Association genetics

Association analysis is aimed at finding associations (or dependencies) between trait values and marker alleles in a population of individuals. In association analysis, genetical relationships between the individuals of a population are generally unknown and have to be inferred from marker data. Genetical relationships are usually described by means of a pedigree.

The associations must be due to the fact that markers are (physically) close to genes affecting the trait, i.e. the associations should be due to linkage between genes and markers. QTL (quantitative trait locus) analysis may be considered as a special form of association analysis. 

A GCP funded introduction on the statistical analysis of germplasm data can be found on these pages.
Software for statistical analysis, developed or adapted by the GCP, can be found here and here at Cropforge.

The FtoL-R program was written to convert frequencies of SSR alleles run on an DNA sequencer for bulks of n individuals into length of alleles of n simulated individuals, hypothetically belonging to the bulk.  The allele frequencies of the hypothetical individuals are the same as the allele frequencies of the bulk. The FtoL program generates a “dummy” data set consisting of allele lengths for hypothetical individuals. These individuals correspond to bulk populations and are generated using the frequencies of marker-allele combinations from the bulks.
Find here the user's manual for the applicable for FtoL analysis progam.
The freely available R version of the FtoL program can be found  here. This FtoL-R program must be copied as a script into the R default directory, and generally called using icons in Windows. 

The FREQS-R Program estimates allele frequencies for fingerprinting and genetic diversity studies using bulked heterogeneous populations.
FREQS-R  converts peak heights of SSR alleles run on a DNA sequencer into frequencies of the alleles within the bulk of individuals amplified with the SSR.  FREQS-R is a freely available program written using the R software. It was written as a simplified R version of the MSSC - SAS®/IML program (Dubreuil et al. 2005; Franco et al. 2005).
Find here the user's manual for the applicable for the FREQ-S program.
The freely available R version of the FtoL program can be found here. The FREQS-R program must be copied as a script into the R default directory and called using icons at Windows. 

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