PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

Zhang, Chi; Dong, Shanshan; Xu, Junyang; He, Weiming; Yang, Tie‐Lin

doi:10.1093/bioinformatics/bty875

Cited by 1,016 publications

(732 citation statements)

References 14 publications

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“…We thinned the marker density to 25 586 SNPs using TASSEL 5.0 to reduce the computational cost of linkage disequilibrium (LD) decay analysis. The pairwise LD between 25 586 SNP markers was calculated and expressed as r 2 using the PopLDdecayV3.30 . The LD decay was set when the r 2 value decreased below a threshold level of r 2 < 0.2.…”

Section: Methodsmentioning

confidence: 99%

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Association and genome analyses to propose putative candidate genes for malt quality traits

et al. 2018

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BACKGROUND We studied the genetics of nine malt quality traits using association genetics in a panel of North Dakota, ICARDA, and Ethiopian barley lines. Grain samples harvested from Bekoji in 2011 and 2012 were used. RESULTS The mapping panel revealed strong population structure explained by inflorescence‐type, geographic origin, and breeding history. North Dakota germplasm were superior in malt quality traits and they can be donors to improve malt quality properties. We identified 106 marker‐trait associations (MTAs) for the nine traits, representing 81 genomic regions across all barley chromosomes. Chromosomes 3H, 5H, and 7H contained most of the MTAs (58.5%). Nearly 18.5% of these genomic regions contained two to three malt quality traits. Within ±250 kb of 81 genomic regions, we recovered 348 barley genes, with some potential impacting malt quality. These include invertase, β‐fructofuranosidase, α‐glucosidase, serine carboxypeptidase, and bidirectional sugar transporter SWEET14‐like protein. Eighteen of these genes were also previously reported in the Hordeum Toolbox, and 17 of them highly expressed during the germination process. CONCLUSION The results from this study invite further follow‐up functional characterization experiments to relate the genes with individual malt quality traits with higher confidence. It also provides germplasm resources for malt barley improvement. © 2018 Society of Chemical Industry

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Section: Methodsmentioning

confidence: 99%

“…The pairwise LD between 25 586 SNP markers was calculated and expressed as r 2 using the PopLDdecayV3.30. 17 The LD decay was set when the r 2 value decreased below a threshold level of r 2 < 0.2.…”

Section: Linkage Disequilibrium (Ld)mentioning

confidence: 99%

Association and genome analyses to propose putative candidate genes for malt quality traits

et al. 2018

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“…Linkage disequilibrium between sites, as assessed with the R² statistic, was also computed with VCFtools. Finally, linkage disequilibrium decay along scaffolds was analyzed with PopLDdecay 3.28 (Zhang et al 2019).…”

Section: Genetic Diversity and Association Of Snps With Mating Typesmentioning

confidence: 99%

Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen,Plasmopara viticola

Dussert

Legrand

Mazet

et al. 2020

Preprint

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Mating types are self-incompatibility systems that promote outcrossing in plants, fungi and oomycetes. Mating-type genes have been widely studied in plants and fungi, but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570 kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions.

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“…To prevent the interactive GWAS viewers and the tabular loci browser from operating too slowly, the volume of GWAS results was reduced by filtering out SNPs which had very low significance values (P value > 1e-4). The pairwise LD r 2 values of the remaining SNPs for each trait within 500 Kb windows were calculated using PopLDdecay (51).…”

Section: Mapping Filtering and Visualizing Genetic Locimentioning

confidence: 99%

“…High quality cis-eQTL SNPs were selected by only retaining those with a P value smaller than the Bonferroni corrected P value cutoff of 1/N. The pairwise LD r 2 values of the remaining SNPs for each gene were calculated using PopLDdecay (47).…”

Section: Mapping and Filtering Of Genetic Locimentioning

confidence: 99%

ZEAMAP, a comprehensive database adapted to the maize multi-omics era

Gui

Yang

et al. 2020

Preprint

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As one of the most extensively cultivated crops, maize (Zea mays L.) has been extensively studied by researchers and breeders for over a century. With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte. Integration of this information has the potential to accelerate genetic research and generate improvements in maize agronomic traits. To this end, we constructed ZEAMAP (http://www.zeamap.com), a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions, chromatin interactions, high-quality genetic variants, phenotypes, metabolomics, genetic maps, genetic mapping loci, population structures and domestication selection signals between teosinte and maize. ZEAMAP is user-friendly, with the ability to interactively integrate, visualize and cross-reference multiple different omics datasets. and linkage analysis, the population structure and pedigrees of each germplasm and the selective signals between different teosinte subspecies and maize. ZEAMAP generated comprehensive functional annotations for the annotated gene models in each assembly, and provided useful tools for users to search, analyze and visualize all these different omics data.

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PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

Cited by 1,016 publications

References 14 publications

Association and genome analyses to propose putative candidate genes for malt quality traits

Association and genome analyses to propose putative candidate genes for malt quality traits

Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen,Plasmopara viticola

ZEAMAP, a comprehensive database adapted to the maize multi-omics era

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