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Genome-wide association and biological pathway analysis for milk-fat composition in Danish Holstein and Danish Jersey cattle.

Buitenhuis B, Janss LL, Poulsen NA, Larsen LB, Larsen MK, Sørensen P - BMC Genomics (2014)

Bottom Line: Of these significant SNPs, 108 SNP markers were significant in both DH and DJ (C14-index, BTA26; C16, BTA14; fat percentage (FP), BTA14).In addition genetic correlations between FA showed a similar pattern across DH and DJ.Furthermore the biological pathway analysis suggested that fat digestion and absorption KEGG04975 is important for the traits FP, C14:1, C16 index and C16:1.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Center for Quantitative Genetics and Genomics, Blichers Allé 20, P,O, Box 50, DK-8830 Tjele, Denmark. bart.buitenhuis@mbg.au.dk.

ABSTRACT

Background: The milk fat profile of the Danish Holstein (DH) and Danish Jersey (DJ) show clear differences. Identification of the genomic regions, genes and biological pathways underlying the milk fat biosynthesis will improve the understanding of the biology underlying bovine milk fat production and may provide new possibilities to change the milk fat composition by selective breeding. In this study a genome wide association scan (GWAS) in the DH and DJ was performed for a detailed milk fatty acid (FA) profile using the HD bovine SNP array and subsequently a biological pathway analysis based on the SNP data was performed.

Results: The GWAS identified in total 1,233 SNPs (FDR < 0.10) spread over 18 chromosomes for nine different FA traits for the DH breed and 1,122 SNPs (FDR < 0.10) spread over 26 chromosomes for 13 different FA traits were detected for the DJ breed. Of these significant SNPs, 108 SNP markers were significant in both DH and DJ (C14-index, BTA26; C16, BTA14; fat percentage (FP), BTA14). This was supported by an enrichment test. The QTL on BTA14 and BTA26 represented the known candidate genes DGAT and SCD. In addition we suggest ACSS3 to be a good candidate gene for the QTL on BTA5 for C10:0 and C15:0. In addition, genetic correlations between the FA traits within breed showed large similarity across breeds. Furthermore, the biological pathway analysis revealed that fat digestion and absorption (KEGG04975) plays a role for the traits FP, C14:1, C16 index and C16:1.

Conclusion: There was a clear similarity between the underlying genetics of FA in the milk between DH and DJ. This was supported by the fact that there was substantial overlap between SNPs for FP, C14 index, C14:1, C16 index and C16:1. In addition genetic correlations between FA showed a similar pattern across DH and DJ. Furthermore the biological pathway analysis suggested that fat digestion and absorption KEGG04975 is important for the traits FP, C14:1, C16 index and C16:1.

No MeSH data available.


Enrichment plot for the different fatty acids and groups of fatty acids for both the Danish Holstein and Danish Jersey breeds at different cut-off levels for the P-values. The colour shade from white to dark blue indicates the fold change in enrichment for each trait.
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Fig3: Enrichment plot for the different fatty acids and groups of fatty acids for both the Danish Holstein and Danish Jersey breeds at different cut-off levels for the P-values. The colour shade from white to dark blue indicates the fold change in enrichment for each trait.

Mentions: Figure 3 presents the enrichment of associated SNPs at five different cut-off values for the P-values obtained from the GWAS within each breed. For the traits FP, and C14 index there was a 14 fold higher number of significant SNP markers than expected for both the DH and the DJ at a cut-off value of 10-4. C14:1 showed a 5 fold higher number of significant SNP markers than expected for the DH, whereas for the DJ a 14 fold higher number of significant SNP markers than expected was shown. For DJ, C18:2c6 showed a 12 fold higher number of significant SNP markers than expected. At the cut-off value for the P-values of 10-4 it was shown that there was significant overlap in SNP markers between the DH and DJ for the traits FP, C14 index, C14:1, C16 index and C16:1 (Figure 4).Figure 3


Genome-wide association and biological pathway analysis for milk-fat composition in Danish Holstein and Danish Jersey cattle.

