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Whole genome analysis of infectious bovine keratoconjunctivitis in Angus cattle using Bayesian threshold models.

Kizilkaya K, Tait RG, Garrick DJ, Fernando RL, Reecy JM - BMC Proc (2011)

Bottom Line: Bayes-C threshold models were used to estimate SNP effects by classifying IBK into two, three or nine ordered categories.Magnitudes of genetic variances estimated in localized regions across the genome indicated that SNP within the most informative regions accounted for much of the genetic variance of IBK and pointed out some degree of association to IBK.There are many candidate genes in these regions which could include a gene or group of genes associated with bacterial disease in cattle.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Science, Iowa State University, Ames, IA 50011 USA. jreecy@iastate.edu.

ABSTRACT
Infectious bovine keratoconjunctivitis (IBK), also known as pinkeye, is characterized by damage to the cornea and is an economically important, lowly heritable, categorical disease trait in beef cattle. Scores of eye damage were collected at weaning on 858 Angus cattle. SNP genotypes for each animal were obtained from BovineSNP50 Infinium-beadchips. Simultaneous associations of all SNP with IBK phenotype were determined using Bayes-C that treats SNP effects as random with equal variance for an assumed fraction (π=0.999) of SNP having no effect on IBK scores. Bayes-C threshold models were used to estimate SNP effects by classifying IBK into two, three or nine ordered categories. Magnitudes of genetic variances estimated in localized regions across the genome indicated that SNP within the most informative regions accounted for much of the genetic variance of IBK and pointed out some degree of association to IBK. There are many candidate genes in these regions which could include a gene or group of genes associated with bacterial disease in cattle.

No MeSH data available.


Related in: MedlinePlus

Genetic variances determined in the chromosomal regions ordered by map position from chromosome 1 to X defined by sliding windows of five consecutive SNP through the whole genome for IBK score classified into two, three or nine categories.
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Figure 2: Genetic variances determined in the chromosomal regions ordered by map position from chromosome 1 to X defined by sliding windows of five consecutive SNP through the whole genome for IBK score classified into two, three or nine categories.

Mentions: Genetic variances explained by SNP were calculated in the chromosomal regions defined by 5 contiguous SNP sliding windows. The 1000 largest genetic variance windows across the genome are shown in Figure 2 by plotting them with respect to their genomic locations (relative SNP positions). For IBK scored in two, three or nine categories, each categorisation indicated different degree of association to IBK in certain genomic regions. Furthermore, it appears that certain chromosomal regions on the genome had different associations according to the categorisation scale.


Whole genome analysis of infectious bovine keratoconjunctivitis in Angus cattle using Bayesian threshold models.

Kizilkaya K, Tait RG, Garrick DJ, Fernando RL, Reecy JM - BMC Proc (2011)

Genetic variances determined in the chromosomal regions ordered by map position from chromosome 1 to X defined by sliding windows of five consecutive SNP through the whole genome for IBK score classified into two, three or nine categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108217&req=5

Figure 2: Genetic variances determined in the chromosomal regions ordered by map position from chromosome 1 to X defined by sliding windows of five consecutive SNP through the whole genome for IBK score classified into two, three or nine categories.
Mentions: Genetic variances explained by SNP were calculated in the chromosomal regions defined by 5 contiguous SNP sliding windows. The 1000 largest genetic variance windows across the genome are shown in Figure 2 by plotting them with respect to their genomic locations (relative SNP positions). For IBK scored in two, three or nine categories, each categorisation indicated different degree of association to IBK in certain genomic regions. Furthermore, it appears that certain chromosomal regions on the genome had different associations according to the categorisation scale.

Bottom Line: Bayes-C threshold models were used to estimate SNP effects by classifying IBK into two, three or nine ordered categories.Magnitudes of genetic variances estimated in localized regions across the genome indicated that SNP within the most informative regions accounted for much of the genetic variance of IBK and pointed out some degree of association to IBK.There are many candidate genes in these regions which could include a gene or group of genes associated with bacterial disease in cattle.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Science, Iowa State University, Ames, IA 50011 USA. jreecy@iastate.edu.

ABSTRACT
Infectious bovine keratoconjunctivitis (IBK), also known as pinkeye, is characterized by damage to the cornea and is an economically important, lowly heritable, categorical disease trait in beef cattle. Scores of eye damage were collected at weaning on 858 Angus cattle. SNP genotypes for each animal were obtained from BovineSNP50 Infinium-beadchips. Simultaneous associations of all SNP with IBK phenotype were determined using Bayes-C that treats SNP effects as random with equal variance for an assumed fraction (π=0.999) of SNP having no effect on IBK scores. Bayes-C threshold models were used to estimate SNP effects by classifying IBK into two, three or nine ordered categories. Magnitudes of genetic variances estimated in localized regions across the genome indicated that SNP within the most informative regions accounted for much of the genetic variance of IBK and pointed out some degree of association to IBK. There are many candidate genes in these regions which could include a gene or group of genes associated with bacterial disease in cattle.

No MeSH data available.


Related in: MedlinePlus