Computational approaches and software tools for genetic linkage map estimation in plants

Cheema, Jitender; Dicks, Jo

doi:10.1093/bib/bbp045

Cited by 93 publications

(83 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Inverted segments were identified as two or more independent markers that exhibited reversed ordering between species; inverted segments at the terminal ends of LGs required the misordering of at least one terminal marker and two or more internal markers. Because establishing the correct map position of tightly linked markers in high-density linkage maps can be difficult due to duplicated loci, genotyping errors, segregation distortion, and chiasma interference (Hackett and Broadfoot 2003;Ferreira et al 2006;Cheema and Dicks 2009;Collard et al 2009), minor ordering errors can arise. As such, a 2-cM threshold was applied for declaring noncollinearity (Hudson et al 2011).…”

Section: Synteny Assessmentmentioning

confidence: 99%

Chromosomal Evolution and Patterns of Introgression inHelianthus

et al. 2014

View full text Add to dashboard Cite

Knowledge of the nature and extent of karyotypic differences between species provides insight into the evolutionary history of the genomes in question and, in the case of closely related species, the potential for genetic exchange between taxa. We constructed high-density genetic maps of the silverleaf sunflower (Helianthus argophyllus) and Algodones Dune sunflower (H. niveus ssp. tephrodes) genomes and compared them to a consensus map of cultivated sunflower (H. annuus) to identify chromosomal rearrangements between species. The genetic maps of H. argophyllus and H. niveus ssp. tephrodes included 17 linkage groups each and spanned 1337 and 1478 cM, respectively. Comparative analyses revealed greater divergence between H. annuus and H. niveus ssp. tephrodes (13 inverted segments, 18 translocated segments) than between H. annuus and H. argophyllus (10 inverted segments, 8 translocated segments), consistent with their known phylogenetic relationships. Marker order was conserved across much of the genome, with 83 and 64% of the H. argophyllus and H. niveus ssp. tephrodes genomes, respectively, being syntenic with H. annuus. Population genomic analyses between H. annuus and H. argophyllus, which are sympatric across a portion of the natural range of H. annuus, revealed significantly elevated genetic structure in rearranged portions of the genome, indicating that such rearrangements are associated with restricted gene flow between these two species.C HROMOSOMAL rearrangements are of considerable interest because they are often associated with barriers to gene flow between related species, either due to their direct effects on the fitness of heterozygotes or through the indirect effects of genic barriers embedded within them (White 1978;Barton and Bengtsson 1986;Rieseberg et al. 1995bRieseberg et al. , 1999Rieseberg 2001;Navarro and Barton 2003;Kirkpatrick and Barton 2006; reviewed in Faria and Navarro 2010;Gimenez et al. 2012). As such, detailed information on karyotypic differences between species provides insight into the nature of reproductive isolation and, more pragmatically, informs attempts to introgress beneficial alleles from wild species into crop gene pools (Chetelat and Meglic 2000;Foulongne et al. 2003;Dirlewanger et al. 2004). An improved understanding of synteny across species can also facilitate the identification and localization of functionally important genes in a taxon of interest through the extrapolation of gene order from model species (e.g., Choi et al. 2004;Dilbirligi et al. 2006).The genus Helianthus, which is composed of 49 species native to the Americas (Timme et al. 2007) and includes cultivated sunflower (Helianthus annuus L.; 2n = 2x = 34; hereafter referred to as ANN), has emerged as a model for genetic studies of adaptation, hybridization, and speciation (Rieseberg et al. 1995a,b;Lai et al. 2005;Reagon and Snow 2006;Massinga et al. 2009;Gutierrez et al. 2010;Vekemans 2010;Roumet et al. 2013). Insight into the nature and extent of reproductive barriers within Helianthus will ...

show abstract

Section: Synteny Assessmentmentioning

confidence: 99%

Chromosomal Evolution and Patterns of Introgression inHelianthus

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Double reduction occurs randomly in polysomic species and only introduces a small bias into recombination frequency estimates . This means that, ignoring the possible influence of double reduction, diploid mapping software can generally be used for simplex marker sets at any ploidy level and for any type of meiotic pairing behaviour (Figure 4), opening up a very wide range of diploid-specific software options (Cheema and Dicks, 2009 Cotton, Gossypium hirsutum (4x)…”

Section: Linkage Mapsmentioning

confidence: 99%

Genetic mapping in polyploids

Bourke¹

View full text Add to dashboard Cite

“…Likelihood: For high-density data, map estimation is typically carried out on the basis of the two-point estimates of the recombination fractions (Cheema and Dicks 2009), primarily due to computational issues. Fundamentally, map uncertainty is due to the sampling error attached to these estimates, which will propagate through to the final map estimate.…”

Section: Asymptotic Distributionmentioning

confidence: 99%

“…Many approaches to genetic map estimation have been proposed and are reviewed along with common challenges in Cheema and Dicks (2009). Perhaps the most challenging step in map construction is ordering markers within a linkage group.…”

mentioning

confidence: 99%

Characterizing Uncertainty in High-Density Maps from Multiparental Populations

et al. 2014

View full text Add to dashboard Cite

Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations. However, errors in map construction can have significant impact on QTL discovery in later stages of analysis, and few methods have been developed to quantify the uncertainty attached to the reported order of markers or intermarker distances. Current methods are computationally intensive or limited to assessing uncertainty only for order or distance, but not both simultaneously. We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances. This approach allows us to construct hypothesis tests and confidence intervals for simultaneously assessing marker-order instability and distance uncertainty. We investigate the effects of marker density, population size, and founder distribution patterns on map confidence in multiparental populations through simulations. Using these data, we provide guidelines on sample sizes necessary to map markers at sub-centimorgan densities with high certainty. We apply these approaches to data from a bread wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population genotyped using the Illumina 9K SNP chip to assess regions of uncertainty and validate them against the recently released pseudomolecule for the wheat chromosome 3B.

show abstract

Computational approaches and software tools for genetic linkage map estimation in plants

Cited by 93 publications

References 27 publications

Chromosomal Evolution and Patterns of Introgression inHelianthus

Chromosomal Evolution and Patterns of Introgression inHelianthus

Genetic mapping in polyploids

Characterizing Uncertainty in High-Density Maps from Multiparental Populations

Contact Info

Product

Resources

About