Buitenhuis B, Janss LL, Poulsen NA, Larsen LB, Larsen MK, Sørensen P - BMC Genomics (2014)

Enrichment plot for the different fatty acids and groups of fatty acids for both the Danish Holstein and Danish Jersey breeds at different cut-off levels for the P-values. The colour shade from white to dark blue indicates the fold change in enrichment for each trait.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4377848&req=5

Fig3: Enrichment plot for the different fatty acids and groups of fatty acids for both the Danish Holstein and Danish Jersey breeds at different cut-off levels for the P-values. The colour shade from white to dark blue indicates the fold change in enrichment for each trait.
Mentions: Figure 3 presents the enrichment of associated SNPs at five different cut-off values for the P-values obtained from the GWAS within each breed. For the traits FP, and C14 index there was a 14 fold higher number of significant SNP markers than expected for both the DH and the DJ at a cut-off value of 10-4. C14:1 showed a 5 fold higher number of significant SNP markers than expected for the DH, whereas for the DJ a 14 fold higher number of significant SNP markers than expected was shown. For DJ, C18:2c6 showed a 12 fold higher number of significant SNP markers than expected. At the cut-off value for the P-values of 10-4 it was shown that there was significant overlap in SNP markers between the DH and DJ for the traits FP, C14 index, C14:1, C16 index and C16:1 (Figure 4).Figure 3

Bottom Line: Of these significant SNPs, 108 SNP markers were significant in both DH and DJ (C14-index, BTA26; C16, BTA14; fat percentage (FP), BTA14).In addition genetic correlations between FA showed a similar pattern across DH and DJ.Furthermore the biological pathway analysis suggested that fat digestion and absorption KEGG04975 is important for the traits FP, C14:1, C16 index and C16:1.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Center for Quantitative Genetics and Genomics, Blichers Allé 20, P,O, Box 50, DK-8830 Tjele, Denmark. bart.buitenhuis@mbg.au.dk.

ABSTRACT

Background: The milk fat profile of the Danish Holstein (DH) and Danish Jersey (DJ) show clear differences. Identification of the genomic regions, genes and biological pathways underlying the milk fat biosynthesis will improve the understanding of the biology underlying bovine milk fat production and may provide new possibilities to change the milk fat composition by selective breeding. In this study a genome wide association scan (GWAS) in the DH and DJ was performed for a detailed milk fatty acid (FA) profile using the HD bovine SNP array and subsequently a biological pathway analysis based on the SNP data was performed.

Results: The GWAS identified in total 1,233 SNPs (FDR < 0.10) spread over 18 chromosomes for nine different FA traits for the DH breed and 1,122 SNPs (FDR < 0.10) spread over 26 chromosomes for 13 different FA traits were detected for the DJ breed. Of these significant SNPs, 108 SNP markers were significant in both DH and DJ (C14-index, BTA26; C16, BTA14; fat percentage (FP), BTA14). This was supported by an enrichment test. The QTL on BTA14 and BTA26 represented the known candidate genes DGAT and SCD. In addition we suggest ACSS3 to be a good candidate gene for the QTL on BTA5 for C10:0 and C15:0. In addition, genetic correlations between the FA traits within breed showed large similarity across breeds. Furthermore, the biological pathway analysis revealed that fat digestion and absorption (KEGG04975) plays a role for the traits FP, C14:1, C16 index and C16:1.

Conclusion: There was a clear similarity between the underlying genetics of FA in the milk between DH and DJ. This was supported by the fact that there was substantial overlap between SNPs for FP, C14 index, C14:1, C16 index and C16:1. In addition genetic correlations between FA showed a similar pattern across DH and DJ. Furthermore the biological pathway analysis suggested that fat digestion and absorption KEGG04975 is important for the traits FP, C14:1, C16 index and C16:1.

No MeSH data available.