Grafgen: Analysis of the genomic composition of individuals in inbred pedigrees

Key Features of grafgen:

A program to estimate the genomic composition of individuals issued from complex pedigrees.

An easy way to compute transition probabilities and perform numerical recursions that are almost impossible to do by hand.

Can work with any number of generations involving any combination of hybrid crossing, selfing, random mating or doubled haploids.

Can work with multiple loci (more than three); number of loci is bounded by memory size.

Provides precision graphical genotypes picturing the segregation patterns of parental alleles on the genome of offspring (extends the concept of graphical genotypes initiated by Young and Tanksley, 1989)

Presentation

Many experiments in the genetics of plants or model organisms are based on pedigrees where founders are inbred lines. Through several generations of crossing, possibly with selection, a population of final individuals is produced that segregates for the founder alleles. Such populations can be used for QTL detection and/or screened for selection candidates. In both cases, precise estimate of the contributions of the founders to the genomes of final individuals is a key issue, but is essentially known only for particular pedigrees (e.g. F2, backcrosses, Recombinant Inbred Lines or Doubled Haploids populations). However, more complex pedigrees are often used in practice. For example, Intermated Recombinant Inbred Lines are produced by a few generations of random mating followed by repeated selfing. Also, after individuals carrying favorable QTL alleles have been identified in a mapping population they can be used in further crosses to perform marker assisted selection; the resulting pedigree is then a complex history of crosses.

grafgen was written to analyse the genomic composition of individuals issued from such complex pedigrees. It allows to use all available information on these crosses, such as intermediate genotyping data and multilocus genotypes. The program allows to focus the analysis on particular regions of interest ( e.g. QTL segments or gene introgressions).

Download

Grafgen package: includes binaries for windows and linux + source code + PDF manual [ ZIP ]::[ TGZ ]

Grafgen documentation [PDF]

grafgen is a free software distributed under the GNU General Public Licence (GPL).

Examples of studies using grafgen

Lecomte L, Duffe P, Buret M, Servin B, Hospital F, Causse M.,2004, Marker-assisted introgression of five QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic backgrounds. Theor Appl Genet. 109(3):658-68. [Abstract]

Thabuis A., A. Pallois, B. Servin, A.M. Daubèze, P. Signoret, F.Hospital and V. Lefebvre, 2004, Marker-assisted introgression of 4 Phytophthora capsici resistance QTL alleles into a bell pepper line: validation of additive and epistatic effects. Molecular Breeding 14:9-20. [Abstract]

Citing grafgen

Reference: Servin B. and Hospital F., grafgen: A program to analyse the genomic composition of individuals in inbred pedigrees. submitted

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