Agriculture Reference
In-Depth Information
Table 2.5.
Software used for association mapping.
Name
Speci
cations
Reference
STRAT
Companion to structure, various tests designed to
deal with population structure
Pritchard and
Rosenberg 1999
Tassel
Association study, evaluating evolutionary
relationships, analysis of linkage disequilibrium,
principal component analysis, cluster analysis,
missing data calculations and data visualization
Bradbury et al.
2007
Bimbam
Bayesian imputation-based association mapping
Suitable for single-SNP analyses in large studies
(e.g., genome scans) and multi-SNP analyses in
smaller studies (candidate regions or genes)
GENSTAT 11
software
General biostatistical tool with association mapping
and linkage mapping components. Works with
large sample numbers.
VI. ASSOCIATION MAPPING COMPARED WITH LINKAGE
MAPPING
Although linkage mapping and association genetics are commonly
thought of as different approaches, both exploit chromosomal crossing
over to break up allele associations into new haplotypes that can be
correlated with phenotypic variation (Myles et al. 2009). The key
difference between the two approaches is the level of control the
researcher has over recombination events. In linkage mapping, the
researcher generates biparental populations, and therefore controls
the possibility for recombination events in the progeny, but usually
has a corresponding loss in mapping resolution compared with AM. The
alternative of using association panels in AM can be seen as a more
natural experiment since there is no control over the number of
recombination events that produce the genotypes tested. The negative
consequence of this lack of control is re
ected in spurious associations.
Two principal advantages are presented by AM over linkage mapping.
The
first is the high resolution of the technique and the second is the
ability to test multiple alleles for associations in the same experiment.
Additionally, in linkage mapping there is a tendency to create popula-
tions with only highly positive alleles versus negative alleles, while in
AM there is a range of phenotypic values for the alleles present in a
population. The presence of multiple alleles, multiple loci, and various
genetic sources for a trait can be advantageous in breeding situations
where plant improvement is a number game to accumulate the most
