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A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle.

Sahana G, Iso-Touru T, Wu X, Nielsen US, de Koning DJ, Lund MS, Vilkki J, Guldbrandtsen B - Genet. Sel. Evol. (2016)

Bottom Line: Among this haplotype's alleles, HAPQTL had a large negative effect on stillbirth.No animals were found to be homozygous for HAPQTL.A deleted region of approximately 500 kb that spans three genes on BTA23 was identified and is a strong candidate QTL with a large effect on BI by increasing stillbirth.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark. goutam.sahana@mbg.au.dk.

ABSTRACT

Background: A whole-genome association study of 4631 progeny-tested Nordic Red dairy cattle bulls using imputed next-generation sequencing data revealed a major quantitative trait locus (QTL) that affects birth index (BI) on Bos taurus autosome (BTA) 23. We analyzed this QTL to identify which of the component traits of BI are affected and understand its molecular basis.

Results: A genome-wide scan of BI in Nordic Red dairy cattle detected major QTL on BTA6, 14 and 23. The strongest associated single nucleotide polymorphism (SNP) on BTA23 was located at 13,313,896 bp with [Formula: see text]. Analyses of component traits showed that the QTL had a large effect on stillbirth. Based on the 10 most strongly associated SNPs with stillbirth, we constructed a haplotype. Among this haplotype's alleles, HAPQTL had a large negative effect on stillbirth. No animals were found to be homozygous for HAPQTL. Analysis of stillbirth records that were categorized by carrier status for HAPQTL of the sire and maternal grandsire suggested that this haplotype had a recessive mode of inheritance. Illumina BovineHD BeadChip genotypes and genotype intensity data indicated a chromosomal deletion between 12.28 and 12.81 Mbp on BTA23. An independent set of Illumina Bovine50k BeadChip genotypes identified a recessive lethal haplotype that spanned the deleted region.

Conclusions: A deleted region of approximately 500 kb that spans three genes on BTA23 was identified and is a strong candidate QTL with a large effect on BI by increasing stillbirth.

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Single-variant association signal plots for birth index (BI) (light gray dots) and single-variant analysis with the 10-SNP haplotype as a cofactor (blue dots). Haplotypes were constructed with the 10 top associated SNPs at the QTL peak and fitted as covariates in the model (blue dots)
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Fig4: Single-variant association signal plots for birth index (BI) (light gray dots) and single-variant analysis with the 10-SNP haplotype as a cofactor (blue dots). Haplotypes were constructed with the 10 top associated SNPs at the QTL peak and fitted as covariates in the model (blue dots)

Mentions: BI and three calving traits (SB, CE and CS) were analyzed for association with SNPs in the target region on BTA23 using a LMM. The SNPs that were most strongly associated with each trait are in Table 1. The strongest association signal was observed for SBL (light gray dots in Fig. 3), followed by BI (light gray dots in Fig. 4) and SBF (light gray dots in Fig. 5), with a peak at 13,313,896 bp (rs722178836). Association peaks for both CE and CS were positioned at 17.63 Mbp (see Additional file 2: Figures S1, S2). The values were between 15.9 and 24.4, i.e. much smaller than those observed for SB and BI.Fig. 3


A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle.

Sahana G, Iso-Touru T, Wu X, Nielsen US, de Koning DJ, Lund MS, Vilkki J, Guldbrandtsen B - Genet. Sel. Evol. (2016)

Single-variant association signal plots for birth index (BI) (light gray dots) and single-variant analysis with the 10-SNP haplotype as a cofactor (blue dots). Haplotypes were constructed with the 10 top associated SNPs at the QTL peak and fitted as covariates in the model (blue dots)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835938&req=5

Fig4: Single-variant association signal plots for birth index (BI) (light gray dots) and single-variant analysis with the 10-SNP haplotype as a cofactor (blue dots). Haplotypes were constructed with the 10 top associated SNPs at the QTL peak and fitted as covariates in the model (blue dots)
Mentions: BI and three calving traits (SB, CE and CS) were analyzed for association with SNPs in the target region on BTA23 using a LMM. The SNPs that were most strongly associated with each trait are in Table 1. The strongest association signal was observed for SBL (light gray dots in Fig. 3), followed by BI (light gray dots in Fig. 4) and SBF (light gray dots in Fig. 5), with a peak at 13,313,896 bp (rs722178836). Association peaks for both CE and CS were positioned at 17.63 Mbp (see Additional file 2: Figures S1, S2). The values were between 15.9 and 24.4, i.e. much smaller than those observed for SB and BI.Fig. 3

Bottom Line: Among this haplotype's alleles, HAPQTL had a large negative effect on stillbirth.No animals were found to be homozygous for HAPQTL.A deleted region of approximately 500 kb that spans three genes on BTA23 was identified and is a strong candidate QTL with a large effect on BI by increasing stillbirth.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark. goutam.sahana@mbg.au.dk.

ABSTRACT

Background: A whole-genome association study of 4631 progeny-tested Nordic Red dairy cattle bulls using imputed next-generation sequencing data revealed a major quantitative trait locus (QTL) that affects birth index (BI) on Bos taurus autosome (BTA) 23. We analyzed this QTL to identify which of the component traits of BI are affected and understand its molecular basis.

Results: A genome-wide scan of BI in Nordic Red dairy cattle detected major QTL on BTA6, 14 and 23. The strongest associated single nucleotide polymorphism (SNP) on BTA23 was located at 13,313,896 bp with [Formula: see text]. Analyses of component traits showed that the QTL had a large effect on stillbirth. Based on the 10 most strongly associated SNPs with stillbirth, we constructed a haplotype. Among this haplotype's alleles, HAPQTL had a large negative effect on stillbirth. No animals were found to be homozygous for HAPQTL. Analysis of stillbirth records that were categorized by carrier status for HAPQTL of the sire and maternal grandsire suggested that this haplotype had a recessive mode of inheritance. Illumina BovineHD BeadChip genotypes and genotype intensity data indicated a chromosomal deletion between 12.28 and 12.81 Mbp on BTA23. An independent set of Illumina Bovine50k BeadChip genotypes identified a recessive lethal haplotype that spanned the deleted region.

Conclusions: A deleted region of approximately 500 kb that spans three genes on BTA23 was identified and is a strong candidate QTL with a large effect on BI by increasing stillbirth.

Show MeSH