Population genetic simulation and data analysis with Plabsoft

Maurer, Hans Peter; Melchinger, Albrecht E.; Frisch, Matthias

doi:10.1007/s10681-007-9493-4

Cited by 63 publications

(36 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Associations among the 184 clones were revealed with principal coordinate analysis (Gower 1966) on the basis of RD estimates between pairs of clones. These analyses were performed on the basis of the 31 SSRs using the software PLABSOFT (Maurer et al 2008), which is implemented as an extension of the statistical software R (R Development Core Team 2004).…”

Section: Methodsmentioning

confidence: 99%

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

et al. 2009

View full text Add to dashboard Cite

The oomycete Phytophthora infestans causes late blight, the most relevant disease of potato (Solanum tuberosum) worldwide. Field resistance to late blight is a complex trait. When potatoes are cultivated under long day conditions in temperate climates, this resistance is correlated with late plant maturity, an undesirable characteristic. Identification of natural gene variation underlying late blight resistance not compromised by late maturity will facilitate the selection of resistant cultivars and give new insight in the mechanisms controlling quantitative pathogen resistance. We tested 24 candidate loci for association with field resistance to late blight and plant maturity in a population of 184 tetraploid potato individuals. The individuals were genotyped for 230 single nucleotide polymorphisms (SNPs) and 166 microsatellite alleles. For association analysis we used a mixed model, taking into account population structure, kinship, allele substitution and interaction effects of the marker alleles at a locus with four allele doses. Nine SNPs were associated with maturity corrected resistance (P , 0.001), which collectively explained 50% of the genetic variance of this trait. A major association was found at the StAOS2 locus encoding allene oxide synthase 2, a key enzyme in the biosynthesis of jasmonates, plant hormones that function in defense signaling. This finding supports StAOS2 as being one of the factors controlling natural variation of pathogen resistance.

show abstract

Section: Methodsmentioning

confidence: 99%

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

et al. 2009

View full text Add to dashboard Cite

show abstract

“…Principal coordinate analysis (Gower, 1966) based on the modified Rogers' distances of the individuals (Wright, 1978) was applied to analyze associations among the 924 genotypes, employing the software package Plabsoft (Maurer et al, 2008).…”

Section: Phenotypic Data Analysesmentioning

confidence: 99%

Evaluation of multi-locus models for genome-wide association studies: a case study in sugar beet

Würschum

Kraft²

2014

Heredity

View full text Add to dashboard Cite

Association mapping has become a widely applied genomic approach to dissect the genetic architecture of complex traits. A major issue for association mapping is the need to control for the confounding effects of population structure, which is commonly done by mixed models incorporating kinship information. In this case study, we employed experimental data from a large sugar beet population to evaluate multi-locus models for association mapping. As in linkage mapping, markers are selected as cofactors to control for population structure and genetic background variation. We compared different biometric models with regard to important quantitative trait locus (QTL) mapping parameters like the false-positive rate, the QTL detection power and the predictive power for the proportion of explained genotypic variance. Employing different approaches we show that the multilocus model, that is, incorporating cofactors, outperforms the other models, including the mixed model used as a reference model. Thus, multi-locus models are an attractive alternative for association mapping to efficiently detect QTL for knowledgebased breeding.

show abstract

“…The extent of linkage disequilibrium between pairs of loci was determined by estimating r 2 as described by Hill and Robertson (1968) using the software Plabsoft (Maurer et al, 2008).…”

Section: Genotypic Data Generationmentioning

confidence: 99%

Relatedness severely impacts accuracy of marker-assisted selection for disease resistance in hybrid wheat

et al. 2013

View full text Add to dashboard Cite

The accuracy of genomic selection depends on the relatedness between the members of the set in which marker effects are estimated based on evaluation data and the types for which performance is predicted. Here, we investigate the impact of relatedness on the performance of marker-assisted selection for fungal disease resistance in hybrid wheat. A large and diverse mapping population of 1739 elite European winter wheat inbred lines and hybrids was evaluated for powdery mildew, leaf rust and stripe rust resistance in multi-location field trials and fingerprinted with 9 k and 90 k SNP arrays. Comparison of the accuracies of prediction achieved with data sets from the two marker arrays revealed a crucial role for a sufficiently high marker density in genome-wide association mapping. Cross-validation studies using test sets with varying degrees of relationship to the corresponding estimation sets revealed that close relatedness leads to a substantial increase in the proportion of total genotypic variance explained by the identified QTL and consequently to an overoptimistic judgment of the precision of marker-assisted selection.

show abstract

Population genetic simulation and data analysis with Plabsoft

Cited by 63 publications

References 51 publications

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

Evaluation of multi-locus models for genome-wide association studies: a case study in sugar beet

Relatedness severely impacts accuracy of marker-assisted selection for disease resistance in hybrid wheat

Contact Info

Product

Resources

About