Genetic Issues in Hard Clam Aquaculture
Investigators:
Dr. Patrick Baker, University of Florida, Department of Fisheries and Aquatic
Sciences
Dr. Brian Bowen, University of Hawaii
Leslie Sturmer, University of Florida, Cooperative Extension Service
Funding:
U.S. Department of Agriculture Cooperative State Research, Education, and
Extension Service
Time Period:
2001 - 2003
Objectives:
The genetic variation of wild
and cultured stocks of the Florida hard clam was quantified and compared in
response to both industry and scientific concerns regarding genetic health of
this important commercial aquaculture species. The hatchery-based hard clam
aquaculture industry, while rapidly growing, is in its infancy in terms of stock
management and improvement. Hatchery stocks are often selected for the "notata"
strain, a shell color variation with no other known performance
advantages. Aquaculture geneticists were concerned that selective breeding for
one trait, such as shell color, could have unintended side effects. Among the
major concerns is the loss of useful genetic diversity through unintentional
inbreeding. Specifically, long-term selective breeding could reduce genetic
variability of hatchery stocks. Genetic diversity is believed to be critical
when clams are exposed to variable environmental conditions or diseases.
Successful analysis of within-stock genetic diversity can also provide the basis
for future research on heterozygosity (within-individual genetic diversity),
stock identification via molecular techniques, and correlation of stock
performance (particularly growth, survival, and reproduction) with genetic
parameters, which can be used to guide breeding and stock improvement programs.
This study had two main emphases: 1) To determine whether loss of genetic
diversity has occurred in cultured clam stocks, and 2) To assess the possibility
that depletion of genetic diversity has affected the health and reproductive
capacity of captive brood stocks.
Accomplishments:
Optimizing DNA Primers
Descriptive molecular genetic techniques were used to examine the issue of
stock diversity. Specifically, mitochondrial DNA (mtDNA) and microsatellites
were used to quantify genetic diversity – haplotype and nucleotide diversity for
mtDNA and heterozygosity for microsatellites. A well-studied gene fragment in
the mitochondria (organelles within cells that have their own DNA) known as
cytochrome oxidase I (COI) was examined using standard molecular techniques. The
difference in COI between clams within a sample provides an estimate of the
total genetic diversity of the sample. From this, we were able to compare
genetic diversity (haplotype diversity) of clams from different hatchery stocks
with some wild populations. Genetic efforts in this project initially focused on
optimizing mitrochondrial DNA primers for hard clams. Primers orignally designed
for work with other invertebrates, would bind at multiple sites and produced
multiple signals in DNA sequencing. Thus, a new forward primer was developed. In
addition, cytochrome b primers, which bracket a sequence that appears to
evolve at rates similar to COI within mollusks, was used.
Quantifying Genetic Diversity
The genetic diversity in captive strains from six Florida hatchery stocks
and in clams escaped from aquaculture in west Florida was compared to wild
stocks from east Florida, Georgia and New York. The southern quahog,
Mercenaria campechiensis, a morphologically similar, sympatric congener,
sometimes occurred in samples, but showed distinct genetic distance from M.
mercenaria and was removed prior to statistical analysis. An index of clam
stock health in terms of genetic diversity was developed (see table). Haplotype
diversity ranges from 0 to 1, with anything over about 0.5 being considered
healthy. As can be seen from the table, wild stocks typically have higher
haplotype diversity than hatchery stocks, but some wild stocks may also have
reduced genetic diversity due to pollution, disease, or other factors. High
haplotype diversity was found in COI sequences for all wild populations and most
hatchery stocks. Several hatcheries had significantly reduced – but still
healthy – levels of haplotype diversity. Two hatcheries also had apparent
contamination with M. campechiensis. These findings indicate that some
hatcheries show an effect by selective breeding on overall diversity, but that
genetic diversity has not yet been reduced to levels at which problems are
likely to arise. Further surveys with microsatellite DNA or control region mtDNA
are mandated to assess inbreeding and the comparative performance of breeding
stocks. These efforts represent the first at looking at stock management and
improvement for the emergent clam aquaculture industry in Florida and provide a
basis for further genetic studies.
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