SNPlotz: a generic genome plot tool to aid the SNP association studies

Hu, Zhi-Liang; Fernando, Rex D.; Garrick, Dorian J.; Reecy, James M.

doi:10.1186/1471-2105-11-s4-p4

Cited by 2 publications

(2 citation statements)

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“…SNPLOTz visualized the estimated SNP effects and their genomic location and was dynamically linked to Gbrowse (http://www.animalgenome.org/gbrowse), which allowed visualization of SNP with other types of genome features (i.e., annotated genes, curated QTL, transcripts, etc.) [23]. The SNP positions within a chromosome were based on Bos taurus genome assembly (UMD 3.1).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle

et al. 2013

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BackgroundInfectious Bovine Keratoconjunctivitis (IBK) in beef cattle, commonly known as pinkeye, is a bacterial disease caused by Moraxellabovis. IBK is characterized by excessive tearing and ulceration of the cornea. Perforation of the cornea may also occur in severe cases. IBK is considered the most important ocular disease in cattle production, due to the decreased growth performance of infected individuals and its subsequent economic effects. IBK is an economically important, lowly heritable categorical disease trait. Mass selection of unaffected animals has not been successful at reducing disease incidence. Genome-wide studies can determine chromosomal regions associated with IBK susceptibility. The objective of the study was to detect single-nucleotide polymorphism (SNP) markers in linkage disequilibrium (LD) with genetic variants associated with IBK in American Angus cattle.ResultsThe proportion of phenotypic variance explained by markers was 0.06 in the whole genome analysis of IBK incidence classified as two, three or nine categories. Whole-genome analysis using any categorisation of (two, three or nine) IBK scores showed that locations on chromosomes 2, 12, 13 and 21 were associated with IBK disease. The genomic locations on chromosomes 13 and 21 overlap with QTLs associated with Bovine spongiform encephalopathy, clinical mastitis or somatic cell count.ConclusionsResults of these genome-wide analyses indicated that if the underlying genetic factors confer not only IBK susceptibility but also IBK severity, treating IBK phenotypes as a two-categorical trait can cause information loss in the genome-wide analysis. These results help our overall understanding of the genetics of IBK and have the potential to provide information for future use in breeding schemes.

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Section: Methodsmentioning

confidence: 99%

Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle

et al. 2013

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“…The posterior means of the SNP effects were collectively used to predict the genomic merit of sliding chromosomal regions, and the variance of the DGV of these windows across individuals was expressed as a proportion of the total variance (Fernando and Garrick, 2010). The estimate of the proportion of genetic variation explained by each window obtained from the genome-wide association study was plotted against genome region using SNPLOTz v.1.52 (Hu et al, 2010 ; www.animalgenome.org/bioinfo/tools/snplotz/). Individual SNP in windows that explained the largest proportion of genetic variation were then visualized in GBrowse (Stein et al, 2002; /www.animalgenome.org/cgi-bin/gbrowse/bovine/) to allow for a detailed inspection of the chromosomal region containing the specific SNP.…”

Section: Genome-wide Association Studymentioning

confidence: 99%

Genome-wide association study of concentrations of iron and other minerals in longissimus muscle of Angus cattle1

Mateescu

Garrick

Tait

et al. 2013

Journal of Animal Science

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The objective of this study was to characterize variation and identify SNP and chromosomal regions associated with mineral concentrations in LM of Angus beef cattle. Samples of LM from 2,285 Angus cattle were obtained, and concentrations of 7 minerals, including iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Genomic DNA extracted from the ground beef sample used for mineral composition was genotyped with the Bovine SNP50 Infinium II BeadChip, and effects of SNP on each trait were estimated using the Bayes-Cπ module of GenSel software. Pedigree-based estimates of heritabilities and corresponding genetic variances indicate iron was the only mineral concentration that could be considered a good candidate for manipulation by genomic selection. The amount of variation that could be accounted for by SNP genotypes was concordant with pedigree-based heritabilities and varied from very low for potassium and sodium (<0.09) to medium high (0.37) for iron. Although significant chromosomal regions were identified for all minerals analyzed in this study, further study focused on iron. Seven regions on 6 chromosomes (1, 2, 7, 10, 15, and 28) were identified to have a major effect on the iron content of LM in Angus cattle. The accuracy of direct genomic values (DGV) for iron concentration was estimated using a 5-fold cross-validation strategy. The accuracy of DGV estimated as the genetic correlation between DGV and the phenotype (iron concentration) adjusted for contemporary groups was 0.59. A bivariate animal model was used to estimate genetic correlations between iron concentrations and a reduced set of economically important carcass traits: HCW, rib eye area, calculated USDA yield grade, percent KPH, and marbling score. The genetic correlations between iron concentration and HCW, percentage KPH, marbling score, and rib eye area were small (-0.19 to 0.15) and nonsignificant. Although still weak (0.22), a positive significant genetic correlation was identified between iron content and USDA calculated yield grade. Beef is a major contributor of iron and zinc in the human diet, and this study found that iron content might be effectively manipulated through marker-assisted selection programs, without compromising other carcass and palatability traits.

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SNPlotz: a generic genome plot tool to aid the SNP association studies

Cited by 2 publications

References 1 publication

Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle

Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle

Genome-wide association study of concentrations of iron and other minerals in longissimus muscle of Angus cattle1

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