Computer note. GGT: software for the display of graphical genotypes

Berloo, R. van

doi:10.1093/jhered/90.2.328

Cited by 157 publications

(80 citation statements)

References 3 publications

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“…Recurrent backcrossing programs are planned on the assumption that the proportion of recurrent parent genome is recovered at a rate of 1-(1/2) t+1 for each of t generations of backcrossing (Babu et al, 2004). Graphical representations of molecular data are very useful in determining the proportion and location of introgressions along the chromosomes (van Berloo, 1999). Molecular markers enhance the ability of breeders to determine the inheritance and parentage of specific genomic regions and to monitor the introgression of specific chromosome segments that are linked to desirable traits in breeding lines.…”

Section: Discussionmentioning

confidence: 99%

“…Three different statistical analyses were performed. First, the pro-portion of the donor and recurrent parental genome was calculated using the software package GGT (an acronym of Graphical GenoTypes; http://www.dpw.wau.nl/pv/pub/ggt (Van Berloo, 1999). This approach considers distances between markers in such a way that a chromosomal segment flanked by two markers derived from the donor parent (D'D") is considered to contain 100% donor DNA across the region, while a chromosomal segment flanked by two markers of recipient type (R'R") is considered as 100% recurrent parent DNA, and a chromosomal segment flanked by one marker of donor type and one marker of recipient type (DR) is considered to be a recombinant, with donor DNA extending approximately half way across the interval and recurrent parent DNA across the other half (Young and Tanksley, 1989).…”

Section: Data Scoring and Statistical Analysesmentioning

confidence: 99%

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Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima)

Semagn¹,

Ndjiondjop²,

Lorieux³

et al. 2007

Afr. J. Biotechnol.

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NERICA rices are interspecific inbred progeny derived from crosses between 4% (1,508 cM), while the observed average proportion of O. glaberrima donor genome was 6.3% (108 cM). Non-parental alleles were detected in 83% of the lines and contributed an average of 38 cM per line (~2.2% of genomic DNA). Lines that had undergone eight generations of inbreeding in the field contained significantly more non-parental alleles (av. 2.7%) compared to the DH lines (av. 1.3%) that were developed from BC 2 anthers. Using both cluster and principal component analyses, two major groups were detected in these materials. The NERICA varieties (NERICA 1 to 7) clustered in one group while the remaining 63 lines clustered in another group, suggesting that the second group may offer significant opportunities for further selection and variety development.

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Section: Discussionmentioning

confidence: 99%

Section: Data Scoring and Statistical Analysesmentioning

confidence: 99%

Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima)

Semagn¹,

Ndjiondjop²,

Lorieux³

et al. 2007

Afr. J. Biotechnol.

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“…Data from the F 1 map were subjected to the Graphical GenoTyping program (GGT) (Van Berloo, 1999). This was used to inspect the distribution of crossovers for each chromosome.…”

Section: Framework Linkage Map Constructionmentioning

confidence: 99%

Complete genetic linkage maps from an interspecific cross between Fusarium circinatum and Fusarium subglutinans

Vos

Myburg

Wingfield

et al. 2007

Fungal Genetics and Biology

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The Gibberella fujikuroi complex includes many plant pathogens of agricultural crops and trees, all of which have anamorphs assigned to the genus Fusarium. In this study, an interspecific hybrid cross between Gibberella circinata and Gibberella subglutinans was used to compile a genetic linkage map. A framework map was constructed using a total of 578 AFLP markers together with the mating type (MAT-1 and MAT-2) genes and the histone (H3) gene. Twelve major linkage groups were identified (n = 12). Fifty percent of the markers showed significant deviation from the expected 1:1 transmission ratio in a haploid F 1 cross (P < 0.05). The transmission of the markers on the linkage map was biased towards alleles of the G. subglutinans parent, with an estimated 60% of the genome of F 1 individuals contributed by this parent. This map will serve as a powerful o op pe en nU UP P ( (J Ju ul ly y 2 20 00 07 7) ) tool to study the genetic architecture of interspecific differentiation and pathogenicity in the two parental genomes.

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“…Thirdly, high resolution mapping of major-effect loci (Finkers-Tomczak et al 2009) is supported by a graphical analysis of the recombinants and their trait values, allowing one to zoom in on the remaining interval where candidate genes reside. Graphical genotyping is supported by software packages such as GGT (van Berloo, 1999;2008) or Flapjack ).…”

Section: Graphical Genotypingmentioning

confidence: 99%

Development and application of a 20K SNP array in potato

Vos¹

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Computer note. GGT: software for the display of graphical genotypes

Cited by 157 publications

References 3 publications

Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima)

Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima)

Complete genetic linkage maps from an interspecific cross between Fusarium circinatum and Fusarium subglutinans

Development and application of a 20K SNP array in potato

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