Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach

Pikkuhookana, P; Sillanpää, Mikko J.

doi:10.1038/hdy.2013.111

Cited by 9 publications

(7 citation statements)

References 126 publications

(145 reference statements)

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“…QTLs affecting the phenotypes of interest can be also detected using LD mapping, which takes advantage of historical recombination events within the unobserved pedigree [73].…”

Section: Qtl Mapping and Marker-assisted Selectionmentioning

confidence: 99%

“…The resolution of QTL mapping can also be enhanced by combining linkage maps with LD maps [73]. Indeed, the existence of LD implies there are segments of a chromosome in the population which are descended from the same common ancestor.…”

Section: Qtl Mapping and Marker-assisted Selectionmentioning

confidence: 99%

“…These identical-by-descent (IBD) chromosome segments carry both identical marker haplotypes and identical QTL alleles. This type of QTL mapping is referred to as LDLA (linkage disequilibrium linkage analysis) [73].…”

Section: Qtl Mapping and Marker-assisted Selectionmentioning

confidence: 99%

See 2 more Smart Citations

Biotechnological and Digital Revolution for Climate-Smart Plant Breeding

Taranto

Nicolia²,

Pavan

et al. 2018

Agronomy

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Climate change, associated with global warming, extreme weather events, and increasing incidence of weeds, pests and pathogens, is strongly influencing major cropping systems. In this challenging scenario, miscellaneous strategies are needed to expedite the rate of genetic gains with the purpose of developing novel varieties. Large plant breeding populations, efficient high-throughput technologies, big data management tools, and downstream biotechnology and molecular techniques are the pillars on which next generation breeding is based. In this review, we describe the toolbox the breeder has to face the challenges imposed by climate change, remark on the key role bioinformatics plays in the analysis and interpretation of big “omics” data, and acknowledge all the benefits that have been introduced into breeding strategies with the biotechnological and digital revolution.

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“…QTLs affecting the phenotypes of interest can be also detected using LD mapping, which takes advantage of historical recombination events within the unobserved pedigree [73].…”

Section: Qtl Mapping and Marker-assisted Selectionmentioning

confidence: 99%

Section: Qtl Mapping and Marker-assisted Selectionmentioning

confidence: 99%

See 1 more Smart Citation

Biotechnological and Digital Revolution for Climate-Smart Plant Breeding

Taranto

Nicolia²,

Pavan

et al. 2018

Agronomy

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“…The molecular tools helping in understanding the genetic mechanism of these traits might be very critical for increasing the efficiency of breeding programs. Trait loci affecting the phenotype can be detected by using linkage analysis and linkage disequilibrium mapping or a combination of both (Pikkuhookana and Sillanpaa, 2014). Both procedures use crossovers or recombinations between two loci.…”

Section: Introductionmentioning

confidence: 99%

Preliminary studies of genom-wide association mapping for some selected morphological characters of watermelons

Yağcıoğlu

Gülşen

Yetışır

et al. 2016

Scientia Horticulturae

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Developing more efficient tools for watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) breeding programs may greatly contribute to genetic improvement. The aims of this study were to investigate genome-wide association analysis (GWAS), and to develop regression models for some important watermelon traits such as yield, fruit weight, flesh color, total soluble solid, seed coat color, seed length and flowering time using 96 lines selected from 258 pure lines. An initial analysis was conducted to reduce sample size to 96 in order to avoid identical, highly similar and distant relatives causing low level of polymorphism and rare alleles. These 96 lines were morphologically and genetically characterized for several morphological characters under the eastern Mediterranean conditions, Adana, Turkey and PCR-based molecular markers. Associated markers were estimated by TASSEL program based on general linear model and a regression model because

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“… 10 More recently, this strategy has been modified to accommodate to the estimation of genetic imprinting 11 and genetic variance. 12 Pikkuhookana and Sillanpaa 13 implemented a Bayesian algorithm for parameter estimation from this strategy.…”

Section: Introductionmentioning

confidence: 99%

Constructing a linkage–linkage disequilibrium map using dominant-segregating markers

Zhu

Dong

Jiang

et al. 2015

DNA Res

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The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage–LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage–LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution.

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Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach

Cited by 9 publications

References 126 publications

Biotechnological and Digital Revolution for Climate-Smart Plant Breeding

Biotechnological and Digital Revolution for Climate-Smart Plant Breeding

Preliminary studies of genom-wide association mapping for some selected morphological characters of watermelons

Constructing a linkage–linkage disequilibrium map using dominant-segregating markers

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