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A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies
BackgroundMultilocus analysis on a set of single nucleotide polymorphisms (SNPs) pre-assigned within a gene constitutes a valuable complement to...
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Genome-Wide Association Study Statistical Models: A Review
Statistical models are at the core of the genome-wide association study (GWAS). In this chapter, we provide an overview of single- and multilocus...
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Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique
The African buffalo, Syncerus caffer , is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat...
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Genome-Wide Association Study: A Powerful Approach to Map QTLs in Crop Plants
Genome-wide association studies (GWAS) are powerful for identifying genomic regions, or even directly the causal loci, controlling the variation of...
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Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence ty**
Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused...
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Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar
BackgroundDespite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived...
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Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a...
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Performing Genome-Wide Association Studies with Multiple Models Using GAPIT
Genome-wide association study (GWAS) is based on the linkage disequilibrium (LD) between phenotypes and genetic markers covering the whole genome....
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Hybrid speciation driven by multilocus introgression of ecological traits
Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species
1 ,2 . However, convincing examples of...
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Designing a Genome-Wide Association Study: Main Steps and Critical Decisions
In this introductory chapter, we seek to provide the reader with a high-level overview of what goes into designing a genome-wide association study...
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Multilocus sequence ty** reveals two distinct populations of “Candidatus Phytoplasma sacchari” in China
Sugarcane white leaf (SCWL), associated with the presence of “ Candidatus Phytoplasma sacchari,” is a devastating disease. In this study, a multilocus...
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Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways
Insomnia is a heritable, highly prevalent sleep disorder for which no sufficient treatment currently exists. Previous genome-wide association studies...
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Genome-Wide Association Analyses to Identify SNPs Related to Drought Tolerance
Drought stress is a serious agronomic problem resulting in significant yield losses globally. Breeding cultivars with drought tolerance is an...
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Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice
BackgroundGrain yield is a complex trait that results from interaction between underlying phenotypic traits and climatic, edaphic, and biotic...
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Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies
BackgroundEvolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance...
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Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence ty**
The laboratory surveillance of bacillary dysentery is based on a standardised Shigella ty** scheme that classifies Shigella strains into four...
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Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.)
Genome-wide association study (GWAS) is effective in identifying favorable alleles for traits of interest with high map** resolution in crop...
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An overview of genome-wide association map** studies in Poaceae species (model crops: wheat and rice)
There is a significant interest while utilizing association map** technique to determine the genes which are accountable for numerical...
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The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation
BackgroundThe multiple de novo copy number variant (M dn CNV) phenotype is described by having four or more constitutional de novo CNVs ( dn CNVs)...
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Performance evaluation of core genome multilocus sequence ty** for genoty** of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection
PurposeTo evaluate the performance of core genome multilocus sequence ty** (cgMLST) for genoty** Mycobacterium tuberculosis ( M.tuberculosis )...
