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Estimating Parentage Relationships Using Molecular Markers in Aquaculture (Paperback)
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Estimating Parentage Relationships Using Molecular Markers in Aquaculture (Paperback)
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The inference of parentage relationships between individuals from
their molecular resemblance represents a useful methodology for
genetic improvement in Aquaculture. This makes possible the
reorganisation of broodstock in groups with low relatedness, as
well as the identification of families in selection programs to
avoid the harmful effects of inbreeding and to maintain the highest
diversity as possible across generations. The choice of the
appropriate genetic marker and the statistical methodology is
essential to get the best solution for the questions considered.
Depending on the availability of previous information on the
genealogy, paternity or kinship analysis will be applied. The
simplest approach to paternity inference, involves parent
identification through the exclusion of the remaining candidates.
However, this can lead to more than one solution, solvable after
application of maximum likelihood procedures. The ability to
identify the parents of each offspring depends on the sampling
scenario (number of candidate parents and the fraction sampled), on
the potential of the markers used (polymorphism, genotyping
errors), and on the conformance to theoretical assumptions of the
statistical models applied. A large number of paternity programs
are freely available. They display usually complementary
performances, and there is not the best software for all
situations. When the authors dealt with a single group of
individuals belonging to the same generation or that could not be
separated into known generations, the aim was just to estimate the
degree of genetic relationship between them, usually expressed as
the coancestry coefficient. The basic idea is to determine how much
of the molecular similarity (Identity By State) is due to the
Identity By Descent (the really important parameter). There are two
groups of relationship estimators from the molecular information.
One of them includes methods directed at estimating coancestry for
only a pair of individuals at a time, usually relaying on the
knowledge of the allele frequencies of the reference population.
Estimators within this group can be further divided into those
called Method of Moments Estimators (MME) and those based on
Maximum Likelihood (MLE). The other group of methods uses jointly
the information of all individuals to determine the more probable
population/familiar structure. They perform an explicit
reconstruction of the genealogy leading to the observed population
(at least for one generation above). Depending on the type of
estimator and the assumptions used in their development, each of
them presents some advantages and/or limitations which should be
taken into account when choosing the one to use. In the present
study, the most relevant estimators are presented and, also, a list
of free software available for their application.
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