodstock (candidates were taken from low HPV ponds). Despite such choice, HPV levels in farmed animals were not reduced from 2011 to 2013. Accordingly, the hypothesis that HPV levels can be reduced over time simply by considering average HPV levels in ponds alone is rejected.Different lines of shrimp within the same farm had different HPV levels, but as lines were raised separately, the line differences could be due to either genetic or environmental differences, the latter including possible different rearing effects and differences in vertical transmission.There were large (up to 2-3 LOG fold) differences of HPV levels between families bred and grown together contemporaneously, and the heritability for HPV copy number was estimated to be moderate to large (0.40. ±.0.13). Apart from genetic differences, differences of vertical transmission from dams may contribute to the between family differences, in any case we postulate that selection between families could be an effective method to reduce HPV levels.HPV levels were not genetically correlated with performance traits such as body weight or length, so selection for HPV level should not adversely affect production characteristics.This is the first evidence for an aquacultured species that viral levels, as opposed to survival/resistance to viruses, may have a substantial host genetic component. The heritability reported here for virus copy number was higher that most heritabilities reported for survival to specific pathogens such as white spot, raising the general postulate that selection for virus copy number may be more effective and repeatable than selection for survival to pathogen challenge. © 2015 Elsevier Inc.

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