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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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Manhattan plot for single-variant association analysis for birth index in Nordic Red dairy cattle. Association analyses were carried out using a sire model for whole-genome sequence variants
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Fig1: Manhattan plot for single-variant association analysis for birth index in Nordic Red dairy cattle. Association analyses were carried out using a sire model for whole-genome sequence variants

Mentions: Figure 1 presents the Manhattan plot for the QTL scan for BI based on WGS data in Nordic Red dairy cattle. Additional file 1: Table S1 provides the top associated genome-wide significant SNPs for each chromosome. Strong association signals for BI were observed on BTA6, 14 and 23. Previously, we reported a QTL for BI on BTA6 which increased calf size at birth and adult stature [32] and we attributed the increases in calving difficulties and stillbirth to the increased calf size at birth. In the present study, we focused on the QTL for BI that is located on BTA23. The most strongly associated SNP was located at 13,313,896 bp (rs722178836) and had an allele substitution effect of -0.72 additive genetic standard deviations and (Fig. 2).Fig. 1


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)

Manhattan plot for single-variant association analysis for birth index in Nordic Red dairy cattle. Association analyses were carried out using a sire model for whole-genome sequence variants
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Manhattan plot for single-variant association analysis for birth index in Nordic Red dairy cattle. Association analyses were carried out using a sire model for whole-genome sequence variants
Mentions: Figure 1 presents the Manhattan plot for the QTL scan for BI based on WGS data in Nordic Red dairy cattle. Additional file 1: Table S1 provides the top associated genome-wide significant SNPs for each chromosome. Strong association signals for BI were observed on BTA6, 14 and 23. Previously, we reported a QTL for BI on BTA6 which increased calf size at birth and adult stature [32] and we attributed the increases in calving difficulties and stillbirth to the increased calf size at birth. In the present study, we focused on the QTL for BI that is located on BTA23. The most strongly associated SNP was located at 13,313,896 bp (rs722178836) and had an allele substitution effect of -0.72 additive genetic standard deviations and (Fig. 2).Fig. 1

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