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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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Stillbirth rate (%) by mating type according to the carrier status of the sire (S) and maternal grandsire (MGS) for the lethal haplotype (HAPQTL), based on the top 10 SNPs associated with stillbirth. I noncarrier S × MGS, II noncarrier S × carrier MGS, III carrier S × noncarrier MGS and IV carrier S × MGS matings, FIN Finland, SWE Sweden and DNK Denmark
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Fig6: Stillbirth rate (%) by mating type according to the carrier status of the sire (S) and maternal grandsire (MGS) for the lethal haplotype (HAPQTL), based on the top 10 SNPs associated with stillbirth. I noncarrier S × MGS, II noncarrier S × carrier MGS, III carrier S × noncarrier MGS and IV carrier S × MGS matings, FIN Finland, SWE Sweden and DNK Denmark

Mentions: We analyzed the stillbirth rate for the four mating types (I, II, III and IV) based on the carrier status of the sire and maternal grandsire. The stillbirth rate was approximately 6 % higher for matings in which both the sire and maternal grandsire carried the putative causative haplotype HAPQTL compared to matings in which neither was a carrier (Fig. 6). We consistently observed higher calf mortality rates from carrier-sire by carrier-maternal grandsire matings across the three Nordic countries, in both the first and later calvings (Table 3).Fig. 6


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)

Stillbirth rate (%) by mating type according to the carrier status of the sire (S) and maternal grandsire (MGS) for the lethal haplotype (HAPQTL), based on the top 10 SNPs associated with stillbirth. I noncarrier S × MGS, II noncarrier S × carrier MGS, III carrier S × noncarrier MGS and IV carrier S × MGS matings, FIN Finland, SWE Sweden and DNK Denmark
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: Stillbirth rate (%) by mating type according to the carrier status of the sire (S) and maternal grandsire (MGS) for the lethal haplotype (HAPQTL), based on the top 10 SNPs associated with stillbirth. I noncarrier S × MGS, II noncarrier S × carrier MGS, III carrier S × noncarrier MGS and IV carrier S × MGS matings, FIN Finland, SWE Sweden and DNK Denmark
Mentions: We analyzed the stillbirth rate for the four mating types (I, II, III and IV) based on the carrier status of the sire and maternal grandsire. The stillbirth rate was approximately 6 % higher for matings in which both the sire and maternal grandsire carried the putative causative haplotype HAPQTL compared to matings in which neither was a carrier (Fig. 6). We consistently observed higher calf mortality rates from carrier-sire by carrier-maternal grandsire matings across the three Nordic countries, in both the first and later calvings (Table 3).Fig. 6

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