Agriculture Reference
In-Depth Information
positive alleles and loci possible in the shortest possible time with the
fewest negative associations or the least linkage drag of any sort.
High-resolution power is obtained in AM when there is low LD across
the genomic regions and individuals evaluated in AM. The use of diverse
germplasm for AMensures a high rate of LD decay due to large number of
recombination across the genome compared with linkage mapping. For
this reason marker density in AM studies must be higher than in linkage
studies. Suppose that you have a natural population of diverse individ-
uals that mate at randombetween themselves for 100 years and approach
HWE, resulting in accumulation of many recombination events and low
LD. Compare that with a 100 year population generated from an F
2
based
on two inbreeding parents, where just a few recombination events occur
in the
filial generations followed by selection and LD for most loci
would be very high. Obviously, the mapping resolution would be high in
the
rst
first case and low in the second case. Recombinant inbred lines (RIL)
have a somewhat higher LD decay and are permanent stocks in sel
ng
species, hence are preferred over F
2
populations, but still do not reach
the power of AM populations.
Resolution of linkage maps for locating QTL is on the order of 5
-
10 cM, which leaves space for several hundreds of genes within each
QTL segment (Buckler and Thornsberry 2002). The low resolution of
QTL studies in biparental population makes linkage map-based strate-
gies a time-consuming tool for gene cloning, even more so since it
involves several steps after the
first location of QTL on a linkage map
until the gene is identi
ed and the type of variant or mutation con
rmed
(Salvi and Tuberosa 2005).
Some other advantages emerge when we compare AM with QTL
mapping. The
first is related to population construction. In AM, the
population is either made by sampling or by a strategy that is advanta-
geous for breeding purposes, while in QTL mapping there is always a
constructed population to maintain. The maintenance of hundreds of
breeding lines in the
field or seed room is sometimes onerous (Myles
et al. 2009) compared with germplasm accessions, which are of man-
dated maintenance and potentially have a large number of alleles. New
approaches such as NAM and MAGIC populations also require seed to
be saved and distributed as with RIL populations and sometimes in even
greater numbers than with RILs. However, these population types are
gaining in popularity because they can be phenotyped multiple times
and in detail and sometimes can be used in breeding programs directly
or for backcrosses.
Another advantage of AM over more traditional QTL approaches is
that AM samples a broad set of alleles for study, since in a germplasm
