Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations

Berg, Arthur; He, Qiuling; Shen, Ye; Chen, Ying; Min-ren, Huang; Wu, Rongling

doi:10.2202/1544-6115.1528

Cited by 3 publications

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“…A next step for studying this species should be to understand the pattern of genetic diversity using molecular markers and the evolution of phytochrome function operated by anthocyanins [2] . More recently, we have exploited an array of informative microsatellite markers [30] and also developed a series of statistical models for estimating and testing multiallelic Hardy-Weinberg disequilibria and multiallelic linkage disequilibria with multilocus data [31] . By associating with marker polymorphisms with floral colors, we can identify significant genetic variants that contribute to flower variation, shedding light on the genetic architecture of color formation in L. longituba .…”

Section: Discussionmentioning

confidence: 99%

Natural Variation in Petal Color in Lycoris longituba Revealed by Anthocyanin Components

Shen

Wang

et al. 2011

PLoS ONE

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Lycoris longituba is one of the species belonging to the Amaryllidaceae family. Despite its limited distribution, endemic to central eastern China, this species displays an exceptionally wide diversity of flower colors from purple, red, orange, to yellow, in nature. We study the natural variation of floral color in L. longituba by testing the components of water-soluble vacuolar pigments – anthocyanins – in its petals using high-performance liquid chromatography coupled with photodiode array detection and electrospray ionization mass spectrometry. Four anthocyanins were identified, cyanidin-3-sophoroside (Cy3So), cyanidin-3-xylosylglucoside (Cy3XyGlc), cyanidin-3-sambubioside (Cy3Sa), and pelargonidin-3-xylosylglucoside (Pg3XyGlc), which occur at various amounts in L. longituba petals of different colors. A multivariate analysis was used to explore the relationship between pigments and flower color. Anthocyanins have been thought to play a major role in acting as a UV screen that protects the plant's DNA from sunlight damage and attracting insects for the purpose of pollination. Thus, knowledge about the content and type of anthocyanins determining the petal coloration of Lycoris longituba will help to study the adaptive evolution of flowers and provide useful information for the ornamental breeding of this species.

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Section: Discussionmentioning

confidence: 99%

Natural Variation in Petal Color in Lycoris longituba Revealed by Anthocyanin Components

Shen

Wang

et al. 2011

PLoS ONE

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“…Kim et al [ 11 ] proposed a multi-locus high order linkage disequilibrium with a multiple order Markov chain model. Berg et al [ 12 ] have developed a method for estimation of multi-allelic third order linkage disequilibrium. Nevertheless, no publication exists on the genome-wide levels of third order linkage disequilibrium present in animal populations.…”

Section: Introductionmentioning

confidence: 99%

Extent of third-order linkage disequilibrium in a composite line of Iberian pigs

et al. 2018

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BackgroundPrevious studies on linkage disequilibrium have investigated second order linkage disequilibrium in animal and plant populations. The objective of this paper was to investigate the genome-wide levels of third order linkage disequilibrium in a composite line founded by admixture of four Iberian pig strains. A model for the generation of third order linkage disequilibrium by population admixture is proposed. A computer Expectation-Maximization algorithm is developed and applied to the estimation of third order linkage disequilibrium at inter- and intra-chromosomal level using 26,347 SNPs typed in 306 sows. The relationship of third order linkage disequilibrium with physical distance was investigated over 35 million triplets in SSC12. Basic and normalized estimates of inter and intra-chromosomal third order linkage disequilibrium are reported.ResultsGenome-wide analyses revealed that third order linkage disequilibrium is rather common among linked loci in this Iberian pig line. It is shown that population admixture of multiple populations may explain the observed levels of third order linkage disequilibrium although it could be generated by genetic drift. Third order linkage disequilibrium decreases rapidly up to 4 Mb and then declines slowly. The short distances between consecutive markers explain the maintenance of the observed third order linkage disequilibria levels when using a model incorporating the break-up of disequilibrium by recombination. Genome-wide testing also revealed that only 3.6% of the normalized estimates were different from 1, − 1, 0, or from a not well-defined situation in which there is only one possible value for the third order linkage disequilibrium parameter, given allele frequencies and pairwise linkage disequilibria parameters.ConclusionsThird order linkage disequilibrium is common among linked markers in the analyzed pig line and may have been generated by population admixture of multiple populations or by genetic drift. As with second order linkage disequilibrium, the absolute value of the third order linkage disequilibrium decreases with physical distance. Normalization of third order linkage disequilibrium should be avoided for closely linked bi-allelic loci.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0661-4) contains supplementary material, which is available to authorized users.

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“…Zaykin, Pudovkin & Weir (2008) provided correlation-based estimation of LD between markers with multiple alleles. Berg et al (2010) generalized the estimation of LD with an arbitrary number of alleles and used it to estimate the genetic diversity of an outcrossing population (2009). To enhance the application of trait linkage mapping, Wijsman, Rothstein & Thompson (2006) derived a multipoint analysis for multiallelic markers in a human pedigree.…”

Section: Introductionmentioning

confidence: 99%

Inferring the evolutionary history of outcrossing populations through computing a multiallelic linkage–linkage disequilibrium map

Zhu

Zhao

et al. 2015

Methods Ecol Evol

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1. Linkage disequilibrium (LD), the non-random association of alleles at different loci, has been used as an important parameter to study the genetic diversity and evolutionary history of natural populations. A joint analysis of LD with the linkage of the same marker pair has proven to gain more insight into the genetic signature of population diversification than LD analysis alone. 2. We develop a unifying framework for simultaneously estimating the linkage and LD across pairs of multiallelic markers. The framework has particular power to construct the LD map from any markers with an arbitrary number of alleles per locus. We provide an efficient strategy to manipulate disequilibrium parameters whose number increases exponentially with the number of alleles. 3. The model was tested through extensive simulation studies and validated by analysing a real marker data set from a population genetic research project of euphrates poplar, a desert tree, distributed in the north-western China. For widespread undomesticated natural populations, compared with biallelic markers, multiallelic markers with a high level of polymorphism are more powerful to study their genetic structure and organization of an outcrossing population. 4. The model developed will potentially have an immediate implication for population and evolutionary genetic studies.

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Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations

Cited by 3 publications

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Natural Variation in Petal Color in Lycoris longituba Revealed by Anthocyanin Components

Natural Variation in Petal Color in Lycoris longituba Revealed by Anthocyanin Components

Extent of third-order linkage disequilibrium in a composite line of Iberian pigs

Inferring the evolutionary history of outcrossing populations through computing a multiallelic linkage–linkage disequilibrium map

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