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Linkage Disequilibrium Statistics and Block Visualization
Linkage disequilibrium analysis enables researchers to interrogate the genome for patterns of coinheritance between genetic markers. Visualizing...
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Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET)
Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target...
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Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia
BackgroundDurum wheat is one of the most important crops, especially in the Mediterranean region. Insight into the genetic diversity of germplasm can...
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Long-range linkage disequilibrium in French beef cattle breeds
BackgroundLinkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci...
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Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association map** of yield-related traits
Tall fescue ( Festuca arundinacea ) from Poaceae family is an allohexaploid (2 n =6 x =42) and cross pollinated plant that is used throughout the world as...
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LDkit: a parallel computing toolkit for linkage disequilibrium analysis
BackgroundLinkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps...
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Genetic Effects in Populations Under Linkage Equilibrium
In this chapter, models of genetic effects at the population level are provided that cover all the genetic architectures considered in the previous...
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Genome-wide association for β-glucan content, population structure, and linkage disequilibrium in elite oat germplasm adapted to subtropical environments
High β-glucan content is one of the main goals of oat breeding programs worldwide. However, the genomic regions and genes controlling β-glucan...
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Combined linkage map** and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize
Key messageCombined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 ...
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Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight
Almond [ Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genoty**-by-sequencing (GBS) was applied to 149 almond...
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Genetic dissection of lutein content in common wheat via association and linkage map**
Key messageGenetic architecture controlling grain lutein content of common wheat was investigated through an integration of genome-wide association...
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Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India
The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among...
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Combining genome-wide association study and linkage map** in the genetic dissection of amylose content in maize (Zea mays L.)
Key messageIntegrated linkage and association analysis revealed genetic basis across multiple environments. The genes Zm00001d003102 and Zm00001d015905...
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Map** of genomic regions linked to stemphylium blight (Stemphylium botryosum Wallr.) resistance in lentil using linkage map** and marker-trait association analysis
Stemphylium blight caused by Stemphylium botryosum, is a foliar disease of lentil. It affects the productivity and milling quality of lentil crops,...
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Automatic block-wise genotype-phenotype association detection based on hidden Markov model
BackgroundFor detecting genotype-phenotype association from case–control single nucleotide polymorphism (SNP) data, one class of methods relies on...
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Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium
BackgroundWheat ( Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic...
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Genome-wide association study and linkage map** reveal TaqW-6B associated with water-extractable arabinoxylan content in wheat grain
Key messageA novel QTL, TaqW-6B of water-extractable arabinoxylan content in the wheat grain on chromosome 6BL was identified and fine mapped in a...
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Estimating linkage disequilibrium from genotypes under Hardy-Weinberg equilibrium
BackgroundMeasures of linkage disequilibrium (LD) play a key role in a wide range of applications from disease association to demographic history...
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geneHapR: an R package for gene haplotypic statistics and visualization
BackgroundTogether with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different...
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Haplotype structure of MSTN, IGF1, and BMP2 genes in Tunisian goats (Capra hircus) and their association with morphometric traits
The aim of the present study was to evaluate variability and haplotype structure of twenty-eight single nucleotide polymorphisms (SNPs) at myostatin (
