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Estimating Parentage Relationships Using Molecular Markers in Aquaculture (pp. 59-112) $100.00
Authors:  (Paulino Martinez, University de Santiago de Compostela, Spain, Jesus Fernandez, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, Spain)
The inference of parentage relationships between individuals from their molecular
resemblance represents a useful methodology for genetic improvement in Aquaculture.
This makes possible the reorganization 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 we deal with a single group of individuals belonging to the same generation or
that can not be separated into known generations, the aim is 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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Estimating Parentage Relationships Using Molecular Markers in Aquaculture (pp. 59-112)