De novo construction of polyploid linkage maps using discrete graphical models

@article{Behrouzi2019DeNC,
  title={De novo construction of polyploid linkage maps using discrete graphical models},
  author={Pariya Behrouzi and Ernst C. Wit},
  journal={Bioinformatics},
  year={2019},
  volume={35},
  pages={1083–1093}
}
MOTIVATION Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to… 
View on Wolters Kluwer
library.wur.nl
10 Citations
Background Citations
2
Methods Citations
4

Figures and Tables from this paper

10 Citations

Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models

TLDR
A statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models is presented.

Tools for Genetic Studies in Experimental Populations of Polyploids

TLDR
The tools available to the research community to better understand polyploid inheritance are looked at, including software for assigning marker genotypes, establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulatingpolyploid populations.

Genetic mapping in polyploids

TLDR
This PhD project looked at how DNA information of polyploids should be best analysed, developing methods and new software tools to achieve this.

netgwas: An R Package for Network-Based Genome-Wide Association Studies

TLDR
The R package netgwas is introduced, which is designed based on undirected graphical models to accomplish three important and interrelated goals in genetics: constructing linkage map, reconstructing linkage disequilibrium networks from multi-loci genotype data, and detecting high-dimensional genotype-phenotype networks.

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance

TLDR
This work used genotyping by sequencing of full-sib progeny to relate genomic regions with brown rust phenotypes by establishing a pipeline to identify reliable SNPs in complex polyploid data, which were used for phenotypic prediction via machine learning.

QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population

TLDR
This study is the first to cast light on the genetics of a polyploid kiwifruit and suggest a plausible mechanism for Psa resistance in this species.

A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities: a rabbit model

TLDR
The analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype.

Dietary Intakes of Vegetable Protein, Folate, and Vitamins B-6 and B-12 Are Partially Correlated with Physical Functioning of Dutch Older Adults Using Copula Graphical Models

TLDR
It is determined that vegetable protein, vitamin B-6, folate, and vitamin B -12 intakes are partially correlated with improved functional outcome measurements in Dutch older adults.

Extensions of graphical models with applications in genetics and genomics

De levende cel is een complex systeem van interacterende moleculen, waarin genen gekopieerd worden naar RNA's en vertaald in eiwitten. De meeste biologische karakteristieken komen voort uit complexe…

High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content

Highbush blueberry (Vaccinium corymbosum, 2n = 4x = 48) is the most cultivated type of blueberry, both in New Zealand and overseas. Its perceived nutritional value is conferred by phytonutrients,…

References

SHOWING 1-10 OF 51 REFERENCES

A rapid marker ordering approach for high-density genetic linkage maps in experimental autotetraploid populations using multidimensional scaling

TLDR
This paper proposes and validates a robust method for rapid construction of high-density linkage maps suitable for autotetraploid species and concludes that an initial analysis using unconstrained MDS gives a rapid method to detect and remove problematic markers, and that a subsequent analysis using either constrained MDS or principal curve analysis gives reliable marker orders.

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

TLDR
This paper introduces a novel algorithm to order markers on a genetic linkage map based on a simple yet fundamental mathematical property that proves the validity of this property, and shows that it consistently outperforms the best available methods in the literature.

polymapR—linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

TLDR
PolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi‐parental populations of outcrossing autopolyploids and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit.

Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP.

TLDR
The procedure performs a sequential build-up of the map and, at each step, a numerical search for the best fitting order of markers, and weighted least squares is used for the estimation of map distances.

Building Ultra-Dense Genetic Maps in the Presence of Genotyping Errors and Missing Data

TLDR
The proposed “twins” approach does not need any prior information, and hence can be applied to genetically poorly studied organisms, and enables mapping big sets of markers.

Constructing dense genetic linkage maps

TLDR
A novel combination of techniques for the construction of dense genetic linkage maps using simulated annealing and missing-data imputation and the Metropolis-Hastings algorithm is used to obtain posterior intervals for the positions of markers.

PERGOLA: fast and deterministic linkage mapping of polyploids

TLDR
PerGOLA can be used successfully to calculate linkage maps for diploid and polyploid species and outperforms existing tools in computational time and mapping accuracy.

Detecting epistatic selection with partially observed genotype data by using copula graphical models

TLDR
A method for reconstructing an underlying network of genomic signatures of high dimensional epistatic selection from multilocus genotype data is developed and reveals ‘aberrant’ marker–marker associations that are due to Epistatic selection rather than gametic linkage.

The Use of SNP Markers for Linkage Mapping in Diploid and Tetraploid Peanuts

TLDR
The present study used a previously constructed 1536 GoldenGate SNP assay developed using SNPs identified between two A. duranensis accessions to score SNP markers incorporated into diploid and tetraploid genetic maps of Arachis and were located almost entirely on A genome linkage groups.

The simulation of meiosis in diploid and tetraploid organisms using various genetic models

TLDR
PedigreeSim, a software package that simulates meiosis in both diploid and tetraploid species and uses this to simulate pedigrees and cross populations, is presented, believed to be the first simulation software that implements all features of meiotic in tetraPLoids.
